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Uses of Reactor in org.simBio.bio |
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Subclasses of Reactor in org.simBio.bio | |
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class |
Compartment
Nodes folder, contain no equation. |
class |
parabola
for test. |
Uses of Reactor in org.simBio.bio.cor |
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Subclasses of Reactor in org.simBio.bio.cor | |
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class |
Hodgkin_huxley_squid_axon_1952_modified
Conversion from CellML 1.0 to Java was done using COR (0.9.31.28) Copyright (c) 2002-2005 Oxford Cardiac Electrophysiology Group |
class |
Vanderpol_model_1928
Conversion from CellML 1.0 to Java was done using COR (0.9.31.28) Copyright (c) 2002-2005 Oxford Cardiac Electrophysiology Group |
Uses of Reactor in org.simBio.bio.faber_rudy_2000.current |
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Subclasses of Reactor in org.simBio.bio.faber_rudy_2000.current | |
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class |
Current
sodium background current. |
class |
ICaL
L-type Calcium channnel. |
class |
ICaT
T-Type Calcium Channel. |
class |
IK1
time indipendent potassium channel |
class |
IKpl
plateau potassium channel |
class |
IKr
Rapidly Activating Potassium channel |
class |
IKs
slow time dependent potassium channel |
class |
INa
fast sodium channel |
class |
INaCa
Sodium Calcium exchanger |
class |
INaK
sodium potassium pump current |
class |
IpCa
Sarcolemmal Ca Pump Current |
class |
NSRLeak
leak current from NSR |
class |
RyR
Calcium release channel on SR |
class |
SRCA
SR calcium pump. |
Uses of Reactor in org.simBio.bio.faber_rudy_2000.function |
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Subclasses of Reactor in org.simBio.bio.faber_rudy_2000.function | |
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class |
Diffusion
diffusion. |
class |
Stimulus
Constructor for Stimulus. |
Uses of Reactor in org.simBio.bio.faber_rudy_2000.molecule |
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Subclasses of Reactor in org.simBio.bio.faber_rudy_2000.molecule | |
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class |
CaBuffer
analytic equation of Calcium buffering. |
class |
DualCaBuffer
Faber GM, Rudy Y. Action potential and contractility changes in [Na+]i overloaded cardiac myocytes: a simulation study. Biophy J 2000;78:2392-2404 |
Uses of Reactor in org.simBio.bio.faber_rudy_2000.structure |
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Subclasses of Reactor in org.simBio.bio.faber_rudy_2000.structure | |
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class |
Cell
Cell. |
class |
JSR
Faber GM, Rudy Y. Action potential and contractility changes in [Na+]i overloaded cardiac myocytes: a simulation study. Biophy J 2000;78:2392-2404 |
class |
NSR
Faber GM, Rudy Y. Action potential and contractility changes in [Na+]i overloaded cardiac myocytes: a simulation study. Biophy J 2000;78:2392-2404 |
Uses of Reactor in org.simBio.bio.function |
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Subclasses of Reactor in org.simBio.bio.function | |
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class |
Analytic2state
2 state gateの解析解を求めて現在の解に設定する。 「心臓のフィジオーム」p. |
class |
Function
Abstract super class of function format. |
Uses of Reactor in org.simBio.bio.henriquez_et_al_2001 |
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Subclasses of Reactor in org.simBio.bio.henriquez_et_al_2001 | |
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class |
GapJunction
Voltage-dependent gap junction model developed by Vogel and Weingart. |
Uses of Reactor in org.simBio.bio.himeno_et_al_2008 |
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Subclasses of Reactor in org.simBio.bio.himeno_et_al_2008 | |
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class |
IKACh
ACh channel. |
Uses of Reactor in org.simBio.bio.hodgkin_huxley_1952 |
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Subclasses of Reactor in org.simBio.bio.hodgkin_huxley_1952 | |
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class |
I_K
Potassium Channel. |
class |
I_L
leak component. |
class |
I_Na
Sodium channel. |
class |
I_stim
Stimulus current. |
class |
Membrane
Membrane. |
Uses of Reactor in org.simBio.bio.kurata_et_al_2005.complex |
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Subclasses of Reactor in org.simBio.bio.kurata_et_al_2005.complex | |
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class |
SR
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Uses of Reactor in org.simBio.bio.kurata_et_al_2005.current |
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Subclasses of Reactor in org.simBio.bio.kurata_et_al_2005.current | |
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class |
ICab
|
class |
INab
|
class |
Ito
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Uses of Reactor in org.simBio.bio.kurata_et_al_2005.flux |
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Subclasses of Reactor in org.simBio.bio.kurata_et_al_2005.flux | |
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class |
Leak
leak flux (Jleak) from the uptake site of SRnet (mM/ms). |
class |
Release
|
class |
Transfer
|
class |
Uptake
|
Uses of Reactor in org.simBio.bio.kurata_et_al_2005.molecule |
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Subclasses of Reactor in org.simBio.bio.kurata_et_al_2005.molecule | |
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class |
CaBuffer_RK
Calculate using ordinary differential equation, working with analytic buffer. |
Uses of Reactor in org.simBio.bio.kuratomi_et_al_2003.current.carrier |
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Subclasses of Reactor in org.simBio.bio.kuratomi_et_al_2003.current.carrier | |
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class |
Carrier
Abstract class for ping-pong model of the carrier. |
Uses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.contraction |
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Subclasses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.contraction | |
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class |
CrossBridgeLength
Length of cross bridge of NL contraction model, Negroni JA and Lascano EC. |
class |
IsotonicContraction
Calculation of half sarcomere length in isotonic experiments. |
class |
Troponin
troponin of Negroni and Lascano contraction model. |
class |
Troponinmit
Troponin state transition of Cardiac Muscle Model by Negroni and Lascano. |
Uses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.current |
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Subclasses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.current | |
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class |
IRyR
Calcium releasing channel on SR. |
Uses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.current.carrier |
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Subclasses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.current.carrier | |
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class |
ICaPump
Ca pump on network SR. |
class |
IPMCA
Ca pump on cell membrane. |
Uses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.current.cf |
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Subclasses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.current.cf | |
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class |
ICFTR
Cystic fibrosis transmembrane conductance regulator Cl- channel current. |
Uses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.function |
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Subclasses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.function | |
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class |
Average
|
class |
ConcentrationAMP
calculation of AMP concentration (conformed to mass conservation law). |
class |
KoDependency_IK1
Updated [K]o dependency calculation for IK1. |
class |
PA2MS
Average and Convert pA to M/S. |
Uses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.molecule |
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Subclasses of Reactor in org.simBio.bio.kuzumoto_et_al_2007.molecule | |
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class |
BetaAR_Gs
betaAR and Gs signaling module. |
class |
CAMP
cAMP module. |
class |
PKA
PKA module. |
class |
PLB
Phospholamban module. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.complex |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.complex | |
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class |
ATPsynthesis
The lumped model of ATP synthesis. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current | |
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class |
MembraneTransporter
Abstract class of membrane transporters. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.cf |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.cf | |
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class |
CfChannel
calculate current component of Na, K, Ca ion according to the constant field theory. |
class |
Iha
Hyperpolarization-activated cation current, Iha. |
class |
ILCCa
Calcium activated Non-Selective Cation current. |
class |
Ist
Sustained inward current for pacemaker model. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.channel |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.channel | |
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class |
Channel
template of Channel. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.pipette |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.pipette | |
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class |
CurrentClamp
current clamp, external current in the RC membrane model. |
class |
Pipette
external current in the RC membrane model. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.potassium |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.current.potassium | |
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class |
PureKchannel
calculate pure potassium channel current. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.function |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.function | |
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class |
Charge
keep whole cell current from external solution. |
class |
ConstantField
calculate constant field. |
class |
Diffusion_a
The first order ordinary differential equation is solved using analytic equation. |
class |
Diffusion_t
The first order ordinary differential equation is solved using analytic equation. |
class |
KoDependency
dependency of extracellular potassium concentration. |
class |
RateConstant
function, c1/(c2*exp((x+c3)/c4)+c5*exp((x+c6)/c7)) |
class |
RateConstantK
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class |
RateConstantVm
|
class |
ReversalPotential
calculate reversal potential of the specific ion. |
class |
Volume
|
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer | |
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class |
Buffer
abstract of buffer |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca | |
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class |
Analytic
instantaneous Ca buffer, using analytic equation as for Zeng et al, 1995 J. |
class |
Analytic_RK
instantaneous Ca buffer using analytic equation as for Zeng et al, 1995. |
class |
InstantCaBuffer
instantaneous Ca buffer, iterative method. |
class |
TroponinNL
Troponin state transition of Cardiac Muscle Model by Negroni and Lascano. |
class |
TroponinNL_RK
Troponin state transition of Negroni and Lascano contraction model for Runge-Kutta. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme | |
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class |
CrossBridgeNL
Cross bridge kinetics of Cardiac Muscle Model by Negroni and Lascano. |
class |
IsometricContraction
Isometric Contraction |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.exp |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.exp | |
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class |
Anoxia
Anoxia condition on ventricular cell model was occured to regulate the oxygen concentration. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.function |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.function | |
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class |
Acidity
calculation of pH (acidity) of the optional solution. |
class |
ConcentrationCyta2
Calculation of the concentration of Cytochrome a2+ |
class |
ConcentrationPi
calculation of iorganic phosphate concentration (conformed to mass conservation law) |
class |
GradientP
proton driving force |
class |
GradientpH
proton gradient on mitochondrial inner membrane. |
class |
MassConservation
calculation of molecular concentration conformed to mass conservation law |
class |
MassConservation2
calculation of molecular concentration conformed to mass conservation law |
class |
MembranePotential
membrane potential on mitochondrial inner membrane. |
class |
MetalFreeConcentration
free concentration of metal affinity molecule |
class |
PartialPotential
calcuration of partial potential. |
class |
PressureToConcentration
calculation of concentration of gas-molecule from partial pressure. |
class |
RedoxPotential
Calculation of the redox potential. |
class |
RedoxPotentialCyta
Calculation of the redox potential of cytochrome a |
class |
VolumeRatio
Calculation of volume ratio between cell and organella. |
class |
Zvalue
calculation of z value. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.function.chemical |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.function.chemical | |
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class |
CN
effect of CN addition. |
class |
FCCP
effect of FCCP addition. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule | |
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class |
SubstrateDehydrogenation
NADH dehydrogenation. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer | |
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class |
HBuffering
Buffering capacity coefficient for H+ (rbuffer). |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme | |
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class |
AK
Adenylate Kinase (AK) System |
class |
CK
Creatine Kinase (CK) System. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain | |
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class |
ATPsynthase
Mitochondrial F1/F0 ATP Synthase. |
class |
ComplexI
NADH-Ubiquinone oxidoreductase (complex I). |
class |
ComplexIII
Cytochrome bc1 Complex (complex III). |
class |
ComplexIV
Cytochrome c Oxidase (complex IV). |
class |
OxidativePhosphorylation
Differential equation for reactions of oxidattive phosphorylation. |
Uses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter |
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Subclasses of Reactor in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter | |
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class |
ANT
ADP/ATP carrier, ADP/ATP translocase, SLC25A4. |
class |
PhosphateCarrier
Phosphate Transporter. |
class |
ProtonLeak
Proton leak from cytosol to intremitochondoria. |
Uses of Reactor in org.simBio.bio.negroni_lascano_1996 |
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Subclasses of Reactor in org.simBio.bio.negroni_lascano_1996 | |
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class |
CrossBridge
Cross bridge kinetics of Cardiac Muscle Model by Negroni and Lascano. |
class |
Qpump
equation 8 in the Negroni and Lascano, 1996 Qpump=Kp/(1+(Km/[Ca2+])^2) |
class |
Qrel
equation 9 in the Negroni and Lascano, 1996 |
Uses of Reactor in org.simBio.bio.negroni_lascano_1996.exp |
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Subclasses of Reactor in org.simBio.bio.negroni_lascano_1996.exp | |
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class |
LChange
muscle length is set with the controlled step and duration |
class |
Model
Cardiac Muscle Model by Negroni and Lascano. |
Uses of Reactor in org.simBio.bio.oka_et_al_2006.function |
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Subclasses of Reactor in org.simBio.bio.oka_et_al_2006.function | |
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class |
JunctionalConductance
Calculate the junctional conductance (nS). |
class |
JunctionalPotential
Calculate the trans-junctional potential between neighbouring two cells. |
Uses of Reactor in org.simBio.bio.oka_et_al_2006.function.kinetics |
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Subclasses of Reactor in org.simBio.bio.oka_et_al_2006.function.kinetics | |
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class |
IndependentGate
Calculate the mean open probability of the gating model consisting of multiple independent gates. |
class |
MultiStateModel
Ligand-operated multi transition model. |
class |
RateConstantCaGate
Calculate the forward and backward rate constans of two-state model by using time constant, pKd and Hill coefficient |
class |
TwoStateModel
Two-state model. |
Uses of Reactor in org.simBio.bio.oka_et_al_2006.structure |
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Subclasses of Reactor in org.simBio.bio.oka_et_al_2006.structure | |
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class |
GapJunctionK
Gap junction model. |
Uses of Reactor in org.simBio.bio.sarai_et_al_2006.function |
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Subclasses of Reactor in org.simBio.bio.sarai_et_al_2006.function | |
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class |
Rate
Rate. |
class |
Ratio
Ratio. |
Uses of Reactor in org.simBio.bio.sarai_noma_2004 |
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Subclasses of Reactor in org.simBio.bio.sarai_noma_2004 | |
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class |
VoltageClamp
apply square voltage pulse |
Uses of Reactor in org.simBio.bio.sarai_noma_2004.fourState |
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Subclasses of Reactor in org.simBio.bio.sarai_noma_2004.fourState | |
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class |
MonteCarlo
|
class |
NaChannel
4 state gate of fast Sodium channel calculated by Monte Carlo method and ordinary differential Equations. |
class |
ODE
Created on 2003/10/30 |
Uses of Reactor in org.simBio.bio.takeuchi_et_al_2006.current |
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Subclasses of Reactor in org.simBio.bio.takeuchi_et_al_2006.current | |
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class |
PMCA
sarcolemmal Ca2+ pump. |
Uses of Reactor in org.simBio.bio.takeuchi_et_al_2006.function |
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Subclasses of Reactor in org.simBio.bio.takeuchi_et_al_2006.function | |
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class |
Electroneutrality
Calculate difference between total amounts of cations and anions. |
class |
ENaCa
equilibrium potential for Na+/Ca2+ exchanger. |
class |
Ouabain
Calculate ouabain effect on amplitude of INaK. |
Uses of Reactor in org.simBio.bio.tenTusscher_et_al_2004.current |
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Subclasses of Reactor in org.simBio.bio.tenTusscher_et_al_2004.current | |
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class |
IbCa
Background Ca2+ current. |
class |
IbNa
Background Na+ current. |
class |
ICa
L-type Ca2+ current. |
class |
IpK
Plateau K current. |
class |
Ito_endo
Transient outward current. |
Uses of Reactor in org.simBio.bio.tenTusscher_et_al_2004.flux |
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Subclasses of Reactor in org.simBio.bio.tenTusscher_et_al_2004.flux | |
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class |
UpTake
Pump current taking up calcium into SR. |
Uses of Reactor in org.simBio.bio.tenTusscher_et_al_2004.function |
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Subclasses of Reactor in org.simBio.bio.tenTusscher_et_al_2004.function | |
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class |
ReversalPotential2
calculate reversal potential of the specific Ion. |
Uses of Reactor in org.simBio.bio.terashima_et_al_2006.complex |
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Subclasses of Reactor in org.simBio.bio.terashima_et_al_2006.complex | |
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class |
WaterFlux
Water flux across the cell membrane [um3/ms]. |
Uses of Reactor in org.simBio.bio.terashima_et_al_2006.current.carrier |
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Subclasses of Reactor in org.simBio.bio.terashima_et_al_2006.current.carrier | |
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class |
NKCC
Flux via Na+-K+-2Cl- cotransporter [amol/msec]. |
Uses of Reactor in org.simBio.bio.terashima_et_al_2006.current.cf |
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Subclasses of Reactor in org.simBio.bio.terashima_et_al_2006.current.cf | |
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class |
IClb
|
class |
IVRCC
volume-regulated Cl- current. |
Uses of Reactor in org.simBio.bio.terashima_et_al_2006.current.potassium |
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Subclasses of Reactor in org.simBio.bio.terashima_et_al_2006.current.potassium | |
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class |
IKATP
ATP-sensitive potassium current. |
Uses of Reactor in org.simBio.bio.terashima_et_al_2006.experiment |
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Subclasses of Reactor in org.simBio.bio.terashima_et_al_2006.experiment | |
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class |
StepChanger
Change the value in a step manner. |
class |
StepChanger2
step change |
class |
TonicityChange
Change extracellular fluid tonicity |
Uses of Reactor in org.simBio.bio.terashima_et_al_2006.function |
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Subclasses of Reactor in org.simBio.bio.terashima_et_al_2006.function | |
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class |
AmplitudeNaK
Calculate volume-dependency of INaK amplitude. |
class |
KoDependency2
Calculate Ko dependency for IKATP. |
class |
Tonicity
Tonicity of extracellular fluid . |
class |
TotalVolume
Calculate total cell volume from cell volume accessible for ion diffusion. |
Uses of Reactor in org.simBio.core |
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Subclasses of Reactor in org.simBio.core | |
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class |
Conductor
root instance to conduct integration. |
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