ModelDB open source code for HH model with time-depended ion concentrations
** 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@physik.hu-berlin.de skype: markus.dahlem
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Markus A Dahlem