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molecules_rxns.mdl
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molecules_rxns.mdl
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/******************************************************/
/* A simple model of a single AZ at the calyx of Held */
/* */
/* Definition of AMPARs */
/* */
/* Matthias Hennig */
/* [email protected] */
/* Updated by Jacob Czech */
/* [email protected] */
/******************************************************/
/* the transmitter in question */
DEFINE_MOLECULES
{
Glu { DIFFUSION_CONSTANT_3D = D }
AMPAR_C0 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_C1 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_C2 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_C3 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_C4 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_O1 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_O2 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_O3 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_O4 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_D1 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_D2 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_D3 { DIFFUSION_CONSTANT_2D = 0 }
AMPAR_D4 { DIFFUSION_CONSTANT_2D = 0 }
}
DEFINE_REACTIONS
{
/*C0[>C1{ Rb:+Glu,POSITIVE_POLE}]*/
AMPAR_C0' + Glu' -> AMPAR_C1' [Rb]
/*C1[>C2{2*Rb:+Glu,POSITIVE_POLE}][>O1{Ro1}] [>C0{4*Ru1:-Glu,POSITIVE_POLE}][>D1{Rd0}]*/
AMPAR_C1' + Glu' -> AMPAR_C2' [2*Rb]
AMPAR_C1' -> AMPAR_O1' [Ro1]
AMPAR_C1' -> AMPAR_C0' + Glu' [4*Ru1]
AMPAR_C1' -> AMPAR_D1' [Rd0]
/*C2[>C3{3*Rb:+Glu,POSITIVE_POLE}][>O2{Ro1*2}][>C1{3*Ru1:-Glu,POSITIVE_POLE}][>D2{Rd1*2}]*/
AMPAR_C2' + Glu' -> AMPAR_C3' [3*Rb]
AMPAR_C2' -> AMPAR_O2' [Ro1*2]
AMPAR_C2' -> AMPAR_C1' + Glu' [3*Ru1]
AMPAR_C2' -> AMPAR_D2' [Rd1*2]
/*C3[>C4{4*Rb:+Glu,POSITIVE_POLE}][>O3{Ro1*3}][>C2{2*Ru1:-Glu,POSITIVE_POLE}][>D3{Rd1*3}]*/
AMPAR_C3' + Glu' -> AMPAR_C4' [4*Rb]
AMPAR_C3' -> AMPAR_O3' [Ro1*3]
AMPAR_C3' -> AMPAR_C2' + Glu' [2*Ru1]
AMPAR_C3' -> AMPAR_D3' [Rd1*3]
/*C4[>O4{Ro1*4}][>C3{Ru1:-Glu,POSITIVE_POLE}][>D4{Rd1*4}]*/
AMPAR_C4' -> AMPAR_O4' [Ro1*4]
AMPAR_C4' -> AMPAR_C3' + Glu' [Ru1]
AMPAR_C4' -> AMPAR_D4' [Rd1*4]
/*O1[>C1{Rc1}]*/
AMPAR_O1' -> AMPAR_C1' [Rc1]
/*O2[>C2{Rc1}]*/
AMPAR_O2' -> AMPAR_C2' [Rc1]
/*O3[>C3{Rc1}]*/
AMPAR_O3' -> AMPAR_C3' [Rc1]
/*O4[>C4{Rc1}]*/
AMPAR_O4' -> AMPAR_C4' [Rc1]
/*D1[>C1{Rr1}][>D2{Rd2:+Glu,POSITIVE_POLE}]*/
AMPAR_D1' -> AMPAR_C1' [Rr1]
AMPAR_D1' + Glu' -> AMPAR_D2' [Rd2]
/*D2[>C2{Rr1}][>D3{2*Rd2:+Glu,POSITIVE_POLE}][>D1{3*Rr2:-Glu,POSITIVE_POLE}]*/
AMPAR_D2' -> AMPAR_C2' [Rr1]
AMPAR_D2' + Glu' -> AMPAR_D3' [2*Rd2]
AMPAR_D2' -> AMPAR_D1' + Glu' [3*Rr2]
/*D3[>C3{Rr1}][>D4{3*Rd2:+Glu,POSITIVE_POLE}][>D2{2*Rr2:-Glu,POSITIVE_POLE}]*/
AMPAR_D3' -> AMPAR_C3' [Rr1]
AMPAR_D3' + Glu' -> AMPAR_D4' [3*Rd2]
AMPAR_D3' -> AMPAR_D2' + Glu' [2*Rr2]
/*D4[>C4{Rr1}][>D3{Rr2:-Glu,POSITIVE_POLE}]*/
AMPAR_D4' -> AMPAR_C4' [Rr1]
AMPAR_D4' -> AMPAR_D3' + Glu' [Rr2]
}
/* AMPA receptor kinetics */
/*DEFINE_REACTION AMPAR {*/
/* C0[>C1{ Rb:+Glu,POSITIVE_POLE}]*/
/* C1[>C2{2*Rb:+Glu,POSITIVE_POLE}][>O1{Ro1}] [>C0{4*Ru1:-Glu,POSITIVE_POLE}][>D1{Rd0}]*/
/* C2[>C3{3*Rb:+Glu,POSITIVE_POLE}][>O2{Ro1*2}][>C1{3*Ru1:-Glu,POSITIVE_POLE}][>D2{Rd1*2}]*/
/* C3[>C4{4*Rb:+Glu,POSITIVE_POLE}][>O3{Ro1*3}][>C2{2*Ru1:-Glu,POSITIVE_POLE}][>D3{Rd1*3}]*/
/* C4[>O4{Ro1*4}][>C3{Ru1:-Glu,POSITIVE_POLE}][>D4{Rd1*4}]*/
/* O1[>C1{Rc1}]*/
/* O2[>C2{Rc1}]*/
/* O3[>C3{Rc1}]*/
/* O4[>C4{Rc1}]*/
/* D1[>C1{Rr1}][>D2{Rd2:+Glu,POSITIVE_POLE}]*/
/* D2[>C2{Rr1}][>D3{2*Rd2:+Glu,POSITIVE_POLE}][>D1{3*Rr2:-Glu,POSITIVE_POLE}]*/
/* D3[>C3{Rr1}][>D4{3*Rd2:+Glu,POSITIVE_POLE}][>D2{2*Rr2:-Glu,POSITIVE_POLE}]*/
/* D4[>C4{Rr1}][>D3{Rr2:-Glu,POSITIVE_POLE}]*/
/* REFERENCE_STATE C0 {*/
/* Glu*/
/* NUMBER_BOUND = 0*/
/* }*/
/*}*/