Search found 11 matches

by brocke
Fri Jul 08, 2016 8:32 am
Forum: Other questions
Topic: order in the solution vector CVODE operates with
Replies: 4
Views: 4572

Re: order in the solution vector CVODE operates with

Michael, thank you for an answer. The size of the input vector for the f function should be equal to the number of all state variables in the system. This is how I understand from the documentation. My intention is to be able to operate ( or to call f function for example) voltage variables separate...
by brocke
Wed Jul 06, 2016 11:13 am
Forum: Other questions
Topic: order in the solution vector CVODE operates with
Replies: 4
Views: 4572

Re: order in the solution vector CVODE operates with

Let me try to answer myself in case someone needs. I apologize if information is incorrect or not precise. It seems like the solution vector has some order of the kind [voltage,gates,..]. The number of voltage variables can be retrieved from CvodeThreadData class, field name: v_node_count_. About th...
by brocke
Wed Jul 06, 2016 5:41 am
Forum: Other questions
Topic: integration of HH channel gating states
Replies: 3
Views: 4324

Re: integration of HH channel gating states

Thank you for a quick reply. Your understanding is incorrect. How did you arrive at it? I tried the default SOLVE statement and I tried SOLVE statement with cnexp to solve HH like channel gates. While debugging in both cases the channel gate variables were calculated by the integration of analytic s...
by brocke
Tue Jul 05, 2016 1:44 pm
Forum: Other questions
Topic: order in the solution vector CVODE operates with
Replies: 4
Views: 4572

order in the solution vector CVODE operates with

Hi, is there an appropriate way or interface how to dissect the solution vector y into voltages and conductance from the CVODE part of the code ? For instance, in the CVodeMalloc the Y0 is given as one state vector. Is there a specific order how the state variables (in particular voltages and channe...
by brocke
Tue Jul 05, 2016 1:23 pm
Forum: Other questions
Topic: integration of HH channel gating states
Replies: 3
Views: 4324

integration of HH channel gating states

Hi,

do I understand correct, that HH-like gating states are *always* integrated using analytic method independently which method I specify in the SOLVE statement in the mod file? If it's wrong, how to manipulate the integration method?

thank you in advance,
e.brocke
by brocke
Mon Apr 13, 2015 6:48 am
Forum: Other questions
Topic: Jacobian calculation
Replies: 1
Views: 1238

Jacobian calculation

Dear developers,

how expensive is one Jacobian evaluation in the adaptive solver in NEURON implementation? Can it be compared to one ode call or is it rather multiplied by the dimension of the system?

thank you in advance,
Brocke
by brocke
Thu Mar 05, 2015 9:15 am
Forum: Adding new mechanisms and functions to NEURON
Topic: HH gate probability integration in mod files
Replies: 1
Views: 1628

HH gate probability integration in mod files

Hi, I've noticed that sometimes the integration formula for HH gates probabilities is formulated using tau/inf variables (most of the time) and sometimes alpha/beta variables. Do I understand it correctly, tau/inf formulation is usually used to account for the temperature? or are there other reasons...
by brocke
Wed Sep 04, 2013 9:21 am
Forum: Other questions
Topic: HH mechanism implemented in Matlab
Replies: 6
Views: 2826

Re: HH mechanism implemented in Matlab

Finally success. After comparing for the 5th time all the digits, I've found an extra 0 in exp term in Matlab code:

Code: Select all

beta(2)  = 1000/(exp(1000*(-V1-0.035))+1);%1.0 /(exp(-(V1+35.0)/10.0)+1);
Sorry for this post. I don't think it can be of an help for anyone. Shall I remove it?

thank you Ted.
by brocke
Tue Sep 03, 2013 10:59 am
Forum: Other questions
Topic: HH mechanism implemented in Matlab
Replies: 6
Views: 2826

Re: HH mechanism implemented in Matlab

The first question to ask is: are you sure that what's in the computer is the same as what you think is in the computer? Specifically, are the geometries and biophysical properties identical to what you think they should be? I believe yes. The second question, which is related to the first, is: do ...
by brocke
Tue Sep 03, 2013 9:20 am
Forum: Other questions
Topic: HH mechanism implemented in Matlab
Replies: 6
Views: 2826

Re: HH mechanism implemented in Matlab

Interestingly, when I do this trick in Matlab: V1 = V1*1e3; %------ m alpha(1) = 1e3*0.1*vtrap((-V1-40.0),10.0); beta(1) = 1e3*4.0*exp((-V1-65.0)/18.0); %------ h alpha(2) = 1e3*0.07*exp((-V1-65.0)/20.0); beta(2) = 1e3*1.0 /(exp((-V1-35.0)/10.0)+1); %------ n alpha(3) = 1e3*0.01*vtrap((-55.0-V1 ),10...
by brocke
Tue Sep 03, 2013 5:47 am
Forum: Other questions
Topic: HH mechanism implemented in Matlab
Replies: 6
Views: 2826

HH mechanism implemented in Matlab

Dear group, I've tried to replicate voltage and current traces in Matlab with HH mechanism, but the traces don't look similar. Probably, there is a trick, and it was discussed already. If it's so, excuse me for this, I really searched and didn't find. I have a simple one isopotentional section and H...