Search found 104 matches

by shailesh
Sat May 18, 2013 3:01 pm
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 8214

Re: Setting Resting Membrane Potential

Regarding your question: My mistake! I had gone about modeling my own hh mechanism (using Example 9.4 from the Neuron book and hh.mod from the library) more for nmodl practice than anything else. There I had ignored the leakage current and hence my reason for adding pas in addition to my 'modified h...
by shailesh
Wed May 15, 2013 4:46 am
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 8214

Setting Resting Membrane Potential

Hi, I have recently begun working with active ion channels in my model and wanted some help in setting the resting membrane potential. I am modeling a myelinated axon. A quick summary: > Soma : pas and hh mechanisms > Nodes: pas and hh mechanisms > Internodes/Myelins: only pas mechanism I require to...
by shailesh
Mon May 13, 2013 8:54 pm
Forum: Other questions
Topic: lambda_f undefined function - when used inside template
Replies: 3
Views: 1803

Re: lambda_f undefined function - when used inside template

Thanks Ted for pointing that out.
It is working fine now with the 'external' command.
by shailesh
Mon May 13, 2013 12:43 am
Forum: Other questions
Topic: lambda_f undefined function - when used inside template
Replies: 3
Views: 1803

lambda_f undefined function - when used inside template

Hi, I am facing an issue when using lambda_f for specifying nseg. The error message is: "lambda_f undefined function" I had read the only other post dealing with such an error on the forum (http://www.neuron.yale.edu/phpbb/viewtopic.php?f=15&t=2017) and double-checked to ensure that I had included '...
by shailesh
Mon Jul 16, 2012 2:20 pm
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8542

Re: Extracellular Resistance as a 3D Grid - Bidomain Model

A BIG thanks for the point by point response. I did see several other posts where extracellular was being modeled in another software (Matlab/Comsol/Maxwell etc). But I did prefer to stick to NEURON for the same and hence will try the second approach that you have suggested. And yes I will go ahead ...
by shailesh
Mon Jul 16, 2012 2:06 pm
Forum: Other questions
Topic: Impedance vs Frequency Plot- DC & AC Current - Gap Junctions
Replies: 4
Views: 4043

Re: Impedance vs Frequency Plot- DC & AC Current - Gap Junct

The voltage clamp method that you suggested does provide an interesting potential alternative. But I decided to play it safe and went about following the former method and it did provide me consistent results (there wasn't much to go wrong there I suppose), though did end up taking quiet long for re...
by shailesh
Sun Jul 15, 2012 12:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Gap Junctions as Resistor and Capacitor in Parallel
Replies: 13
Views: 8479

Re: Gap Junctions as Resistor and Capacitor in Parallel

I did go through ModelDB and other related articles on the Forum and located 2 hoc implementation of gap junctions via LinearMechanism: > Olfactory bulb mitral cell: synchronization by gap junctions (Migliore et al 2005) http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=43039&file=\gap-modeld...
by shailesh
Sun Jul 15, 2012 11:08 am
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8542

Extracellular Resistance as a 3D Grid - Bidomain Model

Hi, I assume it best to explain my objective first so that you could suggest a better approach to tackle my problem. I am attempting to develop a bidomain model (one grid representing cells, coupled via gap junctions, and the other grid their adjacent extracellular space). This would be a passive sy...
by shailesh
Sat Jul 14, 2012 1:39 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Gap Junctions as Resistor and Capacitor in Parallel
Replies: 13
Views: 8479

Re: Gap Junctions as Resistor and Capacitor in Parallel

Hi Ted, Thanks for the quick response. I had actually posted another post ( https://www.neuron.yale.edu/phpBB/viewtopic.php?f=8&t=2650&p=10559#p10559 ) around the same time in which I had used the Linear Circuit Builder for implementing a gap junction with a resistor and capacitor in parallel. But t...
by shailesh
Sat Jul 14, 2012 1:21 am
Forum: Other questions
Topic: Impedance vs Frequency Plot- DC & AC Current - Gap Junctions
Replies: 4
Views: 4043

Re: Impedance vs Frequency Plot- DC & AC Current - Gap Junct

Thanks a lot for pointing that out. So as using the Impedance class is ruled out in my case, would the alternative be to inject sinusoidal currents, over a range of frequencies, and then calculate Zin=peak[v(x)]/i(x) in each case. Would plotting this Zin vs f give me the correct Impedance-Frequency ...
by shailesh
Thu Jul 12, 2012 3:57 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Gap Junctions as Resistor and Capacitor in Parallel
Replies: 13
Views: 8479

Gap Junctions as Resistor and Capacitor in Parallel

Hi, Posting this as a separate query as it was on a different note to the one I posted earlier. I have been trying to extend the NMODL code for implementing a gap junction (as given in the NEURON book) to have both a resistive and capacitive component (i.e. a gap junction represented as a resistor a...
by shailesh
Thu Jul 12, 2012 3:14 pm
Forum: Other questions
Topic: Impedance vs Frequency Plot- DC & AC Current - Gap Junctions
Replies: 4
Views: 4043

Impedance vs Frequency Plot- DC & AC Current - Gap Junctions

Hi, I was using the GUI tool to plot Impedance vs Frequency spectrum for a number of models: (a) a simple passive cell (b) two of these same cells connected via gap junctions (Gap Junctions were modeled in NMODL as purely resisitive - as described in NEURON book) (c) two of these same cells connecte...
by shailesh
Sat Jun 16, 2012 3:51 am
Forum: Other questions
Topic: sinusoid current
Replies: 12
Views: 11190

Negative t values on Current Axis using CVODE

Hi, I was using the Izap.mod file on my model and was getting a few unexpected negative t values when plotting Izap[0].i when CVODE was active. It didn't give any problems with CVODE turned off. To track down the problem, I reduced my code to its very basic (without making any changes to Izap.mod): ...
by shailesh
Tue Mar 15, 2011 10:05 am
Forum: Modeling networks
Topic: Network of cells using gap jucntion
Replies: 1
Views: 2510

Re: Network of cells using Gap Junctions

Hi Irene, I believe you have adapted the gap junction modeling technique provided in The NEURON Book. That example (page 272, Topic 10.1.2.1) was meant for modeling a single gap junction between two cells. Your model involves a 2-Dimensional array of cells and hence the code would require certain tw...