Effect of ionic diffusion on extracellular potentials (Halnes et al 2016)

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Accession:225311
"Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. ..."
Reference:
1 . Halnes G, Mäki-Marttunen T, Keller D, Pettersen KH, Andreassen OA, Einevoll GT (2016) Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue. PLoS Comput Biol 12:e1005193 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular; Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex U1 L6 pyramidal corticalthalamic cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB; NEURON;
Model Concept(s): Extracellular Fields;
Implementer(s): Halnes, Geir [geir.halnes at nmbu.no]; Maki-Marttunen, Tuomo [tuomo.maki-marttunen at tut.fi];
Search NeuronDB for information about:  Neocortex U1 L6 pyramidal corticalthalamic cell;
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haymod_sumcurr
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CaDynamics_E2.mod *
Ih.mod *
Im.mod *
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K_Tst.mod *
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calcsumcurr_manyareagsynmediumtau_parts_fixeddt.py
combinemattomat_fixeddt.m
interpolate.m *
interpolate_multidim.m *
summondata.m
sumrepetitions_seed.m
                            
function summondata
% Returns
% N = number of voxels
% times = times
% jk,   jna, jca: Ion fluxes onto voxels (N x times)
% jx:   flux of unspecified ion into voxels (assumed valence -1)
%       jx contains il, ih and isyn
% icap: capacitive current into voxel
% isyn: synaptic current into voxel (contained in jx)


N = 13;
iica = [];
iina = [];
iik = [];
iix = [];
iicap = [];
it = [];
iimemb = [];
iisyn = [];

str1 = 'currsums_parts_10000areagsynsmediumtau_fixeddt_type2_amp4.2e-05_tstop10000.0_nseg20_dt0.025_';
str2 = '_comb_summed.mat';

for i = 1:10
strseed = ['seed',num2str(i)];
strfile = [str1,strseed,str2];
load(strfile);

iion0 = ik + ina + ica + il + ih;
isyn = imemb - (iion0 + icap);
ix = il + ih + isyn; % all currents of unspecified ion species x

ts2 = ts(:,ts>=1600)-1600 + 8400*(i-1);
ica = ica(:,ts>=1600);
ina = ina(:,ts>=1600);
ik = ik(:,ts>=1600);
ix = ix(:,ts>=1600);
icap = icap(:,ts>=1600);
imemb = imemb(:,ts>=1600);
isyn = isyn(:,ts>=1600);

it = [it,ts2];
iica = [iica,ica];
iina = [iina, ina];
iik = [iik,ik];
iix = [iix,ix];
iicap = [iicap,icap];
iimemb = [iimemb,imemb];
iisyn = [iisyn,isyn];

end

% Convert to SI units
ts = it/1000; %s
icap = iicap*1e-9; % Ampere
imemb = iimemb*1e-9;
isyn = iisyn*1e-9;
ik = iik*1e-9; ina = iina*1e-9; ica = iica*1e-9; ix = iix*1e-9;

% Convert currents to fluxes (j_k = i_k/(z_k*F))
F = 96485.3365; % C/mol
jk = ik/F; % mol/s
jna = ina/F;
jca = ica/2/F;
jx = -ix/F; % I define x as unknown negative ion with valence 1

save('revdata.mat','N', 'ts', 'jk', 'jna', 'jca', 'jx', 'icap', 'isyn', 'imemb');

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