18 Jan
2021
18 Jan
'21
9:32 p.m.
Dear Maryada,
The NMDA channel dynamics are not very clearly described in the original paper by Hill and
Tononi. The model implemented in NEST is in this point mostly based on inspecting the code
of Sean Hill’s Synthesis simulator. Eq (1) and (2) in the NMDA channel section of the
notebook on the model are based on Equation (2) of Vargas-Caballero and Robinson (2003)
[VCR in the following] and text below that equation, from which the slow and fast NMDA
unblocking time constants are also taken. The exponential time courses in VCR Eq 2 are in
NEST modeled by the differential equation (5) in the notebook.
Further, the logic is as follows: m -> 0 corresponds to blocking of NMDA channels. This
happens for small values of V, V < V_act. Blocking is assumed to be instantaneous, and
this is implented by the minimum operation in Eq (4).
What remains is notebook eq (3), giving the steady-state blocking of the NMDA channel for
a given voltage. The equation here is based on VCR eq (1), with our V_act corresponding to
their V_0.5 and our S_act corresponding to their z delta F / RT (I believe some
parentheses in VCR Eq 1 are incorrectly placed), see also VCR Fig 1B.
So V_act is the voltage for which m_inf(V) = ½ and S_act determines the slope of the
sigmoidal activation curve, with large S_act corresponding to a steeper curve.
Synthesis implemented this equation using a look-up table. I obtained the parameter values
for V_act and S_act in ht_neuron by fitting eq (3) to this lookup table.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Department of Data Science
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
On 18/01/2021, 16:49, "Maryada Maryada"
<er.maryada@gmail.com<mailto:er.maryada@gmail.com>> wrote:
Dear Dr. Plesser,
Thanks for your reply. Yes I checked the notebook and in my email I attached a snippet
(see attachment). I couldn't link V_act and S_act with the text in the paper. Could
you please briefly define the two variables? or point me in the right direction?
On Wed, Jan 13, 2021 at 3:32 PM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Dear Maryada,
The model description in Hill & Tononi (2005) is partially incomplete and includes
some typos. In the NEST source code, you will find a Jupyter Notebook describing the
differences between the model description in the paper and the NEST implementation in
directory docs/model_details.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Department of Data Science
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
On 13/01/2021, 12:24, "Maryada Maryada"
<er.maryada@gmail.com<mailto:er.maryada@gmail.com>> wrote:
Dear all,
I am looking for the details of ht_neuron model and referred to DOI:
https://doi.org/10.1152/jn.00915.2004 for details. However, I couldn't find
information on V_act_NMDA and S_act_NMDA. Can anyone please point me in the specific
paragraph/table in the paper or share a one line explanation.
I have attached a screenshot of the equation from the example notebook and also the
complete notebook for quick reference
--
Thanks and Regards
Maryada
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Thanks and Regards
Maryada