Search found 127 matches

by Keivan
Sat Oct 14, 2017 1:35 pm
Forum: NEURON hacks
Topic: 1D Electrodiffusion Cable Model Compatible with NEURON
Replies: 0
Views: 15881

1D Electrodiffusion Cable Model Compatible with NEURON

A few years ago, I and some of my colleagues started to work on a one dimensional electrodiffusion cable model based on Mori 2007 [A Three-Dimensional Model of Cellular Electrical Activity]. Our mathematical endeavours were successful, but we never tested our equations, since I moved to US to get my...
by Keivan
Sun Feb 21, 2016 3:08 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Assertion failed: file init.c, line 823
Replies: 1
Views: 5359

Assertion failed: file init.c, line 823

I have these two new mechanisms (mod files). They compile fine, but when I try to use them, I see this assertion failed bug. Would you please help me understand what is going wrong. TITLE cana Current NEURON { SUFFIX iCaNa USEION na READ nai, nao USEION ca READ cai WRITE ica RANGE ibarna, ica ,cai ,...
by Keivan
Mon Feb 03, 2014 4:03 pm
Forum: MSWin
Topic: nrniv.dll missing after build with cygwin under 64 bit win 8
Replies: 8
Views: 7379

Re: nrniv.dll missing after build with cygwin under 64 bit w

Thank you for fixing that problem. I have cloned the source again and recompiled the code. This is the error: if test "i686" = "x86_64" ; then \ x86_64-w64-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../src/mswin/extra/mos2nrn.cpp ;\ else \ i686-pc-mingw32-g++ -g -O2 -DCYGWIN -o mos2nrn.exe ../../...
by Keivan
Mon Feb 03, 2014 11:39 am
Forum: MSWin
Topic: nrniv.dll missing after build with cygwin under 64 bit win 8
Replies: 8
Views: 7379

Re: nrniv.dll missing after build with cygwin under 64 bit w

for some reason your modification of makefile.am do not work even after re-executing the ./build.sh script and re-configuring. I mean still the x86_64 version of mingw tries to compile the code. I changed the makefile to test the i686 version. Still this error appears nrn/src/nrniv/makefile: mos2nrn...
by Keivan
Mon Feb 03, 2014 12:54 am
Forum: MSWin
Topic: nrniv.dll missing after build with cygwin under 64 bit win 8
Replies: 8
Views: 7379

Re: nrniv.dll missing after build with cygwin under 64 bit w

This is my .bashrc: export HOME=/home/keivan export IV="$HOME/neuron/iv" export N="$HOME/neuron/nrn" export CPU="i686" export host_cpu=$CPU export PATH="$HOME:$PATH:/bin:/usr/bin:/usr/sbin" export PATH="$IV/$CPU/bin:$N/$CPU/bin:$PATH" export CPATH="$CPATH:/usr/include" export LD_LIBRARY_PATH="$LD_LI...
by Keivan
Sat Feb 01, 2014 7:00 am
Forum: MSWin
Topic: nrniv.dll missing after build with cygwin under 64 bit win 8
Replies: 8
Views: 7379

nrniv.dll missing after build with cygwin under 64 bit win 8

For some reason nrniv.dll is missing in my mswin-i686 (with cygwin i686, under 64bit version of windows 8.1) build of neuron. Could you please help me to make my own nrniv.dll. PS: currently, gcc-3 is completely removed from the cygwin repositories that causes some errors in compiling nrn. I have by...
by Keivan
Thu Aug 22, 2013 5:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 2686

Re: Extracellular mechanism with variable e_extracellular

Since it is easy to wire two nodes in the model to each other, I made my ephaptic coupling mechanism. // This mechanism is very simple. // It connects two extracellular voltage nodes to each other // with a low resistance wire so that they become a single node (theoretically) // then we connect this...
by Keivan
Sun Aug 18, 2013 2:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 2686

Re: Extracellular mechanism with variable e_extracellular

Today, I spend some time to understand the LinearMechanism by reading the topic that was suggested by Shailesh. It was really enlightening. I wish that information was explained in the documentation. Anyway, as far as I understood, using LinearMechanism, we can add conductance and capacitance betwee...
by Keivan
Sat Aug 17, 2013 7:12 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 2686

Re: Extracellular mechanism with variable e_extracellular

As far as I know, ephaptic coupling by itself is the sufficient condition for the propagation of action potential from one myocyte to another myocyte. My ephaptic coupling mechanism, however, is unstable. The suggested modifications, as in the xtra mechanism, did not solved the problem. Do you have ...
by Keivan
Thu Aug 15, 2013 5:13 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 2686

Re: Extracellular mechanism with variable e_extracellular

Thank you Ted, I would test the suggested code and reply soon. Thank you Shailesh for pointing me to that topic. From your NMODL code I would guess that a disk has an equivalent circuit something like this Code: Select all A B o--- ra ---+--- rb ---o | rc | gnd where the A terminal is attached to an...
by Keivan
Wed Aug 14, 2013 11:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 2686

Re: Extracellular mechanism with variable e_extracellular

Thank you Ted. I have changed my code the way you suggested. COMMENT Potential in the Intercalated disk This mechanism should be inserted in the pre-junctional compartment phi_c = A*Rc*Ro*(-dv_pre/dx+dv_post/dx) Keivan Moradi, 2013 ENDCOMMENT NEURON { POINT_PROCESS vDisk POINTER v2, vp1, vp2, vc } U...
by Keivan
Mon Aug 12, 2013 1:50 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 2686

Extracellular mechanism with variable e_extracellular

I am trying to make a model of cardiac action potential propagation. Ephaptic coupling has a major role in the propagation of action potentials in these cells. In a simple model of ephaptic coupling, the potential in the cleft between two cells should be calculated. In order to do that I have made a...
by Keivan
Thu Aug 08, 2013 10:48 am
Forum: Reaction-diffusion in NEURON
Topic: Introduction and request for suggestions
Replies: 5
Views: 8285

Re: Introduction and request for suggestions

It is probably too late to answer to this post. Anyway, as far as I have learned about the reaction-diffusion implementation in NEURON 7.3, I am not sure how it can be used in the modeling of dendritic spines since it models ion diffusion along the cable independent of membrane potential. I am also ...
by Keivan
Thu Feb 09, 2012 12:59 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using an appropriate integration method
Replies: 4
Views: 1037

Re: Using an appropriate integration method

It didn't work too. the error is:

Code: Select all

The matrix in the solution method is singular or ill-conditioned
nrniv: scopmath library error
by Keivan
Thu Feb 09, 2012 4:28 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using an appropriate integration method
Replies: 4
Views: 1037

Using an appropriate integration method

I'm working on a model which has 4 states, as follows: A' = -A/tau1 B' = -B/tau2 C' = -C/tau3 g' = (wC*C + wB*B)*(inf-g)/tau When I use "cnexp" the mechanism compiles but there is error during simulation. When I use "sparse" method I cannot compile the mechanism. When i use "runge" method everything...