Search found 11 matches

by Bob02
Thu May 11, 2017 11:08 am
Forum: General questions and discussions about computational neuroscience
Topic: Units in mod file-ca2+ dependent K+ channel
Replies: 10
Views: 13464

Re: Units in mod file-ca2+ dependent K+ channel

Ted, Thank you for the comprehensive explanation. I have only one more question, How does NEURON deal with the "cai" and "vca" equations in this mod file when it solving current balance equation. For example, does NEURON deal with "cai'=  f*(-(alpha*(ican))-(kca*cai))" as: cai'=  f*(-(alpha*(ican*ar...
by Bob02
Mon May 01, 2017 9:38 am
Forum: General questions and discussions about computational neuroscience
Topic: Units in mod file-ca2+ dependent K+ channel
Replies: 10
Views: 13464

Re: Units in mod file-ca2+ dependent K+ channel

Interesting code. Is it based on some other model implemented for NEURON, or what? model or mod file? The original model developed in our lab previously, and it is published few years ago. Now, we are trying to improve and .... The equation for Ca2+ and VCa derived using same method as: 1- Booth et...
by Bob02
Fri Apr 28, 2017 1:17 pm
Forum: General questions and discussions about computational neuroscience
Topic: Units in mod file-ca2+ dependent K+ channel
Replies: 10
Views: 13464

Re: Units in mod file-ca2+ dependent K+ channel

Sorry, I forgot to mention that modlunit says: units: 1000 /m3-sec units: 10 coul/m2-sec I also modified the code as: TITLE Motoneuron Soma channels : Calcium channels + Calcium Dynamics - Soma NEURON { SUFFIX CaSTest4ed NONSPECIFIC_CURRENT ikca NONSPECIFIC_CURRENT ican RANGE gkcabar, gcanbar, eca R...
by Bob02
Fri Apr 28, 2017 10:25 am
Forum: General questions and discussions about computational neuroscience
Topic: Units in mod file-ca2+ dependent K+ channel
Replies: 10
Views: 13464

Re: Units in mod file-ca2+ dependent K+ channel

What does modlunit tell you? For, cai' [mM/ms] = f*(-(alpha*ican [mA/cm2] )-(kca [1/ms] *cai [mM] )) "f" is constant. I know "alpha" have to be mM/mC/cm2 because by substituting [mC/cm2] with [mA/cm2] * [ms] (Q = I * t), we have [mM/ms] = -[mM/mA/cm2] * [mA/cm2]- [mM/ms]. But, I ignored the "alpha"...
by Bob02
Thu Apr 27, 2017 12:16 pm
Forum: General questions and discussions about computational neuroscience
Topic: Units in mod file-ca2+ dependent K+ channel
Replies: 10
Views: 13464

Re: Units in mod file-ca2+ dependent K+ channel

Thank you for your reply. Actually, the DERIVATIVE block contain this equation: cai' = f * ( -alpha * ica - kca * cai) where, f is the percentage of free to bound Ca+2 (set to 0.01 based on report from Helmchen et al. 1996). The parameter alpha (mM/mC/cm2) converts the total ica to Ca+2 concentratio...
by Bob02
Tue Apr 25, 2017 2:44 pm
Forum: General questions and discussions about computational neuroscience
Topic: Units in mod file-ca2+ dependent K+ channel
Replies: 10
Views: 13464

Units in mod file-ca2+ dependent K+ channel

Hi, How can I define the unit of parameter "alpha" in mod file, which converts the total calcium current to Ca2+ concentration? Its unit is "mM/mC/cm2" (mC is "milli Coulomb" and mM is "milli molar"). Is this statement correct? UNITS { (mA) = (milliamp) (mV) = (millivolt) (molar) = (1/liter) (mM-cm2...
by Bob02
Tue Apr 04, 2017 4:40 pm
Forum: General questions and discussions about computational neuroscience
Topic: Current balance equations of multi-compartment
Replies: 8
Views: 12595

Re: Current balance equations of multi-compartment

With those anatomical sizes, that thing is for all practical purposes isopotential--unless cytoplasmic resistivity is at least 3000 ohm cm, i.e. 30 times larger than the typical 100 ohm cm that is usually assumed. But then this is really a mathematician's model anyway, so Ra can be whatever is need...
by Bob02
Tue Apr 04, 2017 4:10 pm
Forum: General questions and discussions about computational neuroscience
Topic: Current balance equations of multi-compartment
Replies: 8
Views: 12595

Re: Current balance equations of multi-compartment

Maybe. Exactly what statements did you use to connect the compartments of your NEURON model to each other? create soma,dend,AH proc topol() { soma { connect dend(0), (0) connect AH(0), (1) } } proc geometry() { soma{ nseg = 1 diam = 30 L = 10 } dend { nseg = 1 diam = 100 L= 200 } AH { nseg = 1 diam...
by Bob02
Tue Apr 04, 2017 12:12 pm
Forum: General questions and discussions about computational neuroscience
Topic: Current balance equations of multi-compartment
Replies: 8
Views: 12595

Re: Current balance equations of multi-compartment

Well, here's one problem: LHS of your ODEs is in pA (because pF*mV/ms = pF*V/s = pA). 1st term of the 1st ODE is in 1e3*nA = pA, which is good, but 2nd term is in 1e3*uS*V = nA. Be sure to check the other terms as well and fix as necessary. Thanks for reply. Actually, the initial conditions of memb...
by Bob02
Mon Apr 03, 2017 12:51 pm
Forum: General questions and discussions about computational neuroscience
Topic: Current balance equations of multi-compartment
Replies: 8
Views: 12595

Re: Current balance equations of multi-compartment

The ODEs that govern membrane potential are correct as far as they go, but I don't see any scale factors related to the facts that, for NEURON, time is in ms and membrane potential is in mV. Yes, there is a scale factor. I’ve multiplied the right side of the current-balance equations to 1000 to hav...
by Bob02
Sun Apr 02, 2017 1:34 pm
Forum: General questions and discussions about computational neuroscience
Topic: Current balance equations of multi-compartment
Replies: 8
Views: 12595

Current balance equations of multi-compartment

I am using XPPAUT/MATLAB to apply bifurcation analysis on a model with soma, dendrite and axon hillock. Then, I will compare/validate the results with ones in NEURON. So, I should use the current-balance equations in XPPAUT/MATLAB same as ones use in NEURON. As XPPAUT/MATLAB are kinds of advanced ca...