Neurite: electrophysiological-mechanical coupling simulation framework (Garcia-Grajales et al 2015)

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Accession:168861
Neurite simulates the electrical signal propagation in myelinated and unmyelinated axons, and in dendritic trees under mechanical loading. Two different solvers are available (explicit and implicit) with sequential (CPU) and parallel (GPUs) versions
Reference:
1 . García-Grajales JA, Rucabado G, García-Dopico A, Peña JM, Jérusalem A (2015) Neurite, a finite difference large scale parallel program for the simulation of electrical signal propagation in neurites under mechanical loading. PLoS One 10:e0116532 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Myelinated neuron;
Channel(s): I Sodium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program;
Model Concept(s): Action Potential Initiation; Axonal Action Potentials; Action Potentials;
Implementer(s): Garcia-Grajales, Julian Andres ;
Search NeuronDB for information about:  I Sodium; I Potassium;
//
//
// File author(s):  <Julian Andres Garcia Grajales>, (C) 2014
//
// Copyright: this software is licenced under the terms stipulated in the license.txt file located in its root directory
//
//

/*!\file coupling.cpp
  \brief This file contains the functions related to the electrical properties that change during the time.
*/

#include "coupling.h"
extern int numStepsX;
extern TYPE tspan;
extern TYPE time_run;

/*! \brief This function calculates the probabilities of the Hodgkin and Huxley model
  @param V_prev Previous potential
  @param alpha Structure with alpha probabilities
  @param beta Structure with beta probabilities
  @param rest_pot Resting potential

*/
extern void hhRate_Const(rate_const &alpha, rate_const &beta, TYPE rest_pot,TYPE potential,TYPE Left_Shift_Na, TYPE Left_Shift_K)  
{

  TYPE V_prevNa=0,V_prevK=0;
  // Original from HH paper
  TYPE scale = 0.001; // In order to have the potential in mV for the HH equations

  // Applying the LS
  V_prevNa = potential + Left_Shift_Na;
  V_prevK = potential + Left_Shift_K;

  V_prevNa = (V_prevNa-rest_pot)/scale; // particular for HH dimensions
  V_prevK = (V_prevK-rest_pot)/scale; // particular for HH dimensions
  // Na gate values
  alpha.m = (2.5-0.1*V_prevNa)/(exp(2.5 - 0.1*V_prevNa)-1);
  beta.m = 4*exp(-V_prevNa/18);

  alpha.h = 0.07*exp(-V_prevNa/20);
  beta.h = 1/(exp(3 - 0.1*V_prevNa) + 1);

  // K gate value
  alpha.n=(0.1 - 0.01*V_prevK)/(exp(1 - 0.1*V_prevK)-1);
  beta.n=0.125*exp(-V_prevK/80);
}




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