Alpha rhythm in vitro visual cortex (Traub et al 2020)

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Accession:263703
The paper describes an experimental model of the alpha rhythm generated by layer 4 pyramidal neurons in a visual cortex slice. The simulation model is derived from that of Traub et al. (2005) J Neurophysiol, developed for thalamocortical oscillations.
Reference:
1 . Traub RD, Hawkins K, Adams NE, Hall SP, Simon A, Whittington MA (2020) Layer 4 pyramidal neuron dendritic bursting underlies a post-stimulus visual cortical alpha rhythm Nature Communications Biology, in press
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Thalamus; Neocortex;
Cell Type(s): Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex layer 4 pyramidal cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron; Neocortex spiny stellate cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: FORTRAN;
Model Concept(s): Brain Rhythms; Dendritic Action Potentials;
Implementer(s): Traub, Roger D [rtraub at us.ibm.com];
Search NeuronDB for information about:  Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; I Na,p; I Na,t; I L high threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
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alpha_rhythm_code_RT
readme.txt
alphaY33.pdf
alphaY67.f
alphaY67.pdf
dexptablebig_setup.f *
dexptablesmall_setup.f *
durand.f *
fnmda.f *
gettime.c *
groucho_gapbld.f *
groucho_gapbld_mix.f *
integrate_deepaxaxx.f *
integrate_deepbaskx.f *
integrate_deepLTSx.f *
integrate_deepng.f *
integrate_nontuftRSXXB.f
integrate_nrtxB.f *
integrate_spinstelldiegoxB.f *
integrate_supaxaxx.f *
integrate_supbaskx.f *
integrate_supLTSX.f *
integrate_supng.f *
integrate_suppyrFRBxPB.f *
integrate_suppyrRSXPB.f
integrate_tcrxB.f *
integrate_tuftIBVx3B.f
integrate_tuftRSXXB.f *
makefile
otis.f *
otis_table_setup.f *
synaptic_compmap_construct.f *
synaptic_map_construct.f *
                            
c Program assumes A, BB1, BB2 defined in calling program
c as follows:
c        A = DEXP(-2.847d0)
c        BB1 = DEXP(-.693d0)
c        BB2 = DEXP(-3.101d0)
        SUBROUTINE FNMDA (VSTOR, OPEN, numcells, numcomps,
     &    MG, L, A, BB1, BB2) 
c Computes "open" for all compartments of cell # L

           integer L, numcells, numcomps, i
       REAL*8 VSTOR(numcomps,numcells), OPEN(numcomps)
       REAL*8 A, BB1, BB2, VM, A1, A2, B1, B2, MG
c modify so that potential is absolute and not relative to
c  "rest"
C  TO DETERMINE VOLTAGE-DEPENDENCE OF NMDA CHANNELS
           DO 1, I = 1, numcomps
           VM = VSTOR(I,L)
           A1 = DEXP(-.016d0*VM - 2.91d0)
           A2 = 1000.d0 * MG * DEXP (-.045d0 * VM - 6.97d0)
           B1 = DEXP(.009d0*VM + 1.22d0)
           B2 = DEXP(.017d0*VM + 0.96d0)
        OPEN(I)     = 1.d0/(1.d0 + (A1+A2)*(A1*BB1 + A2*BB2) /
     X   (A*A1*(B1+BB1) + A*A2*(B2+BB2))  )
C  FROM JAHR & STEVENS, EQ. 4A
C               DO 124, J = 1, 19
C          OPEN(J) = 1./(1.+.667* EXP(-0.07*(VSTOR(J)-60.)) )
C  FROM CHUCK STEVENS
1               CONTINUE
                        END

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