Search found 71 matches

by menica
Fri Dec 15, 2017 10:00 am
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 15
Views: 9737

Re: na_ion mechanism not inserted in section axon

Dear Hines, thanks. This means that it is not possible to have access to the icl produced by the point process in mA/cm2 in the nmodl code. Maybe I should convert it in the hoc code in the post-processing. If I save the syn.icl current in a vector, then I can multiply each value by conversion factor...
by menica
Fri Dec 15, 2017 9:06 am
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 15
Views: 9737

Re: na_ion mechanism not inserted in section axon

Dear Hines and Ted, thanks for your explanation. There is a way in order to know the current generated by the point process that neuron will sum up to the other currents and convert in mA/cm2, directly in mA/cm2? Is this synaptic mechanism wrong? : NEURON { POINT_PROCESS is USEION cl WRITE icl VALEN...
by menica
Wed Dec 13, 2017 12:33 pm
Forum: Other questions
Topic: na_ion mechanism not inserted in section axon
Replies: 15
Views: 9737

Re: na_ion mechanism not inserted in section axon

Hi Ted, I read this thread. In order to know the current generated by a point process, I declared the current as RANGE. How can I access to the conversion in mA/cm2 which neuron does? I tried to convert the current my myself ...but when I look at the total current generated by the point process spec...
by menica
Tue Dec 05, 2017 3:29 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using Ca2+ currents in point and distributed processes
Replies: 6
Views: 4933

Re: Using Ca2+ currents in point and distributed processes

Dear Ted, Thanks. Yes I have a Cl accumulation mechanism and a simple pump mechanism which writes the current passing through the Cl pump icl_pump=const*(cli-cli0). Do you mean that the icl I am using in the accumulation mechanism takes into account the icl of the point process because neuron change...
by menica
Tue Dec 05, 2017 7:21 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using Ca2+ currents in point and distributed processes
Replies: 6
Views: 4933

Re: Using Ca2+ currents in point and distributed processes

hi, I have a similar problem. I have a chloride leak current expressed in mA/cm2 and an accumulation mechanisms. I had a gabaa synapse point process which writes a ligand-gated chloride current in nA. I would like to counterbalance with the cl pump the activity of the leak and cl current generated b...
by menica
Fri Nov 17, 2017 10:00 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 32794

Re: pump kinetic scheme

Dear Ted, thanks! In the meantime, I tried to solve the problem in the other way. I add more complexity to the model (I add the K HH channel and leakage currents for Na, K and non-specific ion, in this way the sodium channel close once the stimulus is over). I obtained the more or less desired behav...
by menica
Mon Nov 13, 2017 11:40 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 32794

Re: pump kinetic scheme

Dear Ted,
I tried out your solution, but it doesn't seem to solve the problem. the nai is not coming back at nai0

Best
Menica
by menica
Sat Oct 28, 2017 4:50 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 32794

Re: pump kinetic scheme

Dear ted Indeed I cannot prove it biologically but I need to have a system that works in this way: input Iclamp current modified the membrane very, this change induces the activation of the voltage gated na channel , the nai increases. The change in nai activates the na pump. The pump is active unti...
by menica
Tue Oct 24, 2017 1:58 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 32794

Re: pump kinetic scheme

Dear Ted, thanks for your input. I read about control theory (new to me) and I understood the steady-state problem of the proportional controllers. One solution to this problem would be adding an integral term (over the change of nai) to the controller, but I don't know how to do this in nmodl. An a...
by menica
Mon Oct 23, 2017 4:56 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 32794

Re: pump kinetic scheme

Dear Raj,
thanks for your answer.
I hope someone will reply to my post.
Best
Menica
by menica
Fri Oct 20, 2017 10:45 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 32794

Re: pump kinetic scheme

Dear Raj, I am dealing with the same problem discussed in this thread. I need to insert a tau term in order to have control on the pump dynamics. I am considering only one soma in which I inserted a voltage-activate Na channel, Na pump and Na accumulation mechanism. Here are the mod files: Na voltag...
by menica
Wed Oct 04, 2017 11:49 am
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16254

Re: load several geomtery file

Hi Ted, now it is working. I am able to open in a loop a series of files objref m m=new Matrix() //m=new Vector() strdef fname objref f for i=1,2 { sprint(fname, "gnacl%d", i) print fname f = new File(fname) f.ropen() m.scanf(f) print m.nrow, m.ncol //print m.size() } the problem is when I want to f...
by menica
Fri Sep 29, 2017 12:22 pm
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16254

Re: load several geomtery file

Dear Ted, I read the documentation and the post, but I don't want to use the command line to pass NEURON a set of parameter. I am always using the same cell and I would like to change only a couple of parameters stored in txt file. I tried to run the example you mentioned but it is not working. Ther...
by menica
Thu Sep 28, 2017 1:21 pm
Forum: Getting started
Topic: load several geomtery file
Replies: 14
Views: 16254

Re: load several geomtery file

hi, I am having a similar problem. I want to load and scan 10 files named "namefile_#number". I tried different ways but I am stuck to this. for i=1:10 { objref m,f f = new File() load_file("gnacl_%d.txt", i) f.ropen("gnacl_%d.txt", i) m = new Matrix() m.scanf(f) print m.nrow, m.ncol } this command ...
by menica
Thu Sep 28, 2017 1:16 pm
Forum: Optimization
Topic: MRF to explore parameter space
Replies: 3
Views: 14592

Re: MRF to explore parameter space

I solved my problem