Search found 104 matches

by shailesh
Sun Aug 18, 2013 2:22 am
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8978

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

One more query to follow-up on: consider a circuit in which two nodes are connected by a conductance G. Let's call them node 0 and node 1, so the voltages at these nodes will be called v0 and v1. The current that leaves node 0 through g is (v0 - v1)*G and the current that leaves node 1 through g is ...
by shailesh
Sat Aug 17, 2013 3:20 am
Forum: Other questions
Topic: Vector Size Error?
Replies: 2
Views: 1452

Re: Vector Size Error?

Thanks for the workaround!
by shailesh
Thu Aug 15, 2013 11:51 pm
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 9557

Re: Setting Resting Membrane Potential

This clinched it for me: For an electrically compact cell, Rm = Rin * surface area in cm2. Hadn't thought of that. Just to complete the above discussion: Rin = 43930 Mohm = 43930* 1e6 ohm So, Rm = Rin * surfacearea = 43930*1e6 ohm * 100*PI*1e-8 = 138065 ohm.cm2 which is very close to out expected va...
by shailesh
Thu Aug 15, 2013 11:43 pm
Forum: Other questions
Topic: Vector Size Error?
Replies: 2
Views: 1452

Vector Size Error?

A seemingly very trivial problem, but I can't figure out whats going wrong with the below code for defining a vector: //Range MINS = 1.2 INCS = 0.05 MAXS = 5 objref vecs vecs = new Vector(((MAXS-MINS)/INCS)+1) print "vector Size: ", vecs.size() print "vector defined Size: ", (((MAXS-MINS)/INCS)+1) p...
by shailesh
Thu Aug 15, 2013 9:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular mechanism with variable e_extracellular
Replies: 9
Views: 4753

Re: Extracellular mechanism with variable e_extracellular

Hi Keivan, Happened to come across your post as I was also working on modeling extracellular fields and found the title interesting. I also ended up having to deal with LinearMechanism.... and yeah it seemed best avoided :p (atleast at first) You might find the following discussion useful: http://ww...
by shailesh
Thu Aug 15, 2013 2:14 am
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 9557

Re: Setting Resting Membrane Potential

Then Rm at the particular potential at which the measurement was made = Di * Dv (read the Ds as upper case delta) is the slope resistance of the membrane. I suppose this is basically equivalent to the slope of an I-V curve - the way we determine input resistance? In that case, wouldn't it be Rin = ...
by shailesh
Wed Aug 14, 2013 11:45 am
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8978

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

Oh ok... I think I see it now! The equation: c*(dy/dt) + g*y = b just involved scalar multiplications, and not the matrix multiplications that I mixed in. I suppose I just got into the flow of things seeing all the matrices, and when I had it on paper, matrix multiplication seemed the most natural w...
by shailesh
Wed Aug 14, 2013 11:28 am
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 9557

Re: Setting Resting Membrane Potential

Sorry for bombarding you with posts, but here is one more: I am not sure I followed you entirely here: If you were to actually measure membrane resistance, you'd apply a small current and observe the resulting change of membrane potential. This would reflect 1/(total conductance of all ion channels)...
by shailesh
Tue Aug 13, 2013 11:50 pm
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8978

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

Thanks Ted. So far so good - I follow you till that point. I attempted such a derivation in that post under the head: APPENDED LATER - The 'correct' approach Only query being what I have posted in the next part there... Suppose we did go ahead with the 'gmat' matrix as in above modeldb files, then e...
by shailesh
Tue Aug 13, 2013 1:22 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURRENT
Replies: 9
Views: 6298

Re: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURR

That pretty much sums it up. Thanks. The membrane current and rest being more or less similar to what? I was referring to rest (as in calculated value of v, vext) being same whether gap junctions were implemented as NONSPECIFIC_CURRENT or ELECTRODE_CURRENT, and that only i_membrane would change. But...
by shailesh
Mon Aug 12, 2013 1:03 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURRENT
Replies: 9
Views: 6298

Re: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURR

Thanks Ted. That list of gap junction implementations is surely going to be handy for many of us. As for, NONSPECIFIC_CURRENT & ELECTRODE_CURRENT, I suppose it would be fair to conclude that the major difference results in the membrane current (i_membrane) and rest being more or less similar. The on...
by shailesh
Sun Aug 11, 2013 1:20 pm
Forum: Other questions
Topic: Extracellular Resistance as a 3D Grid - Bidomain Model
Replies: 12
Views: 8978

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

For the last month or more, I have been trying my hand at using LinearMechanism. Despite having made some headway I am still some way off my goal. Currently, I am stuck with the following errors: "spFactor error: Zero Diagonal" & "spFactor error: Singular". But before going into those, I want to ens...
by shailesh
Sun Aug 11, 2013 4:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURRENT
Replies: 9
Views: 6298

Re: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURR

Found the following post with a whole lot of info on ELECTRODE_CURRENT & NONSPECIFIC_CURRENT: http://www.neuron.yale.edu/phpbb/viewtopic.php?f=16&t=2475#p9807 The following, I believe, relates to a part of my query: Facts which apply to any section that has NEURON's extracellular mechanism: 1. For a...
by shailesh
Sun Aug 11, 2013 4:09 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURRENT
Replies: 9
Views: 6298

Differences between NONSPECIFIC_CURRENT & ELECTRODE_CURRENT

I recently learnt that it is more appropriate to make use of ELECTRODE_CURRENT instead of NONSPECIFIC_CURRENT when extracellular mechanism is present. I went through the NEURON book and this is what I understood: ELECTRODE_CURRENT > Positive values of current would depolarize the cell > Above sugges...
by shailesh
Fri Aug 02, 2013 11:23 am
Forum: Other questions
Topic: Error: "Assertion Failed"
Replies: 11
Views: 3902

Re: Error: "Assertion Failed"

That does explain a lot of what is happening. Thanks for the 'verdict' on the issue. Now that it is known I can work on managing my resources more thriftily. ... and yes in recent times I have begun to wonder whether it would be much better to have my simulations on Linux.... apart from this issue, ...