Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PP1nuc_D34nucPP1nuc+D34nuc PP1nuc_D34nuc_off nucleus MassAction
D3497cyto_PP2BcytoD3497cyto+PP2Bcyto D3497cyto_PP2Bcyto_off cytosol MassAction
PP1nuc_D3497nucPP1nuc+D3497nuc PP1nuc_D3497nuc_off nucleus MassAction
PP1cyto_D34cyto_PP2BcytoPP1nuc_D34nuc_PP2Bnuc PP1cyto_D34cyto_PP2Bcyto_cyto2nuc nucleusmembrane MassAction
PP2ApcytoPP2Apnuc PP2Apcyto2nuc nucleusmembrane MassAction
D97cyto_PKAcytoPKAcyto+D97cyto D97cyto_PKAcyto_off cytosol MassAction
PP1cyto_D3497cyto_PP2BcytoPP1nuc_D3497nuc_PP2Bnuc PP1cyto_D3497cyto_PP2Bcyto_cyto2nuc nucleusmembrane MassAction
D97cyto_PP2ApcytoPP2Apcyto+D97cyto D97cyto_PP2Apcyto_off cytosol MassAction
D97nucD97cyto D97nuc2cyto nucleusmembrane MassAction
D3497cyto+PP2ApcytoD3497cyto_PP2Apcyto D3497cyto_PP2Apcyto_on cytosol MassAction
DcytoDnuc Dcyto2nuc_passive nucleusmembrane MassAction
D34cytoD34nuc D34cyto2nuc_passive nucleusmembrane MassAction
PP2Bcyto+D3497cytoD3497cyto_PP2Bcyto D3497cyto_PP2Bcyto_on cytosol MassAction
PP1nuc_D34nucPP1cyto_D34cyto PP1nuc_D34nuc_nuc2cyto nucleusmembrane MassAction
Dnuc_CK2D97nuc+CK2 Dnuc_CK2_cat nucleus MassAction
D3497nucD3497cyto D3497nuc2cyto nucleusmembrane MassAction
D97nuc_PKAnucD3497nuc+PKAnuc D97nuc_PKAnuc_cat nucleus MassAction
PP2Anuc_PKAnucPP2Apnuc+PKAnuc PP2Anuc_PKAnuc_cat nucleus MassAction
D97nuc_PP2ApnucPP2Apnuc+Dnuc D97nuc_PP2Apnuc_cat nucleus MassAction
PP1nuc_D3497nuc_PP2BnucPP2Bnuc+PP1nuc+D97nuc PP1nuc_D3497nuc_PP2Bnuc_cat nucleus MassAction
PP1nuc_D3497nuc_PP2BnucPP1nuc_D3497nuc+PP2Bnuc PP1nuc_D3497nuc_PP2Bnuc_off nucleus MassAction
PP1cyto_D34cyto_PP2BcytoDcyto+PP2Bcyto+PP1cyto PP1cyto_D34cyto_PP2Bcyto_cat cytosol MassAction
D3497cytoD3497nuc D3497cyto2nuc nucleusmembrane MassAction
D3497nucD3497cyto D3497nuc2cyto_passive nucleusmembrane MassAction
D3497nuc+PP2BnucD3497nuc_PP2Bnuc D3497nuc_PP2Bnuc_on nucleus MassAction
PP2AnucPP2Acyto PP2Anuc2cyto nucleusmembrane MassAction
PP2Acyto_PKAcytoPKAcyto+PP2Apcyto PP2Acyto_PKAcyto_cat cytosol MassAction
PP2Acyto_PKAcytoPKAcyto+PP2Acyto PP2Acyto_PKAcyto_off cytosol MassAction
D34nuc_CK2CK2+D3497nuc D34nuc_CK2_cat nucleus MassAction
DnucDcyto Dnuc2cyto_passive nucleusmembrane MassAction
Dnuc_CK2Dnuc+CK2 Dnuc_CK2_off nucleus MassAction
DMNB_cAMPcAMP photoUncaging_DMNB_cAMP cytosol GeneralKinetics
Dcyto+PKAcytoDcyto_PKAcyto Dcyto_PKAcyto_on cytosol MassAction
Dnuc_PKAnucD34nuc+PKAnuc Dnuc_PKAnuc_cat nucleus MassAction
D97nuc+PKAnucD97nuc_PKAnuc D97nuc_PKAnuc_on nucleus MassAction
D3497cyto_PP2BcytoD3497nuc_PP2Bnuc D3497cyto_PP2Bcyto_cyto2nuc nucleusmembrane MassAction
PP2Bcyto+PP1cyto_D34cytoPP1cyto_D34cyto_PP2Bcyto PP1cyto_D34cyto_PP2Bcyto_on cytosol MassAction
D34nuc+PP2BnucD34nuc_PP2Bnuc D34nuc_PP2Bnuc_on nucleus MassAction
R2+PKAcytoR2C R2_PKAcyto_bind cytosol MassAction
Dcyto_PKAcytoPKAcyto+Dcyto Dcyto_PKAcyto_off cytosol MassAction
D3497cyto_PP2ApcytoD34cyto+PP2Apcyto D3497cyto_PP2Apcyto_cat cytosol MassAction
PP2Anuc+PKAnucPP2Anuc_PKAnuc PP2Anuc_PKAnuc_on nucleus MassAction
PP2BnucPP2Bcyto PP2Bnuc2cyto nucleusmembrane MassAction
PP2Acyto+PKAcytoPP2Acyto_PKAcyto PP2Acyto_PKAcyto_on cytosol MassAction
PP2Bnuc+PP1nuc_D3497nucPP1nuc_D3497nuc_PP2Bnuc PP1nuc_D3497nuc_PP2Bnuc_on nucleus MassAction
R2C+PKAcytoR2C2 R2C_PKAcyto_bind cytosol MassAction
PP1cyto_D3497cytoPP1cyto+D3497cyto PP1cyto_D3497_off cytosol MassAction
D3497cyto_PP2BcytoD97cyto+PP2Bcyto D3497cyto_PP2Bcyto_cat cytosol MassAction
PP1nuc_D34nuc_PP2BnucPP1nuc+Dnuc+PP2Bnuc PP1nuc_D34nuc_PP2Bnuc_cat nucleus MassAction
D34nuc+PP1nucPP1nuc_D34nuc PP1nuc_D34nuc_on nucleus MassAction
Dcyto_PKAcytoPKAcyto+D34cyto Dcyto_PKAcyto_cat cytosol MassAction
PP1cyto_D34cyto_PP2BcytoPP2Bcyto+PP1cyto_D34cyto PP1cyto_D34cyto_PP2Bcyto_off cytosol MassAction
D97cyto_PP2ApcytoD97nuc_PP2Apnuc D97cyto_PP2Apcyto_cyto2nuc nucleusmembrane MassAction
Dnuc+CK2Dnuc_CK2 Dnuc_CK2_on nucleus MassAction
PP1cyto_D34cytoPP1nuc_D34nuc PP1cyto_D34cyto_cyto2nuc nucleusmembrane MassAction
D3497nuc_PP2BnucD3497cyto_PP2Bcyto D3497nuc_PP2Bnuc_nuc2cyto nucleusmembrane MassAction
D3497nuc_PP2ApnucD34nuc+PP2Apnuc D3497nuc_PP2Apnuc_cat nucleus MassAction
D34nuc_PP2BnucPP2Bnuc+Dnuc D34nuc_PP2Bnuc_cat nucleus MassAction
DcytoDnuc Dcyto2nuc nucleusmembrane MassAction
cAMPsourcecAMP+cAMPsource cAMPsource2cAMP cytosol MassAction
D97nuc_PKAnucD97cyto_PKAcyto D97nuc_PKAnuc_nuc2cyto nucleusmembrane MassAction
cAMP_PDE10AAMP+PDE10A cAMP_PDE10A_cat cytosol MassAction
PP1cyto_D34cytoPP1cyto+D34cyto PP1cyto_D34cyto_off cytosol MassAction
PKAnucPKAcyto PKAnuc2cyto nucleusmembrane MassAction
D3497nuc+PP2ApnucD3497nuc_PP2Apnuc D3497nuc_PP2Apnuc_on nucleus MassAction
PKAnuc+DnucDnuc_PKAnuc Dnuc_PKAnuc_on nucleus MassAction
D34cyto_PP2BcytoD34cyto+PP2Bcyto D34cyto_PP2Bcyto_off cytosol MassAction
D3497cyto_PP2ApcytoPP2Apcyto+D3497cyto D3497cyto_PP2Apcyto_off cytosol MassAction
PP1cytoPP1nuc PP1cyto2nuc nucleusmembrane MassAction
D34nuc_CK2CK2+D34nuc D34nuc_CK2_off nucleus MassAction
PP1nuc_D34nuc_PP2BnucPP1nuc_D34nuc+PP2Bnuc PP1nuc_D34nuc_PP2Bnuc_off nucleus MassAction
PP1nuc_D3497nuc_PP2BnucPP1cyto_D3497cyto_PP2Bcyto PP1nuc_D3497nuc_PP2Bnuc_nuc2cyto nucleusmembrane MassAction
D97cyto+PP2ApcytoD97cyto_PP2Apcyto D97cyto_PP2Apcyto_on cytosol MassAction
cAMP4_R2cAMP+cAMP+cAMP+R2+cAMP cAMP4_R2_releasecAMP cytosol MassAction
PP2Anuc_PKAnucPP2Acyto_PKAcyto PP2Anuc_PKAnuc_nuc2cyto nucleusmembrane MassAction
D34nuc_PP2BnucPP2Bnuc+D34nuc D34nuc_PP2Bnuc_off nucleus MassAction
D97cyto_PP2ApcytoDcyto+PP2Apcyto D97cyto_PP2Apcyto_cat cytosol MassAction
PP1cyto_D3497cyto_PP2BcytoPP1cyto+D97cyto+PP2Bcyto PP1cyto_D3497cyto_PP2Bcyto_cat cytosol MassAction
cAMP+R2C2cAMP_R2C2 cAMP_R2C2_onoff cytosol MassAction
D3497nuc_PP2BnucPP2Bnuc+D97nuc D3497nuc_PP2Bnuc_cat nucleus MassAction
D34nuc+CK2D34nuc_CK2 D34nuc_CK2_on nucleus MassAction
D97nuc_PP2ApnucPP2Apnuc+D97nuc D97nuc_PP2Apnuc_off nucleus MassAction
D34cyto_PP2BcytoD34nuc_PP2Bnuc D34cyto_PP2Bcyto_cyto2nuc nucleusmembrane MassAction
cAMP4_R2C2cAMP4_R2C+PKAcyto cAMP4_R2C_PKA_onoff cytosol MassAction
cAMP+cAMP2_R2C2cAMP3_R2C2 cAMP_cAMP2_R2C2_onoff cytosol MassAction
cAMP4_R2CcAMP4_R2+PKAcyto cAMP4_R2_PKA_onoff cytosol MassAction
D97nucD97cyto D97nuc2cyto_passive nucleusmembrane MassAction
Dcyto_PKAcytoDnuc_PKAnuc Dcyto_PKAcyto_cyto2nuc nucleusmembrane MassAction
PP2ApnucPP2Apcyto PP2Apnuc2cyto nucleusmembrane MassAction
PP2Anuc_PKAnucPP2Anuc+PKAnuc PP2Anuc_PKANuc_off nucleus MassAction
PKAcytoPKAnuc PKAcyto2nuc nucleusmembrane MassAction
PP2Acyto_PKAcytoPP2Anuc_PKAnuc PP2Acyto_PKAcyto_cyto2nuc nucleusmembrane MassAction
D3497cyto+PP1cytoPP1cyto_D3497cyto PP1cyto_D3497cyto_on cytosol MassAction
D97nuc_PP2ApnucD97cyto_PP2Apcyto D97nuc_PP2Apnuc_nuc2cyto nucleusmembrane MassAction
PP2ApcytoPP2Acyto PP2Apcytodephosphorylation cytosol MassAction
PP2BcytoPP2Bnuc PP2Bcyto2nuc nucleusmembrane MassAction
PP1cyto_D3497cyto+PP2BcytoPP1cyto_D3497cyto_PP2Bcyto PP1cyto_D3497cyto_PP2Bcyto_on cytosol MassAction
PP1nuc_D34nuc+PP2BnucPP1nuc_D34nuc_PP2Bnuc PP1nuc_D34nuc_PP2Bnuc_on nucleus MassAction
PP2Apnuc+D97nucD97nuc_PP2Apnuc D97nuc_PP2Apnuc_on nucleus MassAction
D34cytoD34nuc D34cyto2nuc nucleusmembrane MassAction
PP2AcytoPP2Anuc PP2Acyto2nuc nucleusmembrane MassAction
PP1cyto_D3497cyto_PP2BcytoPP1cyto_D3497cyto+PP2Bcyto PP1cyto_D3497cyto_PP2Bcyto_off cytosol MassAction
PP1nucPP1cyto PP1nuc2cyto nucleusmembrane MassAction
D97cytoD97nuc D97cyto2nuc_passive nucleusmembrane MassAction
cAMP+cAMP_R2C2cAMP2_R2C2 cAMP_cAMP_R2C2_onoff cytosol MassAction
PP1cyto_D3497cytoPP1nuc_D3497nuc PP1cyto_D3497cyto_cyto2nuc nucleusmembrane MassAction
PP1nuc_D3497nucPP1cyto_D3497cyto PP1nuc_D3497nuc_nuc2cyto nucleusmembrane MassAction
D34cyto_PP2BcytoDcyto+PP2Bcyto D34cyto_PP2Bcyto_cat cytosol MassAction
D34cyto+PP2BcytoD34cyto_PP2Bcyto D34cyto_PP2Bcyto_on cytosol MassAction
D3497nuc_PP2BnucD3497nuc+PP2Bnuc D3497nuc_PP2Bnuc_off nucleus MassAction
D3497cytoD3497nuc D3497cyto2nuc_passive nucleusmembrane MassAction
D34nucD34cyto D34nuc2cyto_passive nucleusmembrane MassAction
D97cyto_PKAcytoD97nuc_PKAnuc D97cyto_PKAcyto_cyto2nuc nucleusmembrane MassAction
D3497nuc_PP2ApnucPP2Apnuc+D3497nuc D3497nuc_PP2Apnuc_off nucleus MassAction
PP2ApnucPP2Anuc PP2Apnucdephosphorylation nucleus MassAction
D3497nuc+PP1nucPP1nuc_D3497nuc PP1nuc_D3497nuc_on nucleus MassAction
D97cyto+PKAcytoD97cyto_PKAcyto D97cyto_PKAcyto_on cytosol MassAction
PP1cyto+D34cytoPP1cyto_D34cyto PP1cyto_D34cyto_on cytosol MassAction
D97cytoD97nuc D97cyto2nuc nucleusmembrane MassAction
Dnuc_PKAnucPKAnuc+Dnuc Dnuc_PKAnuc_off nucleus MassAction
cAMP3_R2C2+cAMPcAMP4_R2C2 cAMP_cAMP3_R2C2_onoff cytosol MassAction
D3497cyto_PP2ApcytoD3497nuc_PP2Apnuc D3497cyto_PP2Apcyto_cyto2nuc nucleusmembrane MassAction
D3497nuc_PP2ApnucD3497cyto_PP2Apcyto D3497nuc_PP2Apnuc_nuc2cyto nucleusmembrane MassAction
D97cyto_PKAcytoD3497cyto+PKAcyto D97cyto_PKAcyto_cat cytosol MassAction
D97nuc_PKAnucD97nuc+PKAnuc D97nuc_PKAnuc_off nucleus MassAction
cAMP+PDE10AcAMP_PDE10A cAMP_PDE10A_onoff cytosol MassAction

Structures

Name
Type
Electrical
cellmembrane Membrane cytosol(+)   c0(-)
nucleusmembrane Membrane nucleus(+)   cytosol(-)
c0 Compartment (+)   (-)
cytosol Compartment (+)   (-)
nucleus Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
cAMPsource cytosol cytosol
D3497cyto cytosol cytosol
PP1cyto cytosol cytosol
PP1cyto_D34cyto cytosol cytosol
Dcyto cytosol cytosol
D97cyto_PP2Apcyto cytosol cytosol
R2 cytosol cytosol
PP2Bcyto cytosol cytosol
PP2Anuc nucleus nucleus
Dnuc_PKAnuc nucleus nucleus
D97nuc_PP2Apnuc nucleus nucleus
PP1cyto_D3497cyto_PP2Bcyto cytosol cytosol
PDE10A cytosol cytosol
cAMP_PDE10A cytosol cytosol
D97cyto_PKAcyto cytosol cytosol
PP1cyto_D34cyto_PP2Bcyto cytosol cytosol
AMP cytosol cytosol
PP1nuc_D34nuc_PP2Bnuc nucleus nucleus
cAMP cytosol cytosol
DMNB_cAMP cytosol cytosol
light_spot cytosol cytosol
R2C cytosol cytosol
D34nuc_CK2 nucleus nucleus
cAMP4_R2C2 cytosol cytosol
cAMP4_R2C cytosol cytosol
cAMP3_R2C2 cytosol cytosol
cAMP_R2C2 cytosol cytosol
cAMP2_R2C2 cytosol cytosol
D34cyto_PP2Bcyto cytosol cytosol
PKAcyto cytosol cytosol
D3497cyto_PP2Apcyto cytosol cytosol
Dcyto_PKAcyto cytosol cytosol
PP2Acyto_PKAcyto cytosol cytosol
Dnuc_CK2 nucleus nucleus
PP2Acyto cytosol cytosol
PP2Anuc_PKAnuc nucleus nucleus
Dnuc nucleus nucleus
cAMP4_R2 cytosol cytosol
D34nuc_PP2Bnuc nucleus nucleus
PP1nuc nucleus nucleus
PP1nuc_D34nuc nucleus nucleus
PP1nuc_D3497nuc nucleus nucleus
PP1nuc_D3497nuc_PP2Bnuc nucleus nucleus
D3497nuc_PP2Apnuc nucleus nucleus
D97nuc nucleus nucleus
D3497nuc_PP2Bnuc nucleus nucleus
CK2 nucleus nucleus
PP2Apcyto cytosol cytosol
PP2Apnuc nucleus nucleus
D97cyto cytosol cytosol
PP1cyto_D3497cyto cytosol cytosol
PP2Bnuc nucleus nucleus
D34cyto cytosol cytosol
D34nuc nucleus nucleus
D3497nuc nucleus nucleus
PKAnuc nucleus nucleus
D97nuc_PKAnuc nucleus nucleus
R2C2 cytosol cytosol
D3497cyto_PP2Bcyto cytosol cytosol

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
cAMPinput_tertiary3 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_secondary3 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_primary3 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_primary1 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_primary2 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_secondary1 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_secondary2 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_tertiary1 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA
cAMPinput_tertiary2 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D) NA

Specifications (Species) - cAMPinput_tertiary3 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cAMPsource (200.0 * (t < 5.0) * (((x >= 150.0) && (x <= 151.8) && (y >= - 12.0) && (y <= - 10.5) && (z >= 5.0) && (z <= 6.0)) + ((x >= 152.0) && (x <= 152.5) && (y >= - 12.0) && (y <= - 10.5) && (z >= 5.0) && (z <= 5.5)))) [uM] 0.0 [um2/s] cytosol
D3497cyto 0.0 [uM] D_d32 [um2/s] cytosol
PP1cyto 5.0 [uM] D_pp1 [um2/s] cytosol
PP1cyto_D34cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
Dcyto 0.0 [uM] D_d32 [um2/s] cytosol
D97cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Bcyto 1.6 [uM] D_pp2b [um2/s] cytosol
PP1cyto_D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
PDE10A 1.0 [uM] D_pde10a [um2/s] cytosol
cAMP_PDE10A 0.0 [uM] D_pde10a [um2/s] cytosol
D97cyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP1cyto_D34cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
AMP 0.0 [uM] 0.0 [um2/s] cytosol
cAMP 0.0 [uM] 100.0 [um2/s] cytosol
DMNB_cAMP 0.0 [uM] 100.0 [um2/s] cytosol
light_spot 0.0 [uM] 0.0 [um2/s] cytosol
R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP4_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP4_R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP3_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP2_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
D34cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PKAcyto 0.0 [uM] D_pkac [um2/s] cytosol
D3497cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
Dcyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP2Acyto_PKAcyto 0.0 [uM] D_pp2apka [um2/s] cytosol
PP2Acyto 2.0 [uM] D_pp2a [um2/s] cytosol
cAMP4_R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Apcyto 0.0 [uM] D_pp2a [um2/s] cytosol
D97cyto 50.0 [uM] D_d32 [um2/s] cytosol
PP1cyto_D3497cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
D34cyto 0.0 [uM] D_d32 [um2/s] cytosol
R2C2 1.0 [uM] D_r2c2 [um2/s] cytosol
D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PP2Anuc 2.0 [uM] D_pp2a [um2/s] nucleus
Dnuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus
D97nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
PP1nuc_D34nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D34nuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
Dnuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
PP2Anuc_PKAnuc 0.0 [uM] D_pp2apka [um2/s] nucleus
Dnuc 0.0 [uM] D_d32 [um2/s] nucleus
D34nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
PP1nuc 5.0 [uM] D_pp1 [um2/s] nucleus
PP1nuc_D34nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D3497nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
D97nuc 30.0 [uM] D_d32 [um2/s] nucleus
D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
CK2 1.0 [uM] D_ck2 [um2/s] nucleus
PP2Apnuc 0.0 [uM] D_pp2a [um2/s] nucleus
PP2Bnuc 1.6 [uM] D_pp2b [um2/s] nucleus
D34nuc 0.0 [uM] D_d32 [um2/s] nucleus
D3497nuc 0.0 [uM] D_d32 [um2/s] nucleus
PKAnuc 0.0 [uM] D_pkac [um2/s] nucleus
D97nuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus

Specifications (Reaction) - cAMPinput_tertiary3 go to Simulations

Name
Enabled?
PP1nuc_D34nuc_off included
D3497cyto_PP2Bcyto_off included
PP1nuc_D3497nuc_off included
PP1cyto_D34cyto_PP2Bcyto_cyto2nuc included
PP2Apcyto2nuc included
D97cyto_PKAcyto_off included
PP1cyto_D3497cyto_PP2Bcyto_cyto2nuc included
D97cyto_PP2Apcyto_off included
D97nuc2cyto included
D3497cyto_PP2Apcyto_on included
Dcyto2nuc_passive included
D34cyto2nuc_passive included
D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_nuc2cyto included
Dnuc_CK2_cat included
D3497nuc2cyto included
D97nuc_PKAnuc_cat included
PP2Anuc_PKAnuc_cat included
D97nuc_PP2Apnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_off included
PP1cyto_D34cyto_PP2Bcyto_cat included
D3497cyto2nuc included
D3497nuc2cyto_passive included
D3497nuc_PP2Bnuc_on included
PP2Anuc2cyto included
PP2Acyto_PKAcyto_cat included
PP2Acyto_PKAcyto_off included
D34nuc_CK2_cat included
Dnuc2cyto_passive included
Dnuc_CK2_off included
photoUncaging_DMNB_cAMP included
Dcyto_PKAcyto_on included
Dnuc_PKAnuc_cat included
D97nuc_PKAnuc_on included
D3497cyto_PP2Bcyto_cyto2nuc included
PP1cyto_D34cyto_PP2Bcyto_on included
D34nuc_PP2Bnuc_on included
R2_PKAcyto_bind included
Dcyto_PKAcyto_off included
D3497cyto_PP2Apcyto_cat included
PP2Anuc_PKAnuc_on included
PP2Bnuc2cyto included
PP2Acyto_PKAcyto_on included
PP1nuc_D3497nuc_PP2Bnuc_on included
R2C_PKAcyto_bind included
PP1cyto_D3497_off included
D3497cyto_PP2Bcyto_cat included
PP1nuc_D34nuc_PP2Bnuc_cat included
PP1nuc_D34nuc_on included
Dcyto_PKAcyto_cat included
PP1cyto_D34cyto_PP2Bcyto_off included
D97cyto_PP2Apcyto_cyto2nuc included
Dnuc_CK2_on included
PP1cyto_D34cyto_cyto2nuc included
D3497nuc_PP2Bnuc_nuc2cyto included
D3497nuc_PP2Apnuc_cat included
D34nuc_PP2Bnuc_cat included
Dcyto2nuc included
cAMPsource2cAMP included
D97nuc_PKAnuc_nuc2cyto included
cAMP_PDE10A_cat included
PP1cyto_D34cyto_off included
PKAnuc2cyto included
D3497nuc_PP2Apnuc_on included
Dnuc_PKAnuc_on included
D34cyto_PP2Bcyto_off included
D3497cyto_PP2Apcyto_off included
PP1cyto2nuc included
D34nuc_CK2_off included
PP1nuc_D34nuc_PP2Bnuc_off included
PP1nuc_D3497nuc_PP2Bnuc_nuc2cyto included
D97cyto_PP2Apcyto_on included
cAMP4_R2_releasecAMP included
PP2Anuc_PKAnuc_nuc2cyto included
D34nuc_PP2Bnuc_off included
D97cyto_PP2Apcyto_cat included
PP1cyto_D3497cyto_PP2Bcyto_cat included
cAMP_R2C2_onoff included
D3497nuc_PP2Bnuc_cat included
D34nuc_CK2_on included
D97nuc_PP2Apnuc_off included
D34cyto_PP2Bcyto_cyto2nuc included
cAMP4_R2C_PKA_onoff included
cAMP_cAMP2_R2C2_onoff included
cAMP4_R2_PKA_onoff included
D97nuc2cyto_passive included
Dcyto_PKAcyto_cyto2nuc included
PP2Apnuc2cyto included
PP2Anuc_PKANuc_off included
PKAcyto2nuc included
PP2Acyto_PKAcyto_cyto2nuc included
PP1cyto_D3497cyto_on included
D97nuc_PP2Apnuc_nuc2cyto included
PP2Apcytodephosphorylation included
PP2Bcyto2nuc included
PP1cyto_D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_PP2Bnuc_on included
D97nuc_PP2Apnuc_on included
D34cyto2nuc included
PP2Acyto2nuc included
PP1cyto_D3497cyto_PP2Bcyto_off included
PP1nuc2cyto included
D97cyto2nuc_passive included
cAMP_cAMP_R2C2_onoff included
PP1cyto_D3497cyto_cyto2nuc included
PP1nuc_D3497nuc_nuc2cyto included
D34cyto_PP2Bcyto_cat included
D34cyto_PP2Bcyto_on included
D3497nuc_PP2Bnuc_off included
D3497cyto2nuc_passive included
D34nuc2cyto_passive included
D97cyto_PKAcyto_cyto2nuc included
D3497nuc_PP2Apnuc_off included
PP2Apnucdephosphorylation included
PP1nuc_D3497nuc_on included
D97cyto_PKAcyto_on included
PP1cyto_D34cyto_on included
D97cyto2nuc included
Dnuc_PKAnuc_off included
cAMP_cAMP3_R2C2_onoff included
D3497cyto_PP2Apcyto_cyto2nuc included
D3497nuc_PP2Apnuc_nuc2cyto included
D97cyto_PKAcyto_cat included
D97nuc_PKAnuc_off included
cAMP_PDE10A_onoff included

Simulations - cAMPinput_tertiary3 go to Specifications

Name
End Time
Output Options
cAMPtertiaryEnd 3600.0

OutputTimeStep 5.0

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1760091997

(Origin: 0.0, -14.0, 0.0; Extent: 155.0, 40.0, 11.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain2 301.60068965661543 [um3] nucleus
Volume Analytical subdomain1 1202.1930494498022 [um3] cytosol
Volume Analytical subdomain0 66696.20626089358 [um3] c0
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 1432.4688299433924 [um2] cellmembrane
Surface subdomain1_subdomain2_membrane subdomain1 | subdomain2 211.84616618489457 [um2] nucleusmembrane

Events

Name Variable Rate Expression

Specifications (Species) - cAMPinput_secondary3 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cAMPsource (200.0 * (t < 5.0) * ((x >= 90.0) && (x <= 91.8) && (y >= - 11.5) && (y <= - 10.0) && (z >= 5.0) && (z <= 5.5))) [uM] 0.0 [um2/s] cytosol
D3497cyto 0.0 [uM] D_d32 [um2/s] cytosol
PP1cyto 5.0 [uM] D_pp1 [um2/s] cytosol
PP1cyto_D34cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
Dcyto 0.0 [uM] D_d32 [um2/s] cytosol
D97cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Bcyto 1.6 [uM] D_pp2b [um2/s] cytosol
PP1cyto_D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
PDE10A 1.0 [uM] D_pde10a [um2/s] cytosol
cAMP_PDE10A 0.0 [uM] D_pde10a [um2/s] cytosol
D97cyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP1cyto_D34cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
AMP 0.0 [uM] 0.0 [um2/s] cytosol
cAMP 0.0 [uM] 100.0 [um2/s] cytosol
DMNB_cAMP 0.0 [uM] 100.0 [um2/s] cytosol
light_spot 0.0 [uM] 0.0 [um2/s] cytosol
R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP4_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP4_R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP3_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP2_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
D34cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PKAcyto 0.0 [uM] D_pkac [um2/s] cytosol
D3497cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
Dcyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP2Acyto_PKAcyto 0.0 [uM] D_pp2apka [um2/s] cytosol
PP2Acyto 2.0 [uM] D_pp2a [um2/s] cytosol
cAMP4_R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Apcyto 0.0 [uM] D_pp2a [um2/s] cytosol
D97cyto 50.0 [uM] D_d32 [um2/s] cytosol
PP1cyto_D3497cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
D34cyto 0.0 [uM] D_d32 [um2/s] cytosol
R2C2 1.0 [uM] D_r2c2 [um2/s] cytosol
D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PP2Anuc 2.0 [uM] D_pp2a [um2/s] nucleus
Dnuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus
D97nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
PP1nuc_D34nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D34nuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
Dnuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
PP2Anuc_PKAnuc 0.0 [uM] D_pp2apka [um2/s] nucleus
Dnuc 0.0 [uM] D_d32 [um2/s] nucleus
D34nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
PP1nuc 5.0 [uM] D_pp1 [um2/s] nucleus
PP1nuc_D34nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D3497nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
D97nuc 30.0 [uM] D_d32 [um2/s] nucleus
D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
CK2 1.0 [uM] D_ck2 [um2/s] nucleus
PP2Apnuc 0.0 [uM] D_pp2a [um2/s] nucleus
PP2Bnuc 1.6 [uM] D_pp2b [um2/s] nucleus
D34nuc 0.0 [uM] D_d32 [um2/s] nucleus
D3497nuc 0.0 [uM] D_d32 [um2/s] nucleus
PKAnuc 0.0 [uM] D_pkac [um2/s] nucleus
D97nuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus

Specifications (Reaction) - cAMPinput_secondary3 go to Simulations

Name
Enabled?
PP1nuc_D34nuc_off included
D3497cyto_PP2Bcyto_off included
PP1nuc_D3497nuc_off included
PP1cyto_D34cyto_PP2Bcyto_cyto2nuc included
PP2Apcyto2nuc included
D97cyto_PKAcyto_off included
PP1cyto_D3497cyto_PP2Bcyto_cyto2nuc included
D97cyto_PP2Apcyto_off included
D97nuc2cyto included
D3497cyto_PP2Apcyto_on included
Dcyto2nuc_passive included
D34cyto2nuc_passive included
D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_nuc2cyto included
Dnuc_CK2_cat included
D3497nuc2cyto included
D97nuc_PKAnuc_cat included
PP2Anuc_PKAnuc_cat included
D97nuc_PP2Apnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_off included
PP1cyto_D34cyto_PP2Bcyto_cat included
D3497cyto2nuc included
D3497nuc2cyto_passive included
D3497nuc_PP2Bnuc_on included
PP2Anuc2cyto included
PP2Acyto_PKAcyto_cat included
PP2Acyto_PKAcyto_off included
D34nuc_CK2_cat included
Dnuc2cyto_passive included
Dnuc_CK2_off included
photoUncaging_DMNB_cAMP included
Dcyto_PKAcyto_on included
Dnuc_PKAnuc_cat included
D97nuc_PKAnuc_on included
D3497cyto_PP2Bcyto_cyto2nuc included
PP1cyto_D34cyto_PP2Bcyto_on included
D34nuc_PP2Bnuc_on included
R2_PKAcyto_bind included
Dcyto_PKAcyto_off included
D3497cyto_PP2Apcyto_cat included
PP2Anuc_PKAnuc_on included
PP2Bnuc2cyto included
PP2Acyto_PKAcyto_on included
PP1nuc_D3497nuc_PP2Bnuc_on included
R2C_PKAcyto_bind included
PP1cyto_D3497_off included
D3497cyto_PP2Bcyto_cat included
PP1nuc_D34nuc_PP2Bnuc_cat included
PP1nuc_D34nuc_on included
Dcyto_PKAcyto_cat included
PP1cyto_D34cyto_PP2Bcyto_off included
D97cyto_PP2Apcyto_cyto2nuc included
Dnuc_CK2_on included
PP1cyto_D34cyto_cyto2nuc included
D3497nuc_PP2Bnuc_nuc2cyto included
D3497nuc_PP2Apnuc_cat included
D34nuc_PP2Bnuc_cat included
Dcyto2nuc included
cAMPsource2cAMP included
D97nuc_PKAnuc_nuc2cyto included
cAMP_PDE10A_cat included
PP1cyto_D34cyto_off included
PKAnuc2cyto included
D3497nuc_PP2Apnuc_on included
Dnuc_PKAnuc_on included
D34cyto_PP2Bcyto_off included
D3497cyto_PP2Apcyto_off included
PP1cyto2nuc included
D34nuc_CK2_off included
PP1nuc_D34nuc_PP2Bnuc_off included
PP1nuc_D3497nuc_PP2Bnuc_nuc2cyto included
D97cyto_PP2Apcyto_on included
cAMP4_R2_releasecAMP included
PP2Anuc_PKAnuc_nuc2cyto included
D34nuc_PP2Bnuc_off included
D97cyto_PP2Apcyto_cat included
PP1cyto_D3497cyto_PP2Bcyto_cat included
cAMP_R2C2_onoff included
D3497nuc_PP2Bnuc_cat included
D34nuc_CK2_on included
D97nuc_PP2Apnuc_off included
D34cyto_PP2Bcyto_cyto2nuc included
cAMP4_R2C_PKA_onoff included
cAMP_cAMP2_R2C2_onoff included
cAMP4_R2_PKA_onoff included
D97nuc2cyto_passive included
Dcyto_PKAcyto_cyto2nuc included
PP2Apnuc2cyto included
PP2Anuc_PKANuc_off included
PKAcyto2nuc included
PP2Acyto_PKAcyto_cyto2nuc included
PP1cyto_D3497cyto_on included
D97nuc_PP2Apnuc_nuc2cyto included
PP2Apcytodephosphorylation included
PP2Bcyto2nuc included
PP1cyto_D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_PP2Bnuc_on included
D97nuc_PP2Apnuc_on included
D34cyto2nuc included
PP2Acyto2nuc included
PP1cyto_D3497cyto_PP2Bcyto_off included
PP1nuc2cyto included
D97cyto2nuc_passive included
cAMP_cAMP_R2C2_onoff included
PP1cyto_D3497cyto_cyto2nuc included
PP1nuc_D3497nuc_nuc2cyto included
D34cyto_PP2Bcyto_cat included
D34cyto_PP2Bcyto_on included
D3497nuc_PP2Bnuc_off included
D3497cyto2nuc_passive included
D34nuc2cyto_passive included
D97cyto_PKAcyto_cyto2nuc included
D3497nuc_PP2Apnuc_off included
PP2Apnucdephosphorylation included
PP1nuc_D3497nuc_on included
D97cyto_PKAcyto_on included
PP1cyto_D34cyto_on included
D97cyto2nuc included
Dnuc_PKAnuc_off included
cAMP_cAMP3_R2C2_onoff included
D3497cyto_PP2Apcyto_cyto2nuc included
D3497nuc_PP2Apnuc_nuc2cyto included
D97cyto_PKAcyto_cat included
D97nuc_PKAnuc_off included
cAMP_PDE10A_onoff included

Simulations - cAMPinput_secondary3 go to Specifications

Name
End Time
Output Options
cAMPsecondaryEnd 3600.0

OutputTimeStep 5.0

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1760091997

(Origin: 0.0, -14.0, 0.0; Extent: 155.0, 40.0, 11.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain2 301.60068965661543 [um3] nucleus
Volume Analytical subdomain1 1202.1930494498022 [um3] cytosol
Volume Analytical subdomain0 66696.20626089358 [um3] c0
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 1432.4688299433924 [um2] cellmembrane
Surface subdomain1_subdomain2_membrane subdomain1 | subdomain2 211.84616618489457 [um2] nucleusmembrane

Events

Name Variable Rate Expression

Specifications (Species) - cAMPinput_primary3 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cAMPsource (200.0 * (t < 5.0) * ((x >= 43.5) && (x <= 45.3) && (y >= 4.5) && (y <= 5.5) && (z >= 5.0) && (z <= 5.5))) [uM] 0.0 [um2/s] cytosol
D3497cyto 0.0 [uM] D_d32 [um2/s] cytosol
PP1cyto 5.0 [uM] D_pp1 [um2/s] cytosol
PP1cyto_D34cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
Dcyto 0.0 [uM] D_d32 [um2/s] cytosol
D97cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Bcyto 1.6 [uM] D_pp2b [um2/s] cytosol
PP1cyto_D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
PDE10A 1.0 [uM] D_pde10a [um2/s] cytosol
cAMP_PDE10A 0.0 [uM] D_pde10a [um2/s] cytosol
D97cyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP1cyto_D34cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
AMP 0.0 [uM] 0.0 [um2/s] cytosol
cAMP 0.0 [uM] 100.0 [um2/s] cytosol
DMNB_cAMP 0.0 [uM] 100.0 [um2/s] cytosol
light_spot 0.0 [uM] 0.0 [um2/s] cytosol
R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP4_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP4_R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP3_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP2_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
D34cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PKAcyto 0.0 [uM] D_pkac [um2/s] cytosol
D3497cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
Dcyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP2Acyto_PKAcyto 0.0 [uM] D_pp2apka [um2/s] cytosol
PP2Acyto 2.0 [uM] D_pp2a [um2/s] cytosol
cAMP4_R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Apcyto 0.0 [uM] D_pp2a [um2/s] cytosol
D97cyto 50.0 [uM] D_d32 [um2/s] cytosol
PP1cyto_D3497cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
D34cyto 0.0 [uM] D_d32 [um2/s] cytosol
R2C2 1.0 [uM] D_r2c2 [um2/s] cytosol
D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PP2Anuc 2.0 [uM] D_pp2a [um2/s] nucleus
Dnuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus
D97nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
PP1nuc_D34nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D34nuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
Dnuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
PP2Anuc_PKAnuc 0.0 [uM] D_pp2apka [um2/s] nucleus
Dnuc 0.0 [uM] D_d32 [um2/s] nucleus
D34nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
PP1nuc 5.0 [uM] D_pp1 [um2/s] nucleus
PP1nuc_D34nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D3497nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
D97nuc 30.0 [uM] D_d32 [um2/s] nucleus
D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
CK2 1.0 [uM] D_ck2 [um2/s] nucleus
PP2Apnuc 0.0 [uM] D_pp2a [um2/s] nucleus
PP2Bnuc 1.6 [uM] D_pp2b [um2/s] nucleus
D34nuc 0.0 [uM] D_d32 [um2/s] nucleus
D3497nuc 0.0 [uM] D_d32 [um2/s] nucleus
PKAnuc 0.0 [uM] D_pkac [um2/s] nucleus
D97nuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus

Specifications (Reaction) - cAMPinput_primary3 go to Simulations

Name
Enabled?
PP1nuc_D34nuc_off included
D3497cyto_PP2Bcyto_off included
PP1nuc_D3497nuc_off included
PP1cyto_D34cyto_PP2Bcyto_cyto2nuc included
PP2Apcyto2nuc included
D97cyto_PKAcyto_off included
PP1cyto_D3497cyto_PP2Bcyto_cyto2nuc included
D97cyto_PP2Apcyto_off included
D97nuc2cyto included
D3497cyto_PP2Apcyto_on included
Dcyto2nuc_passive included
D34cyto2nuc_passive included
D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_nuc2cyto included
Dnuc_CK2_cat included
D3497nuc2cyto included
D97nuc_PKAnuc_cat included
PP2Anuc_PKAnuc_cat included
D97nuc_PP2Apnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_off included
PP1cyto_D34cyto_PP2Bcyto_cat included
D3497cyto2nuc included
D3497nuc2cyto_passive included
D3497nuc_PP2Bnuc_on included
PP2Anuc2cyto included
PP2Acyto_PKAcyto_cat included
PP2Acyto_PKAcyto_off included
D34nuc_CK2_cat included
Dnuc2cyto_passive included
Dnuc_CK2_off included
photoUncaging_DMNB_cAMP included
Dcyto_PKAcyto_on included
Dnuc_PKAnuc_cat included
D97nuc_PKAnuc_on included
D3497cyto_PP2Bcyto_cyto2nuc included
PP1cyto_D34cyto_PP2Bcyto_on included
D34nuc_PP2Bnuc_on included
R2_PKAcyto_bind included
Dcyto_PKAcyto_off included
D3497cyto_PP2Apcyto_cat included
PP2Anuc_PKAnuc_on included
PP2Bnuc2cyto included
PP2Acyto_PKAcyto_on included
PP1nuc_D3497nuc_PP2Bnuc_on included
R2C_PKAcyto_bind included
PP1cyto_D3497_off included
D3497cyto_PP2Bcyto_cat included
PP1nuc_D34nuc_PP2Bnuc_cat included
PP1nuc_D34nuc_on included
Dcyto_PKAcyto_cat included
PP1cyto_D34cyto_PP2Bcyto_off included
D97cyto_PP2Apcyto_cyto2nuc included
Dnuc_CK2_on included
PP1cyto_D34cyto_cyto2nuc included
D3497nuc_PP2Bnuc_nuc2cyto included
D3497nuc_PP2Apnuc_cat included
D34nuc_PP2Bnuc_cat included
Dcyto2nuc included
cAMPsource2cAMP included
D97nuc_PKAnuc_nuc2cyto included
cAMP_PDE10A_cat included
PP1cyto_D34cyto_off included
PKAnuc2cyto included
D3497nuc_PP2Apnuc_on included
Dnuc_PKAnuc_on included
D34cyto_PP2Bcyto_off included
D3497cyto_PP2Apcyto_off included
PP1cyto2nuc included
D34nuc_CK2_off included
PP1nuc_D34nuc_PP2Bnuc_off included
PP1nuc_D3497nuc_PP2Bnuc_nuc2cyto included
D97cyto_PP2Apcyto_on included
cAMP4_R2_releasecAMP included
PP2Anuc_PKAnuc_nuc2cyto included
D34nuc_PP2Bnuc_off included
D97cyto_PP2Apcyto_cat included
PP1cyto_D3497cyto_PP2Bcyto_cat included
cAMP_R2C2_onoff included
D3497nuc_PP2Bnuc_cat included
D34nuc_CK2_on included
D97nuc_PP2Apnuc_off included
D34cyto_PP2Bcyto_cyto2nuc included
cAMP4_R2C_PKA_onoff included
cAMP_cAMP2_R2C2_onoff included
cAMP4_R2_PKA_onoff included
D97nuc2cyto_passive included
Dcyto_PKAcyto_cyto2nuc included
PP2Apnuc2cyto included
PP2Anuc_PKANuc_off included
PKAcyto2nuc included
PP2Acyto_PKAcyto_cyto2nuc included
PP1cyto_D3497cyto_on included
D97nuc_PP2Apnuc_nuc2cyto included
PP2Apcytodephosphorylation included
PP2Bcyto2nuc included
PP1cyto_D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_PP2Bnuc_on included
D97nuc_PP2Apnuc_on included
D34cyto2nuc included
PP2Acyto2nuc included
PP1cyto_D3497cyto_PP2Bcyto_off included
PP1nuc2cyto included
D97cyto2nuc_passive included
cAMP_cAMP_R2C2_onoff included
PP1cyto_D3497cyto_cyto2nuc included
PP1nuc_D3497nuc_nuc2cyto included
D34cyto_PP2Bcyto_cat included
D34cyto_PP2Bcyto_on included
D3497nuc_PP2Bnuc_off included
D3497cyto2nuc_passive included
D34nuc2cyto_passive included
D97cyto_PKAcyto_cyto2nuc included
D3497nuc_PP2Apnuc_off included
PP2Apnucdephosphorylation included
PP1nuc_D3497nuc_on included
D97cyto_PKAcyto_on included
PP1cyto_D34cyto_on included
D97cyto2nuc included
Dnuc_PKAnuc_off included
cAMP_cAMP3_R2C2_onoff included
D3497cyto_PP2Apcyto_cyto2nuc included
D3497nuc_PP2Apnuc_nuc2cyto included
D97cyto_PKAcyto_cat included
D97nuc_PKAnuc_off included
cAMP_PDE10A_onoff included

Simulations - cAMPinput_primary3 go to Specifications

Name
End Time
Output Options
cAMPprimaryEnd 3600.0

OutputTimeStep 5.0

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1760091997

(Origin: 0.0, -14.0, 0.0; Extent: 155.0, 40.0, 11.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain2 301.60068965661543 [um3] nucleus
Volume Analytical subdomain1 1202.1930494498022 [um3] cytosol
Volume Analytical subdomain0 66696.20626089358 [um3] c0
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 1432.4688299433924 [um2] cellmembrane
Surface subdomain1_subdomain2_membrane subdomain1 | subdomain2 211.84616618489457 [um2] nucleusmembrane

Events

Name Variable Rate Expression

Specifications (Species) - cAMPinput_primary1 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cAMPsource (200.0 * (t < 5.0) * ((x >= 20.5) && (x <= 22.3) && (y >= 4.5) && (y <= 5.5) && (z >= 5.0) && (z <= 5.5))) [uM] 0.0 [um2/s] cytosol
D3497cyto 0.0 [uM] D_d32 [um2/s] cytosol
PP1cyto 5.0 [uM] D_pp1 [um2/s] cytosol
PP1cyto_D34cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
Dcyto 0.0 [uM] D_d32 [um2/s] cytosol
D97cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Bcyto 1.6 [uM] D_pp2b [um2/s] cytosol
PP1cyto_D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
PDE10A 1.0 [uM] D_pde10a [um2/s] cytosol
cAMP_PDE10A 0.0 [uM] D_pde10a [um2/s] cytosol
D97cyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP1cyto_D34cyto_PP2Bcyto 0.0 [uM] D_d32pp1pp2b [um2/s] cytosol
AMP 0.0 [uM] 0.0 [um2/s] cytosol
cAMP 0.0 [uM] 100.0 [um2/s] cytosol
DMNB_cAMP 0.0 [uM] 100.0 [um2/s] cytosol
light_spot 0.0 [uM] 0.0 [um2/s] cytosol
R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP4_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP4_R2C 0.0 [uM] D_r2c [um2/s] cytosol
cAMP3_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
cAMP2_R2C2 0.0 [uM] D_r2c2 [um2/s] cytosol
D34cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PKAcyto 0.0 [uM] D_pkac [um2/s] cytosol
D3497cyto_PP2Apcyto 0.0 [uM] D_d32pp2a [um2/s] cytosol
Dcyto_PKAcyto 0.0 [uM] D_d32pkac [um2/s] cytosol
PP2Acyto_PKAcyto 0.0 [uM] D_pp2apka [um2/s] cytosol
PP2Acyto 2.0 [uM] D_pp2a [um2/s] cytosol
cAMP4_R2 0.0 [uM] D_r2 [um2/s] cytosol
PP2Apcyto 0.0 [uM] D_pp2a [um2/s] cytosol
D97cyto 50.0 [uM] D_d32 [um2/s] cytosol
PP1cyto_D3497cyto 0.0 [uM] D_d32pp1 [um2/s] cytosol
D34cyto 0.0 [uM] D_d32 [um2/s] cytosol
R2C2 1.0 [uM] D_r2c2 [um2/s] cytosol
D3497cyto_PP2Bcyto 0.0 [uM] D_d32pp2b [um2/s] cytosol
PP2Anuc 2.0 [uM] D_pp2a [um2/s] nucleus
Dnuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus
D97nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
PP1nuc_D34nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D34nuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
Dnuc_CK2 0.0 [uM] D_d32ck2 [um2/s] nucleus
PP2Anuc_PKAnuc 0.0 [uM] D_pp2apka [um2/s] nucleus
Dnuc 0.0 [uM] D_d32 [um2/s] nucleus
D34nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
PP1nuc 5.0 [uM] D_pp1 [um2/s] nucleus
PP1nuc_D34nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc 0.0 [uM] D_d32pp1 [um2/s] nucleus
PP1nuc_D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp1pp2b [um2/s] nucleus
D3497nuc_PP2Apnuc 0.0 [uM] D_d32pp2a [um2/s] nucleus
D97nuc 30.0 [uM] D_d32 [um2/s] nucleus
D3497nuc_PP2Bnuc 0.0 [uM] D_d32pp2b [um2/s] nucleus
CK2 1.0 [uM] D_ck2 [um2/s] nucleus
PP2Apnuc 0.0 [uM] D_pp2a [um2/s] nucleus
PP2Bnuc 1.6 [uM] D_pp2b [um2/s] nucleus
D34nuc 0.0 [uM] D_d32 [um2/s] nucleus
D3497nuc 0.0 [uM] D_d32 [um2/s] nucleus
PKAnuc 0.0 [uM] D_pkac [um2/s] nucleus
D97nuc_PKAnuc 0.0 [uM] D_d32pkac [um2/s] nucleus

Specifications (Reaction) - cAMPinput_primary1 go to Simulations

Name
Enabled?
PP1nuc_D34nuc_off included
D3497cyto_PP2Bcyto_off included
PP1nuc_D3497nuc_off included
PP1cyto_D34cyto_PP2Bcyto_cyto2nuc included
PP2Apcyto2nuc included
D97cyto_PKAcyto_off included
PP1cyto_D3497cyto_PP2Bcyto_cyto2nuc included
D97cyto_PP2Apcyto_off included
D97nuc2cyto included
D3497cyto_PP2Apcyto_on included
Dcyto2nuc_passive included
D34cyto2nuc_passive included
D3497cyto_PP2Bcyto_on included
PP1nuc_D34nuc_nuc2cyto included
Dnuc_CK2_cat included
D3497nuc2cyto included
D97nuc_PKAnuc_cat included
PP2Anuc_PKAnuc_cat included
D97nuc_PP2Apnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_cat included
PP1nuc_D3497nuc_PP2Bnuc_off included
PP1cyto_D34cyto_PP2Bcyto_cat included
D3497cyto2nuc included
D3497nuc2cyto_passive included
D3497nuc_PP2Bnuc_on included
PP2Anuc2cyto included
PP2Acyto_PKAcyto_cat included
PP2Acyto_PKAcyto_off included
D34nuc_CK2_cat included
Dnuc2cyto_passive included
Dnuc_CK2_off included
photoUncaging_DMNB_cAMP included
Dcyto_PKAcyto_on included
Dnuc_PKAnuc_cat included
D97nuc_PKAnuc_on included
D3497cyto_PP2Bcyto_cyto2nuc included
PP1cyto_D34cyto_PP2Bcyto_on included
D34nuc_PP2Bnuc_on included
R2_PKAcyto_bind included
Dcyto_PKAcyto_off included
D3497cyto_PP2Apcyto_cat included
PP2Anuc_PKAnuc_on included
PP2Bnuc2cyto included
PP2Acyto_PKAcyto_on included
PP1nuc_D3497nuc_PP2Bnuc_on included
R2C_PKAcyto_bind included
PP1cyto_D3497_off included
D3497cyto_PP2Bcyto_cat included
PP1nuc_D34nuc_PP2Bnuc_cat included