Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012)

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Accession:153196
A computational tool to explore the underlying principles of optogenetic neural stimulation. This "light-neuron" model consists of theoretical representations of the light dynamics generated by a fiber optic in brain tissue, coupled to a multicompartment cable model of a cortical pyramidal neuron (Hu et al. 2009, ModelDB #123897) embedded with channelrhodopsin-2 (ChR2) membrane dynamics. Simulations predict that the activation threshold is sensitive to many of the properties of ChR2 (density, conductivity, and kinetics), tissue medium (scattering and absorbance), and the fiber-optic light source (diameter and numerical aperture). This model system represents a scientific instrument to characterize the effects of optogenetic neuromodulation, as well as an engineering design tool to help guide future development of optogenetic technology.
Reference:
1 . Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron. J Neurophysiol 107:3235-45 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon; Channel/Receptor; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I K; I M; I K,Ca; I Sodium; I Calcium; Channelrhodopsin (ChR);
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Detailed Neuronal Models; Action Potentials; Parameter sensitivity; Intracortical Microstimulation; Neuromodulation;
Implementer(s): MacIntyre, CC [ccm4 at case.edu]; Foutz, Thomas J [tfoutz at uw.edu]; Arlow, Richard L [richard.arlow at case.edu];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I K; I M; I K,Ca; I Sodium; I Calcium; Channelrhodopsin (ChR);
/* ----------------------------------------------------------------
    Define the Axon Geometry

    Layer 5 cortical pyramidal cell has a long unmyelinated axon!
    Similar to Mainen et al (Neuron, 1995)
------------------------------------------------------------------*/

n_myelin = 14  // number of myelins and nodes
create ais[2],hill,nakeaxon,myelin[2],node[2]  // forward declaration

proc create_axon() {

  create ais[10],hill,nakeaxon,myelin[n_myelin],node[n_myelin]

  // Acquire the equivalent diameter of soma
  soma {  equiv_diam = sqrt(area(0.5)*nseg/(4*PI))  }   // "*nseg" is needed !!
  if (numarg()) equiv_diam = $1
  // Set axonal diameters
  diamAis=equiv_diam/10
  diamNakeAxon=equiv_diam/12
  diamMyelin=diamAis*1.
  diamNode=diamAis*0.75    // nodes are thinner than axon

  // Initial segment

hill {
    L = 10
    nseg = 10
    diam(	0	:	0.25	) = 	6	:	3.8
    diam(	0.25	:	0.5	) = 	3.8	:	2.8
    diam(	0.5	:	0.75	) = 	2.8	:	1.7
    diam(	0.75	:	1	) = 	1.7	:	1.3

  }


for i=0,9 ais[i] {
    L = 5
    nseg = 10
    diam = 1.22
  }

ais[0]	{
    diam(	0	:	1	) = 	1.7	:	1.5
	}

ais[1]	{
    diam(	0	:	1	) = 	1.5	:	1.22
	}


  // Unmylined axon
  nakeaxon {
    L = 400
    nseg = 100
    diam = diamNakeAxon
  }

  // Myelinated axon with nodes of Ranvier
  for i=0,n_myelin-1 {
    myelin[i] {         // myelin element
      nseg = 5
      L = 100
      diam = diamMyelin
    }
    node[i] {           // nodes of Ranvier
      nseg = 1
      L = 1
      diam = diamNode
    }
  }

  // Connecting

  soma connect hill(0), axonOnSoma       // dend11 -> soma(0) -> soma(1) -> hill
  hill connect ais[0] (0), 1      // hill -> ais[0]
  for i=0,8 ais[i] {              // ais[0] -> ... -> ais[9]
    connect ais[i+1] (0), 1
  }
  ais[9] connect nakeaxon(0), 1        // ais[9] -> nakeaxon
  nakeaxon connect myelin[0] (0), 1    // nakeaxon -> myelin[0]
  myelin[0] connect node[0](0), 1            // myelin[0] -> node[0]
  for i=1,n_myelin-1  {                    // (myelin[0] node[0]) -> ... -> (myelin[n_myelin] node[n_myelin])
      node[i-1] connect myelin[i](0), 1
      myelin[i] connect node[i](0), 1
  }

}

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