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Name - SpermCalcium

BioModel ID - 211839191

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
CaRNE1CaIn	leakRNE RNEmem	MassAction	CaRNE1CaIn
		reaction rate (J): ((Kf * CaRNE1) - (Kr * CaIn))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (((kleakrne * RNE) / RNEmem) * 602.0)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1]
CaInCaRNE1	SPCA RNEmem	GeneralKinetics	CaInCaRNE1
		reaction rate (J): (602.0 * Vspca * (CaIn ^ 2.0) * Cytosole / RNEmem / ((Kspca ^ 2.0) + (CaIn ^ 2.0)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kspca): 0.27[tbd]
CaIn	CatSper Cytosole	GeneralKinetics	CaIn
		reaction rate (J): ((((Vcatsper * (t > 25.0)) * (t < 700.0)) + (Vcatsper / p_k * (t > 700.0))) * (x < 28.0))[uM.s-1] user defined (Vcatsper): 0.7[uM.s-1]
IP3	PLCd m0	GeneralKinetics	IP3
		reaction rate (J): (((1.7 * 1800.0 * (CaIn * (x > 28.0) / (Kplc + CaIn))) * HeadMembaneToAllMembraneRatio) / m0)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (HeadMembaneToAllMembraneRatio): 3.0[molecules.s-1] user defined (Kplc): 0.7[uM]
IP3	IP3K Cytosole	GeneralKinetics	IP3
		reaction rate (J): ((IP3 * 7.6) / (IP3 + 3.0))[uM.s-1]
CaIn	LeakPP m0	GeneralLumpedKinetics	CaIn
		lumped current (LumpedI): 0.0[pA] lumped reaction rate (LumpedJ): ((leakparam * Cytosole * 602.0) * leakmax)[molecules.s-1] net charge valence (netValence): 1.0[1] user defined (leakmax): 0.15[tbd]
CaIn+CaPrCaBuf	CalMod Cytosole	MassAction	CaIn+CaPrCaBuf
		reaction rate (J): (((Kf * CaIn) * CaPr) - (Kr * CaBuf))[uM.s-1] forward rate constant (Kf): 10.0[s-1.uM-1] reverse rate constant (Kr): (Kf * Kd_CalModfast)[s-1] user defined (Kd_CalModfast): 1.0[uM]
CaRNE1+CaReticCaReticCal	CaRetFast RNE	MassAction	CaRNE1+CaReticCaReticCal
		reaction rate (J): (((Kf * CaRNE1) * CaRetic) - (Kr * CaReticCal))[uM.s-1] forward rate constant (Kf): 0.01[s-1.uM-1] reverse rate constant (Kr): (Kf * Kd_CaRetic_slow)[s-1]
CaRNE1+CaRet_SlowCaRetSlow_Calcium	CaRetSlow RNE	MassAction	CaRNE1+CaRet_SlowCaRetSlow_Calcium
		reaction rate (J): (((Kf * CaRNE1) * CaRet_Slow) - (Kr * CaRetSlow_Calcium))[uM.s-1] forward rate constant (Kf): 0.1[s-1.uM-1] reverse rate constant (Kr): (Kf * 2000.0)[s-1]
CaIn	PMCA m0	GeneralKinetics	CaIn
		reaction rate (J): (Vpmca * ((602.0 * (CaIn ^ 2.0) * Cytosole * (x < 28.0) / m0 / ((Kpmca ^ 2.0) + (CaIn ^ 2.0))) * PP_membrane_to_all_membr_ratio))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Vpmca): 1.0[tbd] user defined (Kpmca): 0.2[tbd] user defined (PP_membrane_to_all_membr_ratio): 1.55[tbd]
CaIn+caMSlowCaMSlowCa	CaM_slow Cytosole	MassAction	CaIn+caMSlowCaMSlowCa
		reaction rate (J): (((Kf * CaIn) * caMSlow) - (Kr * CaMSlowCa))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 260.0[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
RNE	Compartment (+) (-)

outside	Compartment (+) (-)

Cytosole	Compartment (+) (-)

m0	Membrane N/A

RNEmem	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
CaIn	Cytosole

CaRNE1	RNE

IP3	Cytosole

Ip3buf	Cytosole

CaPr	Cytosole

CaBuf	Cytosole

CaRetic	RNE

CaReticCal	RNE

CaRet_Slow	RNE

CaRetSlow_Calcium	RNE

caMSlow	Cytosole

CaMSlowCa	Cytosole

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Application0	Deterministic (ODE) Spatial (3D)

Application - Application0

Specifications(Species) - Application0 See in Dashboard
Species	Initial Condition	Diffusion Constant
CaRNE1	1000.0 [uM]	20.0 [um2/s]
CaRetic	((3000.0 * 18.0 / 602.0 / RNE) * 1.0) [uM]	20.0 [um2/s]
CaReticCal	0.0 [uM]	20.0 [um2/s]
CaRet_Slow	((3000.0 * 18.0 / 602.0 / RNE) * 18.0) [uM]	20.0 [um2/s]
CaRetSlow_Calcium	0.0 [uM]	20.0 [um2/s]
CaIn	0.1 [uM]	Diffusion [um2/s]
IP3	0.0 [uM]	8.0 [um2/s]
Ip3buf	0.0 [uM]	0.0 [um2/s]
CaPr	((1000.0 * 2.0) * 18.0 / 602.0 / Cytosole) [uM]	Diffusion [um2/s]
CaBuf	0.0 [uM]	Diffusion [um2/s]
caMSlow	((1000.0 * 2.0) * 18.0 / 602.0 / Cytosole) [uM]	Diffusion [um2/s]
CaMSlowCa	0.0 [uM]	Diffusion [um2/s]

Specifications(Reaction) - Application0 See in Dashboard
Name	Reaction Mapping
leakRNE	included
SPCA	included
CatSper	included
PLCd	included
IP3K	included
LeakPP	included
CalMod	included
CaRetFast	included
CaRetSlow	included
PMCA	included
CaM_slow	included
IP3R	included

Simulations - Application0 See in Dashboard
Name	End Time	Output Options
Calcium diffusionvariationosc	1000.0 [s]	OutputTimeStep 1.0

Geometry Geometry1120118915 See in Dashboard
(Origin: -12.5, 3.0, 3.9; Extent: 50.0, 3.5, 2.5[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain2		0.12512500000000001 [um3]	RNE
Volume	Analytical	subdomain1		18.032437500000004 [um3]	Cytosole
Volume	Analytical	subdomain0		419.3424375000001 [um3]	outside
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	96.30630517752202 [um2]	m0
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	1.033529612708134 [um2]	RNEmem

Global Parameters

Global Parameters See in Dashboard
Name	Expression
kcatABHD	3.0[tbd]

Vabhd	0.0[tbd]

KmABHD	66.0[tbd]

CatSper_0	0.0[tbd]

CatSper0	0.0[tbd]

IC50AG	0.35[tbd]

K_abhdProgf	0.0[tbd]

K_abhdProgb	0.0[tbd]

K_CatSperf	0.0[tbd]

Popen	0.0[tbd]

K2	30.0[tbd]

K3	0.005[tbd]

K5	0.25[tbd]

Z	(1.0 + (CaIn * K3 / (K1 * K2)) + (CaIn / K5) + ((CaIn ^ 2.0) * K3 / (K5 * K1 * K2)) + (IP3 / K1) + (IP3 * CaIn / (K1 * K2)) + (IP3 * CaIn / (K1 * K5)) + (IP3 * CaIn * CaIn / (K1 * K2 * K5))) [tbd]

w11	(IP3 * CaIn * 1.0 / (K1 * K5 * Z))[tbd]

K1	0.13[tbd]

DOLYA	(CaIn / (CaIn + 0.7))[tbd]

NIP3R	1850.0[tbd]

Kserca	0.27[tbd]

Vserca	0.92[tbd]

kleakrne	0.1[tbd]

g0	0.0[tbd]

leakparam	((x < 28.0) * (t < 700.0))[tbd]

Vcatsperfake	0.7[tbd]

Diffusion	4.0[tbd]

Kd_CaRetic_slow	1.0[uM]

Vspca	0.93[tbd]

p_k	1.8[1]