[Comp-neuro] ModelDB open source code for HH model with time-depended ion concentrations

Markus A Dahlem dahlem at physik.hu-berlin.de
Fri Oct 10 15:17:38 CEST 2014


** We made our source code from two recent papers and one accepted
manuscript now available on ModelDB **

*The code simulates the Hodgkin-Huxley model with time-dependent ion
concentrations.*


Briefly, the Hodgkin-Huxley (HH) model has 4 dynamical variables.
Including Na+,K+, and Cl- extra-  and intracellular ion concentrations
introduces 6 further variables.

Various simple reduction techniques, such as adiabatic elimination,
synchronization,
mass conservation, and electroneutrality have been used to reduce this
extended
HH formalism to again only 5 dynamical variables, while the model still
retains adequate
biophysical realism. For example, bursting and cortical spreading
depression (SD) can
be simulated. The model conserves the HH action potential dynamics. See
Refs. [1,2]

The accession number for the  HH model with time-dependent
ion concentrations is 167714.
http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=167714

Moreover, the ModelDB accession number for a wild-type and
mutant SD model described in paper Ref [3] is 167715.
http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=167715

The model can be further reduced to only 4 dynamic variables (without Cl-).
For dynamic volume control and further features, please get in contact with
me, see below.

This models require XPP, which is freely available from:
http://www.math.pitt.edu/~bard/xpp/xpp.html

Refs
[1]  N. Huebel, E. Schöll, and M. A. Dahlem, Bistable dynamics underlying
excitability of ion homeostasis in neuron models, PLOS Comp. Biology.  10,
e1003551 (2014)
[2] N. Huebel and M. A. Dahlem, Dynamics from seconds to hours in
Hodgkin–Huxley model with time–dependent ion concentrations and buffer
reservoirs (accepted PLoS Comp Biol, arXiv 1404.3031)
[3]  M. A. Dahlem, J. Schumacher, and N. Huebel. Linking a genetic defect
in migraine to spreading depression in a computational model, PeerJ, 2:e379
(2014).


--

Dr. Markus Dahlem
Web: https://sites.google.com/site/markusadahlem
Max Planck Institute for the Physics of Complex Systems
Department Biological Physics
Nöthnitzer Straße 38
01187 Dresden
Germany
   and
Humboldt-Universität zu Berlin
AG NLD Cardiovascular Physics
Robert-Koch-Platz 4
10115 Berlin
Germany

phone: +49 (0)351 871 2402
email: dahlem at physik.hu-berlin.de
skype: markus.dahlem
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