Search found 104 matches

by shailesh
Mon Jun 02, 2014 1:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Gap Junctions as Resistor and Capacitor in Parallel
Replies: 13
Views: 8478

Re: Gap Junctions as Resistor and Capacitor in Parallel

That clears up quite a bit. Just a few more queries on this: 1> Under what conditions do we get the following message on "Print Matrix Info" in LCB: Circuit equations have X inconsistencies X: number>=0 Am I correct in believing that it would come-up when we have an incomplete/invalid circuit? 2> Bu...
by shailesh
Fri May 30, 2014 4:54 am
Forum: Other questions
Topic: Mismatch between NEURON results and Circuit Output?
Replies: 9
Views: 3286

Re: Mismatch between NEURON results and Circuit Output?

Remark; One could equivalently compute vi in a BEFORE BREAKPOINT block but in this case there would be no numerical difference. I was wondering about this. I tested it on two cells (nseg = 1) connected via gap junctions for a simulation duration of 0.1 ms. vi in BEFORE BREAKPOINT: oc>cella.v(0.5) -...
by shailesh
Thu May 29, 2014 4:51 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Gap Junctions as Resistor and Capacitor in Parallel
Replies: 13
Views: 8478

Re: Gap Junctions as Resistor and Capacitor in Parallel

Just after posting the earlier query, I was about to add that interestingly when we 'Create Class' from LCB, the LinearMechanism hoc code consists of only 2x2 matrices as opposed to 3x3 when we 'Print Matrix Info' - and why the difference? - But your post already answers that. I edited my "lincir1.h...
by shailesh
Wed May 28, 2014 6:33 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Gap Junctions as Resistor and Capacitor in Parallel
Replies: 13
Views: 8478

Re: Gap Junctions as Resistor and Capacitor in Parallel

Returning to this discussion after a long hiatus... I took your advice and decided to model R-C gap junctions using LinearMechanism. Though by now I have some grip on using LinearMechanisms, I decided to make use of the Linear Circuit Builder (LCB) to start off with and take a look at the LinearMech...
by shailesh
Tue May 20, 2014 11:30 pm
Forum: MSWin
Topic: Require help with Mercurial on Windows
Replies: 2
Views: 8033

Re: Require help with Mercurial on Windows

Thanks for the alpha installer... certainly much easier to get up and running! Will try out the parallel gap junction implementation with this. But since I had attempted the compile on the mercurial release, I am just a tad curious to know what I did wrong. My package versions are: Shailesh@Centurio...
by shailesh
Tue May 20, 2014 3:30 pm
Forum: Other questions
Topic: Mismatch between NEURON results and Circuit Output?
Replies: 9
Views: 3286

Re: Mismatch between NEURON results and Circuit Output?

Thanks Michael, that was real quick! I was eager to test it out but having some trouble in compiling the latest code from Mercurial. I believe the query would be more apt under a different head and hence have posted it here: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=5&t=3094 Would be great i...
by shailesh
Tue May 20, 2014 3:27 pm
Forum: MSWin
Topic: Require help with Mercurial on Windows
Replies: 2
Views: 8033

Require help with Mercurial on Windows

I was trying to compile the latest development code throught Mercurial (so as to make use of http://www.neuron.yale.edu/hg/neuron/nrn/rev/294dac40175f ). I followed the instructions given here: Link 1: http://www.neuron.yale.edu/neuron/download/getdevel Link 2: http://www.neuron.yale.edu/neuron/down...
by shailesh
Mon May 19, 2014 2:21 am
Forum: Other questions
Topic: Mismatch between NEURON results and Circuit Output?
Replies: 9
Views: 3286

Re: Mismatch between NEURON results and Circuit Output?

Yes I can see that would become an issue in parallel implementation of gap junctions (in presence of extracellular mechanism). Is a workaround possible in the current NEURON framework for parallel simulations? I haven't done any serious work with Parallel sims yet and so don't have much clue. I did ...
by shailesh
Fri May 16, 2014 1:23 am
Forum: Other questions
Topic: Mismatch between NEURON results and Circuit Output?
Replies: 9
Views: 3286

Re: Mismatch between NEURON results and Circuit Output?

Thanks Michael! That did it. It did not occur to me to think about how the extracellular mechanism could have been interfering with the regular gap junction implementation (felt it was more likely to do with an incorrect circuit implemenation or some worrying number crunching). Glad that you were ab...
by shailesh
Thu May 08, 2014 2:59 pm
Forum: Other questions
Topic: Mismatch between NEURON results and Circuit Output?
Replies: 9
Views: 3286

Mismatch between NEURON results and Circuit Output?

Hi, I have been trying to develop a network model involving extracellular mechanism as well as constructs using LinearMechanism. Since neither of these are intuitive (and prone to user errors), I made a small dummy model just to test my understanding of what was happening (with the LinearMechanisms ...
by shailesh
Sun Dec 15, 2013 4:41 am
Forum: Getting started
Topic: AlphaSynapse and Alpha Function
Replies: 4
Views: 7086

Re: AlphaSynapse and Alpha Function

As far as I can tell, they just appear to be different ways of obtaining the same (or extremely) similar shape.
If results are normalized, there doesn't seem to be anything to tell them apart. Pilot simulations seem to suggest the same.
by shailesh
Fri Dec 13, 2013 1:52 am
Forum: Getting started
Topic: AlphaSynapse and Alpha Function
Replies: 4
Views: 7086

Re: AlphaSynapse and Alpha Function

What are the peak amplitudes of functions 1 and 2? They appear to only dictate the shape, as peak amplitudes have not been explicitly stated (nor used in calculations). Reason, I suppose, being the study was more to do with regards to the time courses of junction potentials, and so amplitudes were ...
by shailesh
Thu Dec 12, 2013 1:56 pm
Forum: Getting started
Topic: AlphaSynapse and Alpha Function
Replies: 4
Views: 7086

AlphaSynapse and Alpha Function

This is more of a general query hence posting here. I was having some confusion over the way the alpha function is implemented for modeling current/conductance. This is what I have seen at different places: 1>> Some books (e.g. Jack, Noble & Tsien, 1975) and papers (e.g. Purves, 1976) implement alph...
by shailesh
Wed Aug 21, 2013 11:30 am
Forum: Other questions
Topic: Drift in Resting Membrane Potential for Coupled Cells
Replies: 1
Views: 1157

Drift in Resting Membrane Potential for Coupled Cells

Here is the scenario: > Three cells (A,B,C) coupled via gap junctions forming a chain: A ----- B ----- C > All cells have been assigned identical biophysical parameters. They are equipped with some custom active channels. > When isolated (i.e. no gap juntions), each cell has a resting potential of -...
by shailesh
Tue Aug 20, 2013 12:39 pm
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8541

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

Ok...... I think I got it this time. A more general query: I was just wondering that there are so many models on modeldb, but I have rarely come across models where: > there are two or more cells and > all these cells have extracellular fields (ecf) and > the ecfs of these cells should be linked (i....