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BIOMD0000000246 - Vasalou2010_Pacemaker_Neuron_SCN

 

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Reference Publication
Publication ID: 20300645
Vasalou C, Henson MA.
A multiscale model to investigate circadian rhythmicity of pacemaker neurons in the suprachiasmatic nucleus.
PLoS Comput. Biol. 2010 Mar; 6(3): e1000706
Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America.  [more]
Model
Original Model: BIOMD0000000246.xml.origin
Submitter: Lukas Endler
Submission ID: MODEL1004080000
Submission Date: 08 Apr 2010 03:38:32 UTC
Last Modification Date: 31 Aug 2011 20:01:44 UTC
Creation Date: 08 Apr 2010 23:39:53 UTC
Encoders:  Lukas Endler
set #1
bqmodel:isDerivedFrom BioModels Database Leloup2003_CircClock_LD_REV-ERBalpha
BioModels Database Leloup2003_CircClock_LD
BioModels Database Leloup2003_CircClock_DD_REV-ERBalpha
BioModels Database Leloup2003_CircClock_DD
PubMed 11316338
set #2
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
bqbiol:occursIn FMA FMA:67883
set #3
bqbiol:hasTaxon Taxonomy Mammalia
Notes

This the single cell model from the article:
A multiscale model to investigate circadian rhythmicity of pacemaker neurons in the suprachiasmatic nucleus.
Vasalou C, Henson MA. PLoS Comput Biol 2010 Mar 12;6(3):e1000706. PMID: 20300645 , DOI: 10.1371/journal.pcbi.1000706 ;

Abstract:
The suprachiasmatic nucleus (SCN) of the hypothalamus is a multicellular system that drives daily rhythms in mammalian behavior and physiology. Although the gene regulatory network that produces daily oscillations within individual neurons is well characterized, less is known about the electrophysiology of the SCN cells and how firing rate correlates with circadian gene expression. We developed a firing rate code model to incorporate known electrophysiological properties of SCN pacemaker cells, including circadian dependent changes in membrane voltage and ion conductances. Calcium dynamics were included in the model as the putative link between electrical firing and gene expression. Individual ion currents exhibited oscillatory patterns matching experimental data both in current levels and phase relationships. VIP and GABA neurotransmitters, which encode synaptic signals across the SCN, were found to play critical roles in daily oscillations of membrane excitability and gene expression. Blocking various mechanisms of intracellular calcium accumulation by simulated pharmacological agents (nimodipine, IP3- and ryanodine-blockers) reproduced experimentally observed trends in firing rate dynamics and core-clock gene transcription. The intracellular calcium concentration was shown to regulate diverse circadian processes such as firing frequency, gene expression and system periodicity. The model predicted a direct relationship between firing frequency and gene expression amplitudes, demonstrated the importance of intracellular pathways for single cell behavior and provided a novel multiscale framework which captured characteristics of the SCN at both the electrophysiological and gene regulatory levels.

Originally created by libAntimony v1.3 (using libSBML 4.1.0-b1)

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use .
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 20300645 Submission Date: 08 Apr 2010 03:38:32 UTC Last Modification Date: 31 Aug 2011 20:01:44 UTC Creation Date: 08 Apr 2010 23:39:53 UTC
Mathematical expressions
Reactions
vo v_ca_out v1 v2
v3 v_Ca_leak MP_transcription MP_decay
MC_transcription MC_decay MB_transcription MB_decay
PC_translation PC_degradation PC_phosphorylation PCC_formation
CC_translation CC_degradation CC_phosphorylation PCP_degradation
CCP_degradation PCC_shuttling PCC_phosphorylation PCC_degradation
PCCP_degradation PCN_phosphorylation PCN_degradation PCNP_degradation
IN_formation IN_degradation BC_translation BC_phosphorylation
BC_shuttling BC_degradation BCP_degradation BN_phosphorylation
BN_degradation BNP_degradation CB_activation VIP_accumulation
VIP_depletion      
Rules
Assignment Rule (variable: GABA) Assignment Rule (variable: K_in) Assignment Rule (variable: Na_in) Assignment Rule (variable: v_K)
Assignment Rule (variable: f_r) Assignment Rule (variable: beta) Assignment Rule (variable: v_sPc) Assignment Rule (variable: E_Na)
Assignment Rule (variable: E_K) Assignment Rule (variable: E_L) Assignment Rule (variable: E_Ca) Assignment Rule (variable: Cl_in)
Assignment Rule (variable: E_inhib) Assignment Rule (variable: P_K) Assignment Rule (variable: theta_Na) Assignment Rule (variable: theta_K)
Assignment Rule (variable: alpha) Assignment Rule (variable: beta_a) Assignment Rule (variable: c) Assignment Rule (variable: psi)
Assignment Rule (variable: V_rest) Assignment Rule (variable: theta) Assignment Rule (variable: V_reset) Assignment Rule (variable: R)
Assignment Rule (variable: I_Na) Assignment Rule (variable: g_K) Assignment Rule (variable: I_Na_abs) Assignment Rule (variable: g_ex)
Assignment Rule (variable: g_L) Assignment Rule (variable: g_Ca) Assignment Rule (variable: gK_Ca) Assignment Rule (variable: I_star)
Assignment Rule (variable: R_star) Assignment Rule (variable: tau_m)    
Physical entities
Compartments Species
extra Ca_ex Cl_ex K_ex
Na_ex    
cytoplasm Ca_in M_P M_C
M_B P_C C_C
P_CP C_CP PC_C
PC_CP B_C B_CP
CB VIP Cl_o
GABA GABA_o K_in
Na_in    
store Ca_store    
nucleus PC_N PC_NP B_N
B_NP I_N  
Global parameters
v_vo n_vo K_vo v_kk
n_kk K_kk n_kCa V_M1
beta_IP3 V_M2 n_M2 K_2
V_M3 n_M3 K_R_Ca p_A
K_A k_f v_sP0 C_T
K_C n_BN K_AP v_mP
K_mP kd_mP v_sC K_sC
v_mC K_mC kd_mC v_sB
K_IB m_BN v_mB K_mB
kd_mB ks_P kd_n V1_P
K_p V2_P K_dp k3
k4 ks_C kd_nc V1_C
V2_C v_dPC Kd v_dCC
k1 k2 V1_PC V2_PC
vd_PCC V3_PC V4_PC vd_PCN
k7 k8 vd_IN ksB
V1_B V2_B k5 k6
vd_BC V3_B V4_B vd_BN
v_K K_1_CB vP K_2_CB
WT v_VIP f_r n_VIP
K_VIP k_dVIP n_dVIP v_GABA
K_GABA beta K_D v_sPc
V_MK k_MK V_b k_b
E_Na E_Na_0 T T_abs
T_room E_K E_K_0 E_L
E_L_0 E_Ca k_q Cl_in
K_Cl1 v_Cl1 n_Cl K_Cl2
v_Cl2 E_inhib P_K v_PK
n_PK K_PK theta_Na theta_K
alpha P_Ca P_Na P_Cl
beta_a c psi V_rest
R_g Faraday theta V_theta
V_reset R V_R K_R
I_Na g_Na g_K g_K_0
K_gk v_gk I_Na_abs g_ex
V_ex1 n_ex1 K_ex1 n_ex2
K_ex2 V_ex2 g_L g_Ca
v_Ca n_Ca K_Ca gK_Ca
VK_Ca n_KCa K_KCa I_star
g_inhib E_ex R_star tau_m
Cm PK_o V_phos  
Reactions (41)
 
 vo  ↔ 0.0010 × [Ca_in];   {B_C}
 
 v_ca_out 0.0010 × [Ca_in] ↔ ;   {C_C}
 
 v1  ↔ 0.0010 × [Ca_in];  
 
 v2 0.0010 × [Ca_in] ↔ 0.0010 × [Ca_store];  
 
 v3 0.0010 × [Ca_store] ↔ 0.0010 × [Ca_in];  
 
 v_Ca_leak 0.0010 × [Ca_store] ↔ 0.0010 × [Ca_in];  
 
 MP_transcription  ↔ [M_P];   {CB} , {B_N}
 
 MP_decay [M_P] ↔ ;  
 
 MC_transcription  ↔ [M_C];   {B_N}
 
 MC_decay [M_C] ↔ ;  
 
 MB_transcription  ↔ [M_B];   {B_N}
 
 MB_decay [M_B] ↔ ;  
 
 PC_translation  ↔ [P_C];   {M_P}
 
 PC_degradation [P_C] ↔ ;  
 
 PC_phosphorylation [P_C] ↔ [P_CP];  
 
 PCC_formation [P_C] + [C_C] ↔ [PC_C];  
 
 CC_translation  ↔ [C_C];   {M_C}
 
 CC_degradation [C_C] ↔ ;  
 
 CC_phosphorylation [C_C] ↔ [C_CP];  
 
 PCP_degradation [P_CP] ↔ ;  
 
 CCP_degradation [C_CP] ↔ ;  
 
 PCC_shuttling [PC_C] ↔ [PC_N];  
 
 PCC_phosphorylation [PC_C] ↔ [PC_CP];  
 
 PCC_degradation [PC_C] ↔ ;  
 
 PCCP_degradation [PC_CP] ↔ ;  
 
 PCN_phosphorylation [PC_N] ↔ [PC_NP];  
 
 PCN_degradation [PC_N] ↔ ;  
 
 PCNP_degradation [PC_NP] ↔ ;  
 
 IN_formation [B_N] + [PC_N] ↔ [I_N];  
 
 IN_degradation [I_N] ↔ ;  
 
 BC_translation  ↔ [B_C];   {M_B}
 
 BC_phosphorylation [B_C] ↔ [B_CP];  
 
 BC_shuttling [B_C] ↔ [B_N];  
 
 BC_degradation [B_C] ↔ ;  
 
 BCP_degradation [B_CP] ↔ ;  
 
 BN_phosphorylation [B_N] ↔ [B_NP];  
 
 BN_degradation [B_N] ↔ ;  
 
 BNP_degradation [B_NP] ↔ ;  
 
 CB_activation  ↔ [CB];  
 
 VIP_accumulation  ↔ [VIP];  
 
 VIP_depletion [VIP] ↔ ;  
 
Rules (34)
 
 Assignment Rule (name: GABA) GABA = GABA_o+v_GABA*VIP/(K_GABA+VIP)
 
 Assignment Rule (name: K_in) K_in = K_ex/theta_K
 
 Assignment Rule (name: Na_in) Na_in = Na_ex/theta_Na
 
 Assignment Rule (name: v_K) v_K = V_MK*Ca_in/(k_MK+Ca_in)+V_b*beta/(k_b+beta)
 
 Assignment Rule (name: f_r) f_r = -1/(tau_m*log((theta-R_star*I_star)/(V_reset-R_star*I_star)))
 
 Assignment Rule (name: beta) beta = VIP/(VIP+K_D)
 
 Assignment Rule (name: v_sPc) v_sPc = v_sP0+C_T*CB/(K_C+CB)
 
 Assignment Rule (name: E_Na) E_Na = E_Na_0*(T+T_abs)/(T_room+T_abs)
 
 Assignment Rule (name: E_K) E_K = E_K_0*(T+T_abs)/(T_room+T_abs)
 
 Assignment Rule (name: E_L) E_L = E_L_0*(T+T_abs)/(T_room+T_abs)
 
 Assignment Rule (name: E_Ca) E_Ca = k_q*(T+T_abs)/2*log(Ca_ex/Ca_in)*1000
 
 Assignment Rule (name: Cl_in) Cl_in = Cl_o+M_P/(K_Cl1+M_P)*v_Cl1+GABA^n_Cl/(K_Cl2+GABA^n_Cl)*v_Cl2
 
 Assignment Rule (name: E_inhib) E_inhib = (-k_q)*(T+T_abs)*log(Cl_ex/Cl_in)*1000
 
 Assignment Rule (name: P_K) P_K = v_PK*B_C^n_PK/(K_PK+B_C^n_PK)
 
 Assignment Rule (name: theta_Na) theta_Na = exp(E_Na/(k_q*(T+T_abs)*1000))
 
 Assignment Rule (name: theta_K) theta_K = exp(E_K/(k_q*(T+T_abs)*1000))
 
 Assignment Rule (name: alpha) alpha = 4*P_Ca*Ca_in*10^(-3)+P_K*K_in+P_Na*Na_in+P_Cl*Cl_ex
 
 Assignment Rule (name: beta_a) beta_a = P_K*K_in-P_K*K_ex+P_Na*Na_in-P_Na*Na_ex+P_Cl*Cl_ex-P_Cl*Cl_in
 
 Assignment Rule (name: c) c = -(4*P_Ca*Ca_ex*10^(-3)+P_K*K_ex+P_Na*Na_ex+P_Cl*Cl_in)
 
 Assignment Rule (name: psi) psi = ((beta_a^2-4*alpha*c)^(0.5)-beta_a)/(2*alpha)
 
 Assignment Rule (name: V_rest) V_rest = R_g*(T+T_abs)/Faraday*log(psi)*1000
 
 Assignment Rule (name: theta) theta = V_rest+V_theta
 
 Assignment Rule (name: V_reset) V_reset = V_rest+4
 
 Assignment Rule (name: R) R = V_R*V_rest/(K_R+V_rest)
 
 Assignment Rule (name: I_Na) I_Na = g_Na*(V_rest-E_Na)
 
 Assignment Rule (name: g_K) g_K = g_K_0+M_P/(K_gk+M_P)*v_gk
 
 Assignment Rule (name: I_Na_abs) I_Na_abs = (I_Na^2)^(0.5)
 
 Assignment Rule (name: g_ex) g_ex = V_ex1*I_Na_abs^n_ex1/(K_ex1+I_Na_abs^n_ex1)+Ca_in^n_ex2/(K_ex2+Ca_in^n_ex2)*V_ex2
 
 Assignment Rule (name: g_L) g_L = 1/R
 
 Assignment Rule (name: g_Ca) g_Ca = v_Ca*M_P^n_Ca/(K_Ca+M_P^n_Ca)
 
 Assignment Rule (name: gK_Ca) gK_Ca = VK_Ca*C_C^n_KCa/(K_KCa+C_C^n_KCa)
 
 Assignment Rule (name: I_star) I_star = g_Na*E_Na+g_Ca*E_Ca+g_K*E_K+g_L*E_L+gK_Ca*E_K-g_inhib*E_inhib-g_ex*E_ex
 
 Assignment Rule (name: R_star) R_star = 1/(g_Na+g_K+g_L+g_Ca+gK_Ca-g_inhib-g_ex)
 
 Assignment Rule (name: tau_m) tau_m = Cm*R_star
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_ex
Compartment: extra
Initial concentration: 5.0  (Units: umole)
 
 Cl_ex
Compartment: extra
Initial concentration: 114.5  (Units: mmole)
 
 K_ex
Compartment: extra
Initial concentration: 1.0  (Units: mmole)
 
 Na_ex
Compartment: extra
Initial concentration: 145.0  (Units: mmole)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_in
Compartment: cytoplasm
Initial concentration: 0.1  (Units: umole)
 
 M_P
Compartment: cytoplasm
Initial concentration: 2.8
 
 M_C
Compartment: cytoplasm
Initial concentration: 2.0
 
 M_B
Compartment: cytoplasm
Initial concentration: 7.94
 
 P_C
Compartment: cytoplasm
Initial concentration: 0.4
 
 C_C
Compartment: cytoplasm
Initial concentration: 12.0
 
 P_CP
Compartment: cytoplasm
Initial concentration: 0.13
 
 C_CP
Compartment: cytoplasm
Initial concentration: 9.0
 
 PC_C
Compartment: cytoplasm
Initial concentration: 1.26
 
 PC_CP
Compartment: cytoplasm
Initial concentration: 0.2
 
 B_C
Compartment: cytoplasm
Initial concentration: 2.41
 
 B_CP
Compartment: cytoplasm
Initial concentration: 0.48
 
 CB
Compartment: cytoplasm
Initial concentration: 0.12
 
 VIP
Compartment: cytoplasm
Initial concentration: 0.0
 
 Cl_o
Compartment: cytoplasm
Initial concentration: 1.0  (Units: mmole)
 
  GABA
Compartment: cytoplasm
 
 GABA_o
Compartment: cytoplasm
Initial concentration: 0.2
 
  K_in
Compartment: cytoplasm
  (Units: mmole)
 
  Na_in
Compartment: cytoplasm
  (Units: mmole)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_store
Compartment: store
Initial concentration: 0.1  (Units: umole)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 PC_N
Compartment: nucleus
Initial concentration: 0.16
 
 PC_NP
Compartment: nucleus
Initial concentration: 0.091
 
 B_N
Compartment: nucleus
Initial concentration: 1.94
 
 B_NP
Compartment: nucleus
Initial concentration: 0.32
 
   I_N
Compartment: nucleus
Initial concentration: 0.05
 
Global Parameters (163)
 
   v_vo
Value: 0.09   (Units: uM_per_h)
Constant
 
   n_vo
Value: 4.5   (Units: dimensionless)
Constant
 
   K_vo
Value: 4.5   (Units: nM)
Constant
 
   v_kk
Value: 3.3   (Units: per_uM_per_h)
Constant
 
   n_kk
Value: 0.1   (Units: dimensionless)
Constant
 
   K_kk
Value: 0.02   (Units: nM)
Constant
 
   n_kCa
Value: 2.0   (Units: dimensionless)
Constant
 
   V_M1
Value: 3.0E-4   (Units: uM_per_h)
Constant
 
   beta_IP3
Value: 0.5   (Units: dimensionless)
Constant
 
   V_M2
Value: 149.5   (Units: uM_per_h)
Constant
 
   n_M2
Value: 2.2   (Units: dimensionless)
Constant
 
   K_2
Value: 5.0   (Units: uM)
Constant
 
   V_M3
Value: 400.0   (Units: uM_per_h)
Constant
 
   n_M3
Value: 6.0   (Units: dimensionless)
Constant
 
   K_R_Ca
Value: 3.0   (Units: uM)
Constant
 
   p_A
Value: 4.2   (Units: dimensionless)
Constant
 
   K_A
Value: 0.67   (Units: uM)
Constant
 
   k_f
Value: 0.0010   (Units: per_h)
Constant
 
   v_sP0
Value: 1.0   (Units: nM_per_h)
Constant
 
   C_T
Value: 1.6   (Units: nM_per_h)
Constant
 
   K_C
Value: 0.15   (Units: nM)
Constant
 
   n_BN
Value: 4.0   (Units: dimensionless)
Constant
 
   K_AP
Value: 0.6   (Units: nM)
Constant
 
   v_mP
Value: 1.1   (Units: nM_per_h)
Constant
 
   K_mP
Value: 0.31   (Units: nM)
Constant
 
   kd_mP
Value: 0.01   (Units: per_h)
Constant
 
   v_sC
Value: 1.1   (Units: nM_per_h)
Constant
 
   K_sC
Value: 0.6   (Units: nM)
Constant
 
   v_mC
Value: 1.0   (Units: nM_per_h)
Constant
 
   K_mC
Value: 0.4   (Units: nM)
Constant
 
   kd_mC
Value: 0.01   (Units: per_h)
Constant
 
   v_sB
Value: 1.0   (Units: nM_per_h)
Constant
 
   K_IB
Value: 2.2   (Units: nM)
Constant
 
   m_BN
Value: 2.0   (Units: dimensionless)
Constant
 
   v_mB
Value: 0.8   (Units: nM_per_h)
Constant
 
   K_mB
Value: 0.4   (Units: nM)
Constant
 
   kd_mB
Value: 0.01   (Units: per_h)
Constant
 
   ks_P
Value: 0.6   (Units: per_h)
Constant
 
   kd_n
Value: 0.01   (Units: per_h)
Constant
 
   V1_P
Value: NaN   (Units: nM_per_h)
Constant
 
   K_p
Value: 0.1   (Units: nM)
Constant
 
   V2_P
Value: 0.3   (Units: nM_per_h)
Constant
 
   K_dp
Value: 0.1   (Units: nM)
Constant
 
   k3
Value: 0.4   (Units: per_nM_per_h)
Constant
 
   k4
Value: 0.2   (Units: per_h)
Constant
 
   ks_C
Value: 1.6   (Units: per_h)
Constant
 
   kd_nc
Value: 0.12   (Units: per_h)
Constant
 
   V1_C
Value: 0.6   (Units: nM_per_h)
Constant
 
   V2_C
Value: 0.1   (Units: nM_per_h)
Constant
 
   v_dPC
Value: 0.7   (Units: per_nM_per_h)
Constant
 
   Kd
Value: 0.3   (Units: nM)
Constant
 
   v_dCC
Value: 0.7   (Units: nM_per_h)
Constant
 
   k1
Value: 0.45   (Units: per_h)
Constant
 
   k2
Value: 0.2   (Units: per_h)
Constant
 
   V1_PC
Value: NaN   (Units: nM_per_h)
Constant
 
   V2_PC
Value: 0.1   (Units: nM_per_h)
Constant
 
   vd_PCC
Value: 0.7   (Units: nM_per_h)
Constant
 
   V3_PC
Value: NaN   (Units: nM_per_h)
Constant
 
   V4_PC
Value: 0.1   (Units: nM_per_h)
Constant
 
   vd_PCN
Value: 0.7   (Units: nM_per_h)
Constant
 
   k7
Value: 0.5   (Units: per_nM_per_h)
Constant
 
   k8
Value: 0.1   (Units: per_h)
Constant
 
   vd_IN
Value: 0.8   (Units: nM_per_h)
Constant
 
   ksB
Value: 0.12
Constant
 
   V1_B
Value: 0.5   (Units: nM_per_h)
Constant
 
   V2_B
Value: 0.1   (Units: nM_per_h)
Constant
 
   k5
Value: 0.4
Constant
 
   k6
Value: 0.2
Constant
 
   vd_BC
Value: 0.5   (Units: nM_per_h)
Constant
 
   V3_B
Value: 0.5   (Units: nM_per_h)
Constant
 
   V4_B
Value: 0.2   (Units: nM_per_h)
Constant
 
   vd_BN
Value: 0.6   (Units: nM_per_h)
Constant
 
   v_K
Value: NaN   (Units: nM_per_h)
 
   K_1_CB
Value: 0.01   (Units: nM)
Constant
 
   vP
Value: 1.0   (Units: nM_per_h)
Constant
 
   K_2_CB
Value: 0.01   (Units: nM)
Constant
 
   WT
Value: 1.0   (Units: dimensionless)
Constant
 
   v_VIP
Value: 0.5   (Units: nM_per_h)
Constant
 
   f_r
Value: NaN   (Units: hertz)
 
   n_VIP
Value: 1.9   (Units: dimensionless)
Constant
 
   K_VIP
Value: 15.0
Constant
 
   k_dVIP
Value: 0.5
Constant
 
   n_dVIP
Value: 0.2   (Units: dimensionless)
Constant
 
   v_GABA
Value: 19.0   (Units: nM)
Constant
 
   K_GABA
Value: 3.0   (Units: nM)
Constant
 
   beta
Value: NaN   (Units: dimensionless)
 
   K_D
Value: 0.08
Constant
 
   v_sPc
Value: NaN
 
   V_MK
Value: 5.0
Constant
 
   k_MK
Value: 2.9
Constant
 
   V_b
Value: 2.0
Constant
 
   k_b
Value: 2.0
Constant
 
   E_Na
Value: NaN   (Units: milliVolt)
 
   E_Na_0
Value: 45.0   (Units: milliVolt)
Constant
 
   T
Value: 37.0   (Units: kelvin)
Constant
 
   T_abs
Value: 273.15   (Units: kelvin)
Constant
 
   T_room
Value: 22.0   (Units: kelvin)
Constant
 
   E_K
Value: NaN   (Units: milliVolt)
 
   E_K_0
Value: -97.0   (Units: milliVolt)
Constant
 
   E_L
Value: NaN   (Units: milliVolt)
 
   E_L_0
Value: -29.0   (Units: milliVolt)
Constant
 
   E_Ca
Value: NaN   (Units: milliVolt)
 
   k_q
Value: 8.75E-5
Constant
 
   Cl_in
Value: NaN
 
   K_Cl1
Value: 4.0
Constant
 
   v_Cl1
Value: 15.5
Constant
 
   n_Cl
Value: -0.2
Constant
 
   K_Cl2
Value: 1.0
Constant
 
   v_Cl2
Value: 19.0
Constant
 
   E_inhib
Value: NaN   (Units: milliVolt)
 
   P_K
Value: NaN
 
   v_PK
Value: 1.9
Constant
 
   n_PK
Value: -2.0
Constant
 
   K_PK
Value: 1.0
Constant
 
   theta_Na
Value: NaN   (Units: milliVolt)
 
   theta_K
Value: NaN   (Units: milliVolt)
 
   alpha
Value: NaN
 
   P_Ca
Value: 0.05
Constant
 
   P_Na
Value: 0.036
Constant
 
   P_Cl
Value: 0.3
Constant
 
   beta_a
Value: NaN
 
   c
Value: NaN
 
   psi
Value: NaN
 
   V_rest
Value: NaN   (Units: milliVolt)
 
   R_g
Value: 8.314
Constant
 
   Faraday
Value: 96485.0
Constant
 
   theta
Value: NaN   (Units: milliVolt)
 
   V_theta
Value: 20.0   (Units: milliVolt)
Constant
 
   V_reset
Value: NaN   (Units: milliVolt)
 
   R
Value: NaN
 
   V_R
Value: 0.41
Constant
 
   K_R
Value: 34.0   (Units: milliVolt)
Constant
 
   I_Na
Value: NaN   (Units: microAmpere)
 
   g_Na
Value: 36.0   (Units: nanoSievert)
Constant
 
   g_K
Value: NaN   (Units: nanoSievert)
 
   g_K_0
Value: 9.7   (Units: nanoSievert)
Constant
 
   K_gk
Value: 10.0   (Units: nM)
Constant
 
   v_gk
Value: 10.0   (Units: nanoSievert)
Constant
 
   I_Na_abs
Value: NaN   (Units: microAmpere)
 
   g_ex
Value: NaN   (Units: nanoSievert)
 
   V_ex1
Value: 105.0
Constant
 
   n_ex1
Value: 2.5
Constant
 
   K_ex1
Value: 5.7405E8   (Units: microAmpere)
Constant
 
   n_ex2
Value: -1.0
Constant
 
   K_ex2
Value: 1.0   (Units: per_uM)
Constant
 
   V_ex2
Value: 4.4
Constant
 
   g_L
Value: NaN
 
   g_Ca
Value: NaN
 
   v_Ca
Value: 12.3
Constant
 
   n_Ca
Value: 2.2
Constant
 
   K_Ca
Value: 22.0
Constant
 
   gK_Ca
Value: NaN
 
   VK_Ca
Value: 3.0
Constant
 
   n_KCa
Value: -1.0
Constant
 
   K_KCa
Value: 0.16
Constant
 
   I_star
Value: NaN   (Units: microAmpere)
 
   g_inhib
Value: 12.3   (Units: nanoSievert)
Constant
 
   E_ex
Constant
 
   R_star
Value: NaN
 
   tau_m
Value: NaN
 
   Cm
Value: 5.0
Constant
 
   PK_o
Value: 1.1
Constant
 
   V_phos
Value: 0.4
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000246

Curator's comment: (updated: 09 Apr 2010 04:09:45 BST)

Reproduction of some of the time courses in Fig 3 of the original publication. The calculations were performed using Copasi 4.5.31.

The time courses were aligned at their maximal internal Calcium concentration, but time was not rescaled to the circadian time, giving slightly different graphs.

As described in the article, the Ryanodine blockade was simulated by setting the parameter VM3 (v3 in the article) zero, nimodipine application by setting g_Ca constant and zero.

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