Uses of Interface
org.simBio.core.Node

Packages that use Node

org.simBio.bio	for the biologists.
org.simBio.bio.cor
org.simBio.bio.faber_rudy_2000.current
org.simBio.bio.faber_rudy_2000.function
org.simBio.bio.faber_rudy_2000.molecule
org.simBio.bio.faber_rudy_2000.structure
org.simBio.bio.function
org.simBio.bio.henriquez_et_al_2001
org.simBio.bio.himeno_et_al_2008
org.simBio.bio.hodgkin_huxley_1952	Modifyed Hodgkin Huxley Squid Axon Model 1952
org.simBio.bio.kurata_et_al_2005.complex
org.simBio.bio.kurata_et_al_2005.current
org.simBio.bio.kurata_et_al_2005.flux
org.simBio.bio.kurata_et_al_2005.molecule
org.simBio.bio.kuratomi_et_al_2003.current.carrier
org.simBio.bio.kuzumoto_et_al_2007.contraction
org.simBio.bio.kuzumoto_et_al_2007.current
org.simBio.bio.kuzumoto_et_al_2007.current.carrier
org.simBio.bio.kuzumoto_et_al_2007.current.cf
org.simBio.bio.kuzumoto_et_al_2007.function
org.simBio.bio.kuzumoto_et_al_2007.molecule
org.simBio.bio.matsuoka_et_al_2003.complex
org.simBio.bio.matsuoka_et_al_2003.current
org.simBio.bio.matsuoka_et_al_2003.current.carrier
org.simBio.bio.matsuoka_et_al_2003.current.cf
org.simBio.bio.matsuoka_et_al_2003.current.channel
org.simBio.bio.matsuoka_et_al_2003.current.pipette
org.simBio.bio.matsuoka_et_al_2003.current.potassium
org.simBio.bio.matsuoka_et_al_2003.function	The common functions among models
org.simBio.bio.matsuoka_et_al_2003.molecule.buffer
org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca
org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme
org.simBio.bio.matsuoka_et_al_2004.current.carrier
org.simBio.bio.matsuoka_et_al_2004.exp
org.simBio.bio.matsuoka_et_al_2004.function
org.simBio.bio.matsuoka_et_al_2004.function.chemical
org.simBio.bio.matsuoka_et_al_2004.molecule
org.simBio.bio.matsuoka_et_al_2004.molecule.buffer
org.simBio.bio.matsuoka_et_al_2004.molecule.buffer.Ca
org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme
org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain
org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter
org.simBio.bio.negroni_lascano_1996	The contraction model proposed by Negroni and Lascano, 1996.
org.simBio.bio.negroni_lascano_1996.exp
org.simBio.bio.noble_et_al_1998
org.simBio.bio.oka_et_al_2006.function
org.simBio.bio.oka_et_al_2006.function.kinetics
org.simBio.bio.oka_et_al_2006.structure
org.simBio.bio.sarai_et_al_2003
org.simBio.bio.sarai_et_al_2006.current.carrier
org.simBio.bio.sarai_et_al_2006.current.cf
org.simBio.bio.sarai_et_al_2006.function
org.simBio.bio.sarai_noma_2004	Single Na channel model, Sarai and Noma, 2004.
org.simBio.bio.sarai_noma_2004.fourState
org.simBio.bio.sarai_noma_2004.structure
org.simBio.bio.takeuchi_et_al_2006.current
org.simBio.bio.takeuchi_et_al_2006.function
org.simBio.bio.tenTusscher_et_al_2004.complex
org.simBio.bio.tenTusscher_et_al_2004.current
org.simBio.bio.tenTusscher_et_al_2004.current.carrier
org.simBio.bio.tenTusscher_et_al_2004.flux
org.simBio.bio.tenTusscher_et_al_2004.function
org.simBio.bio.terashima_et_al_2006.complex
org.simBio.bio.terashima_et_al_2006.current	Classes for membrane currents.
org.simBio.bio.terashima_et_al_2006.current.carrier
org.simBio.bio.terashima_et_al_2006.current.cf
org.simBio.bio.terashima_et_al_2006.current.potassium
org.simBio.bio.terashima_et_al_2006.experiment	Classes for experimental manipulation.
org.simBio.bio.terashima_et_al_2006.function	The common functions among models
org.simBio.core	The basal Classes of the simBio simBioの基盤クラス群。 他のクラスは全て、ここにあるクラスを参照もしくは継承もしくは利用しています。
org.simBio.core.integrator
org.simBio.sim.analyzer	analyzers which inherit core.Analyzer, core.Analyserを継承するクラス群
org.simBio.sim.analyzer.csv	CSV maker 計算結果をCSV形式で書き出します。
org.simBio.sim.analyzer.csv.keep
org.simBio.sim.analyzer.csv.result
org.simBio.sim.analyzer.graph
org.simBio.sim.analyzer.graph.simple	2D Graph maker 計算結果を2次元グラフで表示する。
org.simBio.sim.analyzer.measure
org.simBio.util.numerical
org.simBio.util.numerical.methods

Uses of Node in org.simBio.bio

Classes in org.simBio.bio that implement Node

class	Compartment Nodes folder, contain no equation.
class	parabola for test.

Fields in org.simBio.bio declared as Node

Node	parabola.y
Node	parabola.z

Uses of Node in org.simBio.bio.cor

Classes in org.simBio.bio.cor that implement Node

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

Fields in org.simBio.bio.cor declared as Node

Node	Vanderpol_model_1928.Main_x Main_x (dimensionless).
Node	Vanderpol_model_1928.Main_y Main_y (dimensionless).
Node	Hodgkin_huxley_squid_axon_1952_modified.membrane_V membrane_V (millivolt).
Node	Hodgkin_huxley_squid_axon_1952_modified.potassium_channel_n_gate_n potassium_channel_n_gate_n (dimensionless).
Node	Hodgkin_huxley_squid_axon_1952_modified.sodium_channel_h_gate_h sodium_channel_h_gate_h (dimensionless).
Node	Hodgkin_huxley_squid_axon_1952_modified.sodium_channel_m_gate_m sodium_channel_m_gate_m (dimensionless).

Uses of Node in org.simBio.bio.faber_rudy_2000.current

Classes in org.simBio.bio.faber_rudy_2000.current that implement Node

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.

Fields in org.simBio.bio.faber_rudy_2000.current declared as Node

Node	ICaL.Ca
Node	SRCA.Cai
Node	RyR.Cai
Node	IpCa.Cai
Node	INaCa.Cai
Node	IKs.Cai
Node	ICaL.Cai
Node	INaCa.Cao
Node	ICaL.Cao
Node	RyR.Casr
Node	NSRLeak.Casr
Node	ICaL.d
Node	Current.ep
Node	ICaL.f
Node	IKr.gate
Node	ICaT.gate_b
Node	ICaT.gate_g
Node	IKs.gate_xs1
Node	IKs.gate_xs2
Node	INa.h
Node	RyR.iCa
Node	RyR.iTotal
Node	INa.j
Node	ICaL.K
Node	IKs.Ki
Node	ICaL.Ki
Node	INaK.Ko
Node	IKs.Ko
Node	IKr.Ko
Node	IK1.Ko
Node	ICaL.Ko
Node	INa.m
Node	ICaL.Na
Node	INaK.Nai
Node	INaCa.Nai
Node	IKs.Nai
Node	ICaL.Nai
Node	INaK.Nao
Node	INaCa.Nao
Node	IKs.Nao
Node	ICaL.Nao
Node	INaK.T
Node	INaCa.T
Node	IKs.T
Node	ICaL.T
Node	RyR.timeStep
Node	RyR.Vm
Node	Current.Vm

Uses of Node in org.simBio.bio.faber_rudy_2000.function

Classes in org.simBio.bio.faber_rudy_2000.function that implement Node

class	Diffusion diffusion.
class	Stimulus Constructor for Stimulus.

Fields in org.simBio.bio.faber_rudy_2000.function declared as Node

Node	Diffusion.a
Node	Diffusion.b

Uses of Node in org.simBio.bio.faber_rudy_2000.molecule

Classes in org.simBio.bio.faber_rudy_2000.molecule that implement Node

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

Fields in org.simBio.bio.faber_rudy_2000.molecule declared as Node

Node	CaBuffer.buffered
Node	DualCaBuffer.Cafree
Node	CaBuffer.Cafree
Node	DualCaBuffer.Catotal
Node	CaBuffer.Catotal

Uses of Node in org.simBio.bio.faber_rudy_2000.structure

Classes in org.simBio.bio.faber_rudy_2000.structure that implement Node

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

Fields in org.simBio.bio.faber_rudy_2000.structure declared as Node

Node	NSR.Ca
Node	NSR.Cai
Node	JSR.Cai
Node	JSR.CaTotal
Node	Cell.CaTotal
Node	Cell.ICab
Node	Cell.ICaLCa
Node	Cell.ICaLK
Node	Cell.ICaLNa
Node	Cell.ICaT
Node	Cell.Iext
Node	Cell.IK1
Node	Cell.IKpl
Node	Cell.IKr
Node	Cell.IKs
Node	Cell.INa
Node	Cell.INab
Node	Cell.INaCa
Node	Cell.INaK
Node	Cell.IpCa
Node	Cell.itotal
Node	Cell.itotalCa
Node	Cell.itotalK
Node	Cell.itotalNa
Node	Cell.K
Node	NSR.leak
Node	Cell.Na
Node	JSR.ryr
Node	NSR.srca
Node	NSR.trans
Node	JSR.trans
Node	Cell.Vm

Uses of Node in org.simBio.bio.function

Classes in org.simBio.bio.function that implement Node

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.
class	StepChanger Sequentially changes the value at the desired elapsed time.

Fields in org.simBio.bio.function declared as Node

Node	Analytic2state.alfa
Node	Analytic2state.beta
Node	Analytic2state.dt
Node	Analytic2state.previous
Node	StepChanger.target

Uses of Node in org.simBio.bio.henriquez_et_al_2001

Classes in org.simBio.bio.henriquez_et_al_2001 that implement Node

class

GapJunction Voltage-dependent gap junction model developed by Vogel and Weingart.

Fields in org.simBio.bio.henriquez_et_al_2001 declared as Node

Node	GapJunction.gHH conductance of HH state
Node	GapJunction.gHL conductance of HL state
Node	GapJunction.gLH conductance of LH state
Node	GapJunction.gLL conductance of LL state
Node	GapJunction.nHH fraction of HH state
Node	GapJunction.nHL fraction of HL state
Node	GapJunction.nLH fraction of LH state
Node	GapJunction.nLL fraction of LL state
Node	GapJunction.VHL voltage across hemichannel at HL state (mV)
Node	GapJunction.Vj junctional potential (mV)
Node	GapJunction.VLH voltage across hemichannel at LH state (mV)

Uses of Node in org.simBio.bio.himeno_et_al_2008

Classes in org.simBio.bio.himeno_et_al_2008 that implement Node

class	Iha Iha.
class	IKACh ACh channel.
class	Ist Sustained inward current for pacemaker model.

Fields in org.simBio.bio.himeno_et_al_2008 declared as Node

Node	Ist.activation gate variable
Node	ICaL.ATP intracellular ATP concentration (mM)
Node	IKs.Ca intracellular Ca2+ concentration
Node	ICaL.CaDiadic local Ca2+ concentration near the mouth of L-type Ca channel (mM)
Node	Ist.Cai intracellular calcium concentration (mM)
Node	ICaL.Cai intracellular Ca2+ concentration (mM)
Node	Iha.cAMP cAMP concentration
Node	Iha.cAMP_Vshift
Node	Iha.closedState1
Node	Iha.closedState2
Node	IKACh.gate
Node	ICaL.gate ultra-slow gate probability
Node	IKs.gate1 the open probability of voltage-dependent gate
Node	IKs.gate2 the open probability of [Ca2+]i-dependent gate
Node	IKs.gateC2 the C2 state probability of [Ca2+]i-dependent gate
Node	Ist.inactivation gate variable
Node	IKs.KCNQ1
Node	IKs.KCNQ1free
Node	IKs.KCNQ1p
Node	IKs.KCNQ1p_ratio
Node	Iha.openState1
Node	Iha.openState2
Node	ICaL.pAI AI state probability for voltage-dependent gate
Node	ICaL.pAP AP state probability for voltage-dependent gate
Node	ICaL.pC C state probability for calcium-dependent gate
Node	ICaL.PCa
Node	ICaL.PCl
Node	ICaL.PK
Node	Ist.PKA PKA catalitic domain I concentration
Node	IKs.PKA
Node	ICaL.PKA PKA catalitic domain I concentration
Node	ICaL.PKA_fac
Node	ICaL.PNa
Node	IKs.POpen
Node	ICaL.pRP PR state probability for voltage-dependent gate
Node	ICaL.pU U state probability for calcium-dependent gate
Node	ICaL.pUCa UCa state probability for calcium-dependent gate
Node	ICaL.SingleCurrentAMP to see single current amplitude
Node	Ist.slowInactivation gate variable
Node	Ist.Vm membrane potential (mV)
Node	IKs.Vm Membrane Potential (mV)
Node	Iha.Vm
Node	ICaL.Vm membrane potential (mV)

Uses of Node in org.simBio.bio.hodgkin_huxley_1952

Classes in org.simBio.bio.hodgkin_huxley_1952 that implement Node

class	I_K Potassium Channel.
class	I_L leak component.
class	I_Na Sodium channel.
class	I_stim Stimulus current.
class	Membrane Membrane.

Fields in org.simBio.bio.hodgkin_huxley_1952 declared as Node

Node	I_Na.h gate variable (dimensionless)
Node	Membrane.I_K Potassium current (microA_per_cm2)
Node	Membrane.I_L Leak (Chloride) current (microA_per_cm2)
Node	Membrane.I_Na Sodium current (microA_per_cm2)
Node	Membrane.I_stim Stimulus current (microA_per_cm2)
Node	I_Na.m gate variable (dimensionless)
Node	Membrane.Vm membrane potential, V, initial value = -75.0 (millivolt)
Node	I_Na.Vm membrane potential, V, initial value = -75.0 (millivolt)
Node	I_L.Vm membrane potential, V, initial value = -75.0 (millivolt)
Node	I_K.Vm membrane potential, V, initial value = -75.0 (millivolt)

Uses of Node in org.simBio.bio.kurata_et_al_2005.complex

Classes in org.simBio.bio.kurata_et_al_2005.complex that implement Node

class

SR

Fields in org.simBio.bio.kurata_et_al_2005.complex declared as Node

Node	SR.Cai
Node	SR.CarelTotal
Node	SR.Caup
Node	SR.Leak
Node	SR.Release
Node	SR.Transfer
Node	SR.UpTake

Uses of Node in org.simBio.bio.kurata_et_al_2005.current

Classes in org.simBio.bio.kurata_et_al_2005.current that implement Node

class	ICab
class	INab
class	Ito

Fields in org.simBio.bio.kurata_et_al_2005.current declared as Node

Node	IpCa.Cai
Node	INaCa.Cai
Node	ICaL.Cai
Node	ICab.Cai
Node	INaCa.Cao
Node	ICab.Cao
Node	ICaL.dL
Node	Ito.F
Node	INaK.F
Node	INaCa.F
Node	INab.F
Node	INa.F
Node	IKs.F
Node	IKr.F
Node	IK1.F
Node	ICab.F
Node	ICaL.fL
Node	INa.h
Node	Ito.Ki
Node	INa.Ki
Node	IKs.Ki
Node	IKr.Ki
Node	IK1.Ki
Node	Ito.Ko
Node	INaK.Ko
Node	INa.Ko
Node	IKs.Ko
Node	IKr.Ko
Node	IK1.Ko
Node	IKs.n
Node	Ito.Nai
Node	INaK.Nai
Node	INaCa.Nai
Node	INab.Nai
Node	INa.Nai
Node	IKs.Nai
Node	Ito.Nao
Node	INaK.Nao
Node	INaCa.Nao
Node	INab.Nao
Node	INa.Nao
Node	IKs.Nao
Node	IKr.pa
Node	Ito.q
Node	Ito.R
Node	INaK.R
Node	INaCa.R
Node	INab.R
Node	INa.R
Node	IKs.R
Node	IKr.R
Node	IK1.R
Node	ICab.R
Node	Ito.T
Node	INaK.T
Node	INaCa.T
Node	INab.T
Node	INa.T
Node	IKs.T
Node	IKr.T
Node	IK1.T
Node	ICab.T
Node	Ito.Vm
Node	INaK.Vm
Node	INaCa.Vm
Node	INab.Vm
Node	INa.Vm
Node	IKs.Vm
Node	IKr.Vm
Node	IK1.Vm
Node	ICaL.Vm
Node	ICab.Vm

Uses of Node in org.simBio.bio.kurata_et_al_2005.flux

Classes in org.simBio.bio.kurata_et_al_2005.flux that implement Node

class	Leak leak flux (Jleak) from the uptake site of SRnet (mM/ms).
class	Release
class	Transfer
class	Uptake

Fields in org.simBio.bio.kurata_et_al_2005.flux declared as Node

Node	Uptake.Cai [Ca2+]i (mM)
Node	Release.Cai
Node	Leak.Cai [Ca]i (mM)
Node	Transfer.Caj [Ca2+]rel (mM)
Node	Transfer.Can [Ca2+]up (mM)
Node	Release.Carel
Node	Leak.Caup [Ca]up (mM)
Node	Release.dR
Node	Release.fR
Node	Release.ICab
Node	Release.ICaL
Node	Release.INaCa
Node	Release.IpCa
Node	Release.Vm

Uses of Node in org.simBio.bio.kurata_et_al_2005.molecule

Classes in org.simBio.bio.kurata_et_al_2005.molecule that implement Node

class

CaBuffer_RK Calculate using ordinary differential equation, working with analytic buffer.

Fields in org.simBio.bio.kurata_et_al_2005.molecule declared as Node

Node	CaBuffer_RK.Ca free Ca concentration (mM)
Node	CaBuffer_RK.CaTotal total Ca concentration (mM)

Uses of Node in org.simBio.bio.kuratomi_et_al_2003.current.carrier

Classes in org.simBio.bio.kuratomi_et_al_2003.current.carrier that implement Node

class

Carrier Abstract class for ping-pong model of the carrier.

Fields in org.simBio.bio.kuratomi_et_al_2003.current.carrier declared as Node

Node	Carrier.amplitude amplitude factor (A/F)
Node	INaCa.Cai concentration of intracellular Calcium[mM]
Node	INaCa.Cao concentration of intracellular Calcium[mM]
Node	Carrier.gate reduced 2-state gate
Node	INaCa.inActivation inactivation gate
Node	INaCa.Nai concentration of intracellular Sodium [mM]
Node	INaCa.Nao concentration of intracellular Sodium [mM]
Node	INaCa.T absolute temperature[K]
Node	INaCa.Vm membrane potential of cell[mV]

Uses of Node in org.simBio.bio.kuzumoto_et_al_2007.contraction

Classes in org.simBio.bio.kuzumoto_et_al_2007.contraction that implement Node

class	CrossBridgeForce Cross bridge force of NL contraction model, Negroni JA and Lascano EC.
class	CrossBridgeLength Length of cross bridge of NL contraction model, Negroni JA and Lascano EC.
class	ForceEquilibrium Calculation of force equilibrium.
class	IsotonicContraction Calculation of half sarcomere length in isotonic experiments.
class	ParallelElementForce Parallel element force of NL contraction model, Negroni JA and Lascano EC.
class	Troponin troponin of Negroni and Lascano contraction model.
class	Troponinmit Troponin state transition of Cardiac Muscle Model by Negroni and Lascano.

Fields in org.simBio.bio.kuzumoto_et_al_2007.contraction declared as Node

Node	Troponinmit.ADP
Node	Troponin.ATP
Node	Troponin.Ca
Node	Troponin.CaTotal
Node	Troponin.dATP
Node	Troponin.dXdt
Node	CrossBridgeLength.dXdt derivative value of inextensibleLength
Node	ForceEquilibrium.forceExt
Node	Troponin.L
Node	IsotonicContraction.L
Node	CrossBridgeLength.L half sarcomere length
Node	Troponinmit.Pi
Node	Troponin.T
Node	Troponin.TCa
Node	Troponin.TCaCB
Node	CrossBridgeForce.TCaCB
Node	Troponin.TCB
Node	CrossBridgeForce.TCB
Node	CrossBridgeLength.X half length of thick filament + thin filament length over the non-overlap zone
Node	CrossBridgeForce.X

Uses of Node in org.simBio.bio.kuzumoto_et_al_2007.current

Classes in org.simBio.bio.kuzumoto_et_al_2007.current that implement Node

class

IRyR Calcium releasing channel on SR.

Fields in org.simBio.bio.kuzumoto_et_al_2007.current declared as Node

Node	IRyR.CaDiadic local Ca2+ concentration near the mouth of RyR channel.
Node	IRyR.Cai intracellular calcium concentration (mM)
Node	IRyR.Cao calcium concentration in SR release site (mM)
Node	IRyR.CICRfactor
Node	IRyR.close close state probability
Node	IRyR.K1
Node	IRyR.k1xclose
Node	IRyR.K2
Node	IRyR.K3
Node	IK1.Mg the concentration of Mg2+ (mM)
Node	IRyR.open open state probability
Node	IK1.Pspm the probability of being in the SPM block state
Node	IK1.SPM the concentration of Spermine (mM)

Uses of Node in org.simBio.bio.kuzumoto_et_al_2007.current.carrier

Classes in org.simBio.bio.kuzumoto_et_al_2007.current.carrier that implement Node

class	ICaPump Ca pump on network SR.
class	IPMCA Ca pump on cell membrane.

Fields in org.simBio.bio.kuzumoto_et_al_2007.current.carrier declared as Node

Node	IPMCA.ADP
Node	INaK.ADP
Node	ICaPump.ADP
Node	IPMCA.ATP intracellular ATP concentration (mM)
Node	INaK.ATP concentration of ATP[mM]
Node	ICaPump.ATP intracellular ATP concentration (mM)
Node	IPMCA.CaCaM
Node	IPMCA.Cai Ca2+ concentration in cytoplasm (mM)
Node	ICaPump.Cai Ca2+ concentration in cytoplasm (mM)
Node	IPMCA.Cao Ca2+ concentration in external solution (mM)
Node	ICaPump.Cao Ca2+ concentration in SR (mM, uptake site compartment)
Node	INaK.Couabain ouabain concentration
Node	IPMCA.dATP instantaneous rate of the ATP consumption (M/s)
Node	INaK.dATP differential ATP [mM/msec]
Node	ICaPump.dATP variation of ATP concentration (mM/ms)
Node	INaK.Ki concentration of intracellular Potassium[mM]
Node	ICaPump.KmCaCp mM, dissociation const for Ca binding within cytoplasm
Node	INaK.Ko concentration of extracellular Potassium[mM]
Node	INaK.Nai concentration of intracellular Sodium[mM]
Node	INaK.Nao concentration of extracellular Sodium[mM]
Node	IPMCA.Pi
Node	INaK.Pi
Node	ICaPump.Pi
Node	IPMCA.PKA PKA type I concentration (mM)
Node	INaK.PKA PKA phosphorylation parameter *
Node	ICaPump.PLBphos ratio of phosphorylated fraction of phospholamban
Node	INaK.T absolute temperature[K]
Node	IPMCA.Vi cell volume accessible for ion diffusion
Node	INaK.Vi cell volume accessible for ion diffusion[um^3]
Node	ICaPump.Vi cell volume accessible for ion diffusion
Node	INaK.Vm membrane potential of cell[mV]

Uses of Node in org.simBio.bio.kuzumoto_et_al_2007.current.cf

Classes in org.simBio.bio.kuzumoto_et_al_2007.current.cf that implement Node

class

ICFTR Cystic fibrosis transmembrane conductance regulator Cl- channel current.

Fields in org.simBio.bio.kuzumoto_et_al_2007.current.cf declared as Node

Node	ICFTR.ATP concentration of intracellular ATP [mM]
Node	ICaL.ATP intracellular ATP concentration (mM)
Node	IKs.Ca intracellular Ca2+ concentration
Node	ICaL.CaDiadic local Ca2+ concentration near the mouth of L-type Ca channel (mM)
Node	ICaL.Cai intracellular Ca2+ concentration (mM)
Node	ICaL.gate ultra-slow gate probability
Node	IKs.gate1 the open probability of voltage-dependent gate
Node	IKs.gate2 the open probability of [Ca2+]i-dependent gate
Node	IKs.gateC2 the C2 state probability of [Ca2+]i-dependent gate
Node	IKs.KCNQ1
Node	IKs.KCNQ1free
Node	IKs.KCNQ1p
Node	IKs.KCNQ1p_ratio
Node	ICaL.pAI AI state probability for voltage-dependent gate
Node	ICaL.pAP AP state probability for voltage-dependent gate
Node	ICaL.pC C state probability for calcium-dependent gate
Node	ICaL.PCa
Node	ICaL.PCl
Node	ICaL.PK
Node	IKs.PKA
Node	ICFTR.PKA PKA catalitic domain I concentration
Node	ICaL.PKA PKA catalitic domain I concentration
Node	ICaL.PKA_fac
Node	ICaL.PNa
Node	IKs.POpen
Node	ICFTR.POpen open probability
Node	ICaL.pRP PR state probability for voltage-dependent gate
Node	ICaL.pU U state probability for calcium-dependent gate
Node	ICaL.pUCa UCa state probability for calcium-dependent gate
Node	ICaL.SingleCurrentAMP to see single current amplitude
Node	IKs.Vm Membrane Potential (mV)
Node	ICaL.Vm membrane potential (mV)

Uses of Node in org.simBio.bio.kuzumoto_et_al_2007.function

Classes in org.simBio.bio.kuzumoto_et_al_2007.function that implement Node

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.

Fields in org.simBio.bio.kuzumoto_et_al_2007.function declared as Node

Node	ConcentrationAMP.ADPtotal
Node	ConcentrationAMP.ATPtotal
Node	ConcentrationAMP.cAMP
Node	KoDependency_IK1.Ko concentration of extracellular potassium [mM]
Node	Average.sum total amount
Node	Average.target target to sum
Node	PA2MS.Vi internal volume (um^3)

Uses of Node in org.simBio.bio.kuzumoto_et_al_2007.molecule

Classes in org.simBio.bio.kuzumoto_et_al_2007.molecule that implement Node

class	BetaAR_Gs betaAR and Gs signaling module.
class	CAMP cAMP module.
class	PKA PKA module.
class	PLB Phospholamban module.

Fields in org.simBio.bio.kuzumoto_et_al_2007.molecule declared as Node

Node	PKA.A2RCI A2RCI concentration (mM)
Node	PKA.A2RI A2RI concentration (mM)
Node	CAMP.AC Adenylate cyclase concentration (mM)
Node	PLB.ADP ADP concentration (mM)
Node	PKA.ARCI ARCI concentration (mM)
Node	PLB.ATP ATP concentration (mM)
Node	CAMP.ATP ATP concentration (mM)
Node	BetaAR_Gs.beta1_AR free receptor concentration
Node	BetaAR_Gs.beta1_AR_S301 site of 301 phosphorylated receptor concentration
Node	BetaAR_Gs.beta1_AR_S464 site of 464 phosphorylated receptor concentration
Node	BetaAR_Gs.beta1_ARact active receptor concentration
Node	PKA.cAMP cAMP concentration (mM)
Node	CAMP.cAMP Phosphodiesterase concentration (mM)
Node	PKA.cAMPtot total cAMP concentration (mM)
Node	CAMP.cAMPtot total cAMP concentration (mM)
Node	BetaAR_Gs.d_Gs_alpha_GTPtot Multi newton raphson function
Node	BetaAR_Gs.Gs free gs_protein concentration
Node	BetaAR_Gs.Gs_alpha_GDP Multi newton raphson function
Node	CAMP.Gs_alpha_GTP Gs_alpha GTP-form concentration (mM)
Node	CAMP.Gs_alpha_GTP_AC Gs_alpha_GTP and AC complex concentration (mM)
Node	CAMP.Gs_alpha_GTPtot Gs_alpha_GTP total concentration (mM)
Node	BetaAR_Gs.Gs_alpha_GTPtot Multi newton raphson function
Node	BetaAR_Gs.Gs_beta_gamma gs_beta_gamma_protein concentration
Node	BetaAR_Gs.Gstot total gs_protein concentration
Node	PLB.Inhib1 inhibitor-1 concentration (mM)
Node	PLB.Inhib1p phosphorylated inhibitor-1 concentration (mM)
Node	PLB.Inhib1ptot phosphorylated inhibitor-1 total (Inhib1p + PP1_Inhib) concentration (mM)
Node	BetaAR_Gs.Iso total ligand concentration
Node	BetaAR_Gs.L free ligand concentration
Node	BetaAR_Gs.LR ligand-receptor complex concentration
Node	BetaAR_Gs.LRG ligand-receptor-gs_protein complex concentration
Node	CAMP.PDE Phosphodiesterase concentration (mM)
Node	PLB.PKA PKA catalytic domain I concentration (mM)
Node	PKA.PKA PKA concentration (mM)
Node	BetaAR_Gs.PKA PKA catalitic domain I
Node	PKA.PKACI_PKI PKA and PKI complex concentration (mM)
Node	PKA.PKI protein kinase inhibitor (mM)
Node	PLB.PLB PLB concentration (mM)
Node	PLB.PLBp phosphorylated PLB concentration (mM)
Node	PLB.PLBphos percent of PLB phosphorylation
Node	PLB.PP1 protein phosphatase-1 concentration (mM)
Node	PLB.PP1_Inhib1p protein phosphatase-1 and phosphorylated inhibitor-1 complex concentration (mM)
Node	PKA.RCI RCI concentration (mM)
Node	BetaAR_Gs.RG receptor-gs_protein complex concentration

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.complex

Classes in org.simBio.bio.matsuoka_et_al_2003.complex that implement Node

class

ATPsynthesis The lumped model of ATP synthesis.

Fields in org.simBio.bio.matsuoka_et_al_2003.complex declared as Node

Node	ATPsynthesis.ATP ATP concentration ([ATP]).

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.current

Classes in org.simBio.bio.matsuoka_et_al_2003.current that implement Node

class

MembraneTransporter Abstract class of membrane transporters.

Fields in org.simBio.bio.matsuoka_et_al_2003.current declared as Node

Node	Diffusion.Cai concentration of intracellular Ca2+ [mM]
Node	Diffusion.Cao concentration of extracellular Ca2+ [mM]
Node	MembraneTransporter.CCa to see Ca current component
Node	MembraneTransporter.CK to see K current component
Node	MembraneTransporter.CNa to see Na current component
Node	MembraneTransporter.current
Node	MembraneTransporter.currentCa
Node	MembraneTransporter.currentK
Node	MembraneTransporter.currentNa
Node	Diffusion.Ki concentration of intracellular K+ [mM]
Node	Diffusion.Ko concentration of extracellular K+ [mM]
Node	Diffusion.Nai concentration of intracellular Na+ [mM]
Node	Diffusion.Nao concentration of extracellular Na+ [mM]

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.current.carrier

Fields in org.simBio.bio.matsuoka_et_al_2003.current.carrier declared as Node

Node	Carrier.amplitude amplitude factor (A/F)
Node	INaK.ATP concentration of ATP[mM]
Node	ICaPump.ATP intracellular ATP concentration (mM)
Node	INaK.ATPconsumingRate rate of ATP consumption
Node	ICaPump.ATPconsumingRate consuming rate of ATP; (mM/min)
Node	INaK.ATPconsumption ATP consumption[mM]
Node	ICaPump.ATPconsumption ATP consumed at the time t (mM)
Node	INaCa.Cai concentration of intracellular Calcium[mM]
Node	ICaPump.Cai Ca2+ concentration in cytoplasm (mM)
Node	INaCa.Cao concentration of intracellular Calcium[mM]
Node	ICaPump.Cao Ca2+ concentration in SR (mM, uptake site compartment)
Node	INaK.dATP differential ATP [mM/msec]
Node	ICaPump.F Faradey constant
Node	Carrier.gate reduced 2-state gate
Node	INaK.Ki concentration of intracellular Potassium[mM]
Node	INaK.Ko concentration of extracellular Potassium[mM]
Node	INaK.Nai concentration of intracellular Sodium[mM]
Node	INaCa.Nai concentration of intracellular Sodium [mM]
Node	INaK.Nao concentration of extracellular Sodium[mM]
Node	INaCa.Nao concentration of intracellular Sodium [mM]
Node	INaK.T absolute temperature[K]
Node	INaCa.T absolute temperature[K]
Node	INaK.Vi cell volume accessible for ion diffusion[um^3]
Node	ICaPump.Vi cell volume accessible for ion diffusion
Node	INaK.Vm membrane potential of cell[mV]
Node	INaCa.Vm membrane potential of cell[mV]

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.current.cf

Classes in org.simBio.bio.matsuoka_et_al_2003.current.cf that implement Node

class

ILCCa Calcium activated Non-Selective Cation current.

Fields in org.simBio.bio.matsuoka_et_al_2003.current.cf declared as Node

Node	Ist.activation gate variable
Node	ICaT.activation open probability of activation gate
Node	ICaL.ATP intracellular ATP concentration (mM)
Node	ICaL.CaDiadic local Ca2+ concentration near the mouth of L-type Ca channel (mM)
Node	Ist.Cai intracellular calcium concentration (mM)
Node	ILCCa.Cai intracellular calcium concentration (mM)
Node	ICaL.Cai intracellular calcium concentration (mM)
Node	Iha.closedState1
Node	Iha.closedState2
Node	CfChannel.constantFieldCa Ca2+ flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldK K+ flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldNa Na+ flux calculated by constant field theory [mM]
Node	INa.gate ultra-slow gate
Node	ICaL.gate ultra-slow gate probability
Node	Ito.gate1 activation gating variable
Node	Ito.gate2 inactivation gating variable
Node	IKpl.GK channel conductance
Node	Ist.inactivation gate variable
Node	ICaT.inactivation open probability of inactivation gate
Node	Iha.openState1
Node	Iha.openState2
Node	INa.pAI AI state probability for voltage-dependent gate
Node	ICaL.pAI AI state probability for voltage-dependent gate
Node	INa.pAP AP state probability for voltage-dependent gate
Node	ICaL.pAP AP state probability for voltage-dependent gate
Node	ICaL.pC C state probability for calcium-dependent gate
Node	INa.pRP RP state probability for voltage-dependent gate
Node	ICaL.pRP PR state probability for voltage-dependent gate
Node	ICaL.pU U state probability for calcium-dependent gate
Node	ICaL.pUCa UCa state probability for calcium-dependent gate
Node	Ist.slowInactivation gate variable
Node	ICaL.sumCa integration of ICaL
Node	Ito.Vm membrane potential (mV)
Node	Ist.Vm membrane potential (mV)
Node	INa.Vm membrane potential (mV)
Node	IKpl.Vm membrane potential (mV)
Node	Iha.Vm
Node	ICaT.Vm membrane potential
Node	ICaL.Vm membrane potential (mV)

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.current.channel

Classes in org.simBio.bio.matsuoka_et_al_2003.current.channel that implement Node

class

Channel template of Channel.

Fields in org.simBio.bio.matsuoka_et_al_2003.current.channel declared as Node

Node	IRyR.CaDiadic local Ca2+ concentration near the mouth of RyR channel
Node	IRyR.Cai intracellular calcium concentration (mM)
Node	IRyR.Cao extracellular calcium concentration (mM)
Node	IRyR.close close state probability
Node	IRyR.open open state probability
Node	IRyR.sumCa integration of IRyR

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.current.pipette

Classes in org.simBio.bio.matsuoka_et_al_2003.current.pipette that implement Node

class	CurrentClamp current clamp, external current in the RC membrane model.
class	Pipette external current in the RC membrane model.
class	VoltageClamp voltage clamp protocol.

Fields in org.simBio.bio.matsuoka_et_al_2003.current.pipette declared as Node

Node	VoltageClamp.observedCurrent current through the cell membrane
Node	VoltageClamp.timeStep time step for integral calculation
Node	VoltageClamp.Vm membrane potential

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.current.potassium

Classes in org.simBio.bio.matsuoka_et_al_2003.current.potassium that implement Node

class

IKATP ATP-sensitive potassium current.

Fields in org.simBio.bio.matsuoka_et_al_2003.current.potassium declared as Node

Node	IK1.alfa rate constant
Node	IKATP.ATPi concentration of intracellular ATP[mM]
Node	IKs.Ca intracellular Ca2+ concentration
Node	IKACh.gate
Node	IK1.gate gate, blocked by polyamine (time dependent compornent)
Node	IKs.gate1 the open probability of voltage-dependent gate
Node	IKr.gate1 activation gating variable (the rapid component)
Node	IKs.gate2 the open probability of [Ca2+]i-dependent gate
Node	IKr.gate2 activation gating variable (the slow component)
Node	IKr.gate3 inactivation gating variable
Node	PureKchannel.permeabilityK channel permeability for potassium
Node	PureKchannel.reversalPotential reversal potential
Node	PureKchannel.Vm membrane potential (mV)
Node	IKs.Vm Membrane Potential(mV)

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.function

Classes in org.simBio.bio.matsuoka_et_al_2003.function that implement Node

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
class	RateConstantVm
class	ReversalPotential calculate reversal potential of the specific ion.
class	Volume

Fields in org.simBio.bio.matsuoka_et_al_2003.function declared as Node

Node	Charge.Cm membrane capacitance (pF)
Node	Diffusion_a.dt
Node	ReversalPotential.in intracellular ion concentration (mM)
Node	Current.in internal ion concentration (mM)
Node	ConstantField.in intracellular ion concentration (mM)
Node	KoDependency.Ko concentration of extracellular potassium [mM]
Node	ReversalPotential.out extracellular ion concentration (mM)
Node	Current.out external ion concentration (mM)
Node	ConstantField.out extracellular ion concentration (mM)
Node	Volume.ratio ratio
Node	RateConstantK.reversalPotential
Node	Diffusion_t.t
Node	ReversalPotential.T the absolute temperature (K)
Node	ConstantField.T the absolute temperature (K)
Node	Diffusion_t.target
Node	Diffusion_a.target
Node	Volume.total total value
Node	Current.Vi internal volume (um^3)
Node	RateConstantVm.Vm
Node	RateConstantK.Vm
Node	ConstantField.Vm membrane potential (mV)
Node	Charge.Vm membrane potential (mV)
Node	Current.Vo external volume (um^3)

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer

Classes in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer that implement Node

class

Buffer abstract of buffer

Fields in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer declared as Node

Node	Buffer.free free concentration (mM)

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca

Classes in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca that implement Node

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	ODE Ca buffer, using ordinary differential equation (ODE).
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.

Fields in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca declared as Node

Node	TroponinNL.ATP
Node	TroponinNL.ATPconsumingRate
Node	TroponinNL.ATPconsumption
Node	TroponinNL.Ca
Node	ODE.Ca free Ca2+ concentration (mM)
Node	InstantCaBuffer.Ca
Node	Analytic_RK.Ca free calcium concentration (mM)
Node	Analytic.Ca
Node	TroponinNL_RK.CaTotal total Ca concentration
Node	Analytic_RK.CaTotal total calcium concentration (free calcium + buffered calcium + influx/efflux calcium) (mM)
Node	TroponinNL.TCa
Node	TroponinNL.TCaCB
Node	TroponinNL.TCB

Uses of Node in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme

Classes in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme that implement Node

class	CrossBridgeNL Cross bridge kinetics of Cardiac Muscle Model by Negroni and Lascano.
class	IsometricContraction Isometric Contraction

Fields in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme declared as Node

Node	CrossBridgeNL.forceCB
Node	CrossBridgeNL.forceExt
Node	CrossBridgeNL.h
Node	CrossBridgeNL.halfsarcomerelength
Node	CrossBridgeNL.InextensibleLength

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.current.carrier

Fields in org.simBio.bio.matsuoka_et_al_2004.current.carrier declared as Node

Node	INaK.ADP
Node	ICaPump.ADP
Node	INaK.Pi

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.exp

Classes in org.simBio.bio.matsuoka_et_al_2004.exp that implement Node

class

Anoxia Anoxia condition on ventricular cell model was occured to regulate the oxygen concentration.

Fields in org.simBio.bio.matsuoka_et_al_2004.exp declared as Node

Node	Anoxia.elapsedTime
Node	Anoxia.oxygen

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.function

Classes in org.simBio.bio.matsuoka_et_al_2004.function that implement Node

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.

Fields in org.simBio.bio.matsuoka_et_al_2004.function declared as Node

Node	ConcentrationAMP.AdenosineTotal
Node	ConcentrationPi.ADPtcell total ADP concentration in cytosol
Node	ConcentrationAMP.ADPtcell
Node	ConcentrationPi.ADPtmit total ADP concentration in mitochondria
Node	ConcentrationPi.AMP AMP concentration in cytosol
Node	ConcentrationPi.ATPtcell total ATP concentration in cytosol
Node	ConcentrationAMP.ATPtcell
Node	ConcentrationPi.ATPtmit total ATP concentration in mitochondria
Node	RedoxPotentialCyta.dP proton gradient
Node	MembranePotential.dP proton driving force
Node	MembranePotential.dpH proton gradient of mitochondrial matrix to cytosol
Node	GradientP.dpH proton gradient between cytosol and matrix
Node	ConcentrationCyta2.Ema redox potential of cytochrome a
Node	RedoxPotentialCyta.Emc redox potential of cytochrome c
Node	MetalFreeConcentration.metal metal ion concentration
Node	MassConservation.other other concentration of the same molecular group
Node	PressureToConcentration.PartialPressure
Node	ConcentrationPi.PCr phosphocreatine concentration in cytosol
Node	GradientpH.pHcell pH of cytosol
Node	GradientpH.pHmit pH of mitochondrial matrix
Node	ConcentrationPi.Pimit iorganic phosphate concentration in mitochondria
Node	RedoxPotential.Product product and substrate concentrations of reaction
Node	Acidity.Proton
Node	VolumeRatio.ratio volume ratio
Node	ConcentrationPi.Rcm volume ratio between cytosol and mitochondrial matrix
Node	RedoxPotential.Substrate product and substrate concentrations of reaction
Node	PartialPotential.total membrane potential
Node	MetalFreeConcentration.total total concentration
Node	MassConservation.total total concentration
Node	ConcentrationCyta2.Zvalue Z = 2.303 * R * T / F

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.function.chemical

Classes in org.simBio.bio.matsuoka_et_al_2004.function.chemical that implement Node

class	CN effect of CN addition.
class	FCCP effect of FCCP addition.

Fields in org.simBio.bio.matsuoka_et_al_2004.function.chemical declared as Node

Node	CN.CN cyanide concentration
Node	FCCP.FCCP FCCP concentration

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.molecule

Classes in org.simBio.bio.matsuoka_et_al_2004.molecule that implement Node

class

SubstrateDehydrogenation NADH dehydrogenation.

Fields in org.simBio.bio.matsuoka_et_al_2004.molecule declared as Node

Node	Diffusion.external external concentration
Node	Diffusion.internal internal concentration
Node	SubstrateDehydrogenation.NAD NAD+ concentration
Node	SubstrateDehydrogenation.NADH NADH concentration
Node	SubstrateDehydrogenation.Rcm ratio of cytosol active volume and mitochondria volume

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer

Classes in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer that implement Node

class

HBuffering Buffering capacity coefficient for H+ (rbuffer).

Fields in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer declared as Node

Node	HBuffering.pH a measure of the activity of hydrogen ions (H+) in a solution

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer.Ca

Fields in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer.Ca declared as Node

Node	TroponinNL_RK.ADP
Node	TroponinNL_RK.Pi

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme

Classes in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme that implement Node

class	AK Adenylate Kinase (AK) System
class	CK Creatine Kinase (CK) System.

Fields in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme declared as Node

Node	AK.ADPfree free ADP concentration in cytosol
Node	AK.ADPmg Mg binding ADP concentration in cytosol
Node	CK.ADPtotal total ADP concentration in cytosol
Node	AK.ADPtotal total ADP concentration in cytosol
Node	AK.AMP AMP concentration in cytosol
Node	AK.ATPmg Mg binding ATP concentration in cytosol
Node	CK.ATPtotal total ATP concentration in cytosol
Node	AK.ATPtotal total ATP concentration in cytosol
Node	CK.Cr creatine concentration in cytosol
Node	CK.PCr phosphocreatine concentration in cytosol
Node	CK.Proton proton concentration in cytosol

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain

Classes in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain that implement Node

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.

Fields in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain declared as Node

Node	ComplexIV.a2 cytochrome a2+ (reduced) concentration
Node	ATPsynthase.ADPtmito total ADP concentration in mitochondrial matrix
Node	ATPsynthase.ATPtmito total ATP concentration in mitochondrial matrix
Node	ComplexIV.c2 cytochrome c2+ (reduced) concentration
Node	OxidativePhosphorylation.Cytc2 cytochrome c2+ (reduced) concentration
Node	ComplexIII.dP proton driving force of mitochondrial inner membrane
Node	ComplexI.dP proton driving force on mitochondrial inner membrane
Node	ATPsynthase.dP proton driving force on mitochondrial inner membrane
Node	ComplexIII.Emc redox potential for cytochrome c
Node	ComplexI.EmN redox potential for NADH
Node	ComplexIII.EmU redox potential for ubiquinone
Node	ComplexI.EmU redox potential for ubiquinone
Node	ATPsynthase.Hcell proton concentration in cytosol
Node	OxidativePhosphorylation.Hmito proton concentration in mitochondrial matrix
Node	ATPsynthase.Hmito proton concentration in mitochondrial matrix
Node	ComplexIV.kC4 rate constant of complex IV
Node	OxidativePhosphorylation.NADH mitochondrial NADH concentration
Node	ComplexIV.O2 oxygen concentration
Node	OxidativePhosphorylation.Oxygen oxygen concentration
Node	ATPsynthase.Pitmito inorganic phosphate concentration in mitochondrial matrix
Node	OxidativePhosphorylation.rbuffermito buffering capacity for proton in mitochondrial matrix
Node	ATPsynthase.rbuffermito buffering capacity for proton in mitochondrial matrix
Node	OxidativePhosphorylation.Rcm ratio of cytosol volume and mitochondria volume
Node	ATPsynthase.Rcm ratio of cytosol volume and mitochondria volume
Node	OxidativePhosphorylation.UQH2 ubiquinol (UQH2) concentration
Node	OxidativePhosphorylation.vC1 rate of complex I
Node	OxidativePhosphorylation.vC3 rate of complex III
Node	OxidativePhosphorylation.vC4 rate of complex IV

Uses of Node in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter

Classes in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter that implement Node

class	ANT ADP/ATP carrier, ADP/ATP translocase, SLC25A4.
class	PhosphateCarrier Phosphate Transporter.
class	ProtonLeak Proton leak from cytosol to intremitochondoria.

Fields in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter declared as Node

Node	ANT.ADPfcell Mg free ADP concentration in cytosol (mM)
Node	ANT.ADPfmito Mg free ADP concentration in mitohocndria (mM)
Node	ANT.ADPtcell total ADP concentration in cytosol (mM)
Node	ANT.ATPfcell Mg free ATP concentration in cytosol (mM)
Node	ANT.ATPfmito Mg free ATP concentration in mitohocndria (mM)
Node	ANT.ATPtcell total ATP concentration in cytosol (mM)
Node	ANT.ATPtmito total ATP concentration in mitohocndria (mM)
Node	ProtonLeak.dP proton gradient of mitohocndrial inner membrane
Node	ANT.dPsicell membrane potential at matrix side of mitochondrial inner membrane (mV)
Node	ANT.dPsimito membrane potential at matrix side of mitochondrial inner membrane (mV)
Node	ProtonLeak.Hcell proton concentration in cytosol (mM)
Node	PhosphateCarrier.Hcell proton concentration in cytosol (mM)
Node	ProtonLeak.Hmito proton concentration in mitohocndria (mM)
Node	PhosphateCarrier.Hmito proton concentration in mitochondrial matrix (mM)
Node	ANT.Hmito proton concentration in mitohocndria (mM)
Node	ProtonLeak.kLK1 rate constant of proton leak (mM/msec)
Node	PhosphateCarrier.pHcell pH in cytosol
Node	PhosphateCarrier.pHmito pH in mitochondrial matrix
Node	PhosphateCarrier.Pitcell inorganic phosphate concentration in cytosol (mM)
Node	PhosphateCarrier.Pitmito inorganic phosphate concentration in mitochondrial matrix (mM)
Node	ProtonLeak.rbuffermito buffering capacity for proton in mitochondrial matrix
Node	PhosphateCarrier.rbuffermito buffering capacity for proton in mitochondrial matrix
Node	ANT.rbuffermito buffering capacity for proton in mitochondrial matrix
Node	ProtonLeak.Rcm ratio of cytosol volume and mitochondria volume
Node	PhosphateCarrier.Rcm ratio of cytosol volume and mitochondria volume
Node	ANT.Rcm ratio of cytosol volume and mitochondria volume

Uses of Node in org.simBio.bio.negroni_lascano_1996

Classes in org.simBio.bio.negroni_lascano_1996 that implement Node

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

Fields in org.simBio.bio.negroni_lascano_1996 declared as Node

Node	Troponin.Ca
Node	Qrel.Ca
Node	Qpump.Ca
Node	Qrel.CaRest
Node	Troponin.dXdt
Node	CrossBridge.dXdt
Node	Qrel.elapsedTime
Node	CrossBridge.Fb
Node	CrossBridge.Fp
Node	Qrel.Km
Node	Qpump.Km
Node	Qrel.Kp
Node	Qpump.Kp
Node	Troponin.L
Node	CrossBridge.L
Node	Qrel.Qm
Node	Qrel.Qpump
Node	Qrel.QpumpRest
Node	Qrel.Qsr
Node	Qrel.t0
Node	Qrel.t1
Node	Troponin.TCa
Node	Troponin.TCaCB
Node	CrossBridge.TCaCB
Node	Troponin.TCB
Node	CrossBridge.TCB
Node	CrossBridge.X

Uses of Node in org.simBio.bio.negroni_lascano_1996.exp

Classes in org.simBio.bio.negroni_lascano_1996.exp that implement Node

class	LChange muscle length is set with the controlled step and duration
class	Model Cardiac Muscle Model by Negroni and Lascano.

Fields in org.simBio.bio.negroni_lascano_1996.exp declared as Node

Node	Model.Ca
Node	Model.Fb
Node	Model.Fp
Node	Model.L
Node	LChange.L muscle length
Node	Model.TCa
Node	Model.TCaCB
Node	Model.TCB
Node	Model.X

Uses of Node in org.simBio.bio.noble_et_al_1998

Fields in org.simBio.bio.noble_et_al_1998 declared as Node

Node	Model.CaCalmod
Node	Model.Cads
Node	Model.Cai
Node	Model.Carel
Node	Model.CaTrop
Node	Model.Caup
Node	Model.CrossBridge
Node	Model.d
Node	Model.E
Node	Model.f
Node	Model.f2
Node	Model.f2ds
Node	Model.FrAct
Node	Model.FrProd
Node	Model.h
Node	Model.ICaL
Node	Model.IKr
Node	Model.IKs
Node	Model.Istim
Node	Model.Ki
Node	Model.Ko
Node	Model.LightChain
Node	Model.m
Node	Model.Nai
Node	Model.r
Node	Model.s
Node	Model.Tension
Node	Model.xr1
Node	Model.xr2
Node	Model.xs

Uses of Node in org.simBio.bio.oka_et_al_2006.function

Classes in org.simBio.bio.oka_et_al_2006.function that implement Node

class	JunctionalConductance Calculate the junctional conductance (nS).
class	JunctionalPotential Calculate the trans-junctional potential between neighbouring two cells.

Fields in org.simBio.bio.oka_et_al_2006.function declared as Node

Node	JunctionalConductance.gj the unitary conductance of gap junction channels (pS)
Node	JunctionalConductance.pOpen the mean open probability of the gates
Node	JunctionalPotential.Vm1 membrane potential of cell no 1
Node	JunctionalPotential.Vm2 membrane potential of cell no 2

Uses of Node in org.simBio.bio.oka_et_al_2006.function.kinetics

Classes in org.simBio.bio.oka_et_al_2006.function.kinetics that implement Node

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.

Fields in org.simBio.bio.oka_et_al_2006.function.kinetics declared as Node

Node	TwoStateModel.close closed state probability
Node	MultiStateModel.close closed state probability
Node	RateConstantCaGate.k_backward backward rate constant
Node	RateConstantCaGate.k_forward forward rate constant
Node	TwoStateModel.ligand ligand concentration
Node	MultiStateModel.ligand ligand concentration
Node	TwoStateModel.open open state probability
Node	MultiStateModel.open open state probability
Node	RateConstantCaGate.pX p[X].

Uses of Node in org.simBio.bio.oka_et_al_2006.structure

Classes in org.simBio.bio.oka_et_al_2006.structure that implement Node

class

GapJunctionK Gap junction model.

Fields in org.simBio.bio.oka_et_al_2006.structure declared as Node

Node	GapJunction.Cm1 membrane capacitance of cell #1 (pF)
Node	GapJunction.Cm2 membrane capacitance of cell #2 (pS)
Node	GapJunction.conductance conductance of gapjunction (nS)
Node	GapJunctionK.Ki1 intracellular K+ concentration of cell #1 (mM)
Node	GapJunctionK.Ki2 intracellular K+ concentration of cell #2 (mM)
Node	GapJunction.Vm1 membrane potential of cell #1 (mV)
Node	GapJunction.Vm2 membrane potential of cell #2 (mV)
Node	GapJunctionK.volume1 cell volume of cell #1 (um3)
Node	GapJunctionK.volume2 cell volume of cell #2 (um3)

Uses of Node in org.simBio.bio.sarai_et_al_2003

Fields in org.simBio.bio.sarai_et_al_2003 declared as Node

Node	VoltageClamp.observedCurrent total current through the cell membrane (pA)
Node	VoltageClamp.Vm membrane potential (mV)

Uses of Node in org.simBio.bio.sarai_et_al_2006.current.carrier

Fields in org.simBio.bio.sarai_et_al_2006.current.carrier declared as Node

Node	IPMCA.ADP intracellular ADP concentration (mM)
Node	IPMCA.ATP intracellular ATP concentration (mM)
Node	IPMCA.Cai Ca2+ concentration in cytoplasm (mM)
Node	IPMCA.Cao Ca2+ concentration in external solution (mM)
Node	IPMCA.dATP rate of the ATP consumption (mM/ms)
Node	IPMCA.Vi cell volume accessible for ion diffusion

Uses of Node in org.simBio.bio.sarai_et_al_2006.current.cf

Fields in org.simBio.bio.sarai_et_al_2006.current.cf declared as Node

Node	ICaL.ATP intracellular ATP concentration (mM)
Node	ICaL.CaDiadic local Ca2+ concentration near the mouth of L-type Ca channel (mM)
Node	ICaL.Cai intracellular calcium concentration (mM)
Node	ICaL.gate ultra-slow gate probability
Node	ICaL.pAI AI state probability for voltage-dependent gate
Node	ICaL.pAP AP state probability for voltage-dependent gate
Node	ICaL.pC C state probability for calcium-dependent gate
Node	ICaL.pRP PR state probability for voltage-dependent gate
Node	ICaL.pU U state probability for calcium-dependent gate
Node	ICaL.pUCa UCa state probability for calcium-dependent gate
Node	ICaL.sumCa integration of ICaL
Node	ICaL.Vm membrane potential (mV)

Uses of Node in org.simBio.bio.sarai_et_al_2006.function

Classes in org.simBio.bio.sarai_et_al_2006.function that implement Node

class	Rate Rate.
class	Ratio Ratio.

Fields in org.simBio.bio.sarai_et_al_2006.function declared as Node

Node	Ratio.denominator denominator
Node	Ratio.numerator numerator
Node	Rate.sum total amount
Node	Rate.target target to sum

Uses of Node in org.simBio.bio.sarai_noma_2004

Fields in org.simBio.bio.sarai_noma_2004 declared as Node

Node	VoltageClamp.Vm

Uses of Node in org.simBio.bio.sarai_noma_2004.fourState

Classes in org.simBio.bio.sarai_noma_2004.fourState that implement Node

class	MonteCarlo
class	NaChannel 4 state gate of fast Sodium channel calculated by Monte Carlo method and ordinary differential Equations.

Fields in org.simBio.bio.sarai_noma_2004.fourState declared as Node

protected Node	ODE.pAI
protected Node	ODE.pAP
protected Node	ODE.pRP

Uses of Node in org.simBio.bio.sarai_noma_2004.structure

Fields in org.simBio.bio.sarai_noma_2004.structure declared as Node

Node	GapJunction.Cm1 membrane capacitance of cell #1
Node	GapJunction.Cm2 membrane capacitance of cell #2
Node	GapJunction.Vm1 membrane potential of cell #1
Node	GapJunction.Vm2 membrane potential of cell #2

Uses of Node in org.simBio.bio.takeuchi_et_al_2006.current

Classes in org.simBio.bio.takeuchi_et_al_2006.current that implement Node

class

PMCA sarcolemmal Ca2+ pump.

Fields in org.simBio.bio.takeuchi_et_al_2006.current declared as Node

Node	ICaL.ATP intracellular ATP concentration (mM)
Node	IRyR.CaDiadic local Ca2+ concentration near the mouth of RyR channel
Node	ICaL.CaDiadic local Ca2+ concentration near the mouth of L-type Ca channel (mM)
Node	PMCA.Cai concentration of intracellular Ca2+ [mM]
Node	IRyR.Cai intracellular calcium concentration (mM)
Node	INaCa.Cai concentration of intracellular Ca2+ [mM]
Node	ICaL.Cai intracellular Ca2+ concentration (mM)
Node	INaCa.Cao concentration of extracellular Ca2+ [mM]
Node	IRyR.Carel calcium concentration in SR rel (mM)
Node	IRyR.close close state probability
Node	CfChannel.constantFieldCa Ca2+ flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldCl Cl- flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldK K+ flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldNa Na+ flux calculated by constant field theory [mM]
Node	ICaL.gate ultra-slow gate probability
Node	INaCa.inActivation1 I1 probability for inactivation gate 1 (Na-dependent)
Node	INaCa.inActivation2 I2 probability for inactivation gate 2 (Ca-dependent)
Node	INaCa.Nai concentration of intracellular Na+ [mM]
Node	INaCa.Nao concentration of extracellular Na+ [mM]
Node	IRyR.open open state probability
Node	ICaL.pAI AI state probability for voltage-dependent gate
Node	ICaL.pAP AP state probability for voltage-dependent gate
Node	ICaL.pC C state probability for Ca2+-dependent gate
Node	INaCa.pE1total E1 probability
Node	PMCA.permeabilityCa factor to define the maximum PMCA current [pA/pF]
Node	CfChannel.permeabilityCa channel permeability for Ca2+
Node	CfChannel.permeabilityCl channel permeability for Cl- [pA/pF/mM]
Node	CfChannel.permeabilityK channel permeability for K+ [pA/pF/mM][pA/pF/mM]
Node	CfChannel.permeabilityNa channel permeability for Na+ [pA/pF/mM]
Node	ICaL.pRP PR state probability for voltage-dependent gate
Node	ICaL.pU U state probability for Ca2+-dependent gate
Node	ICaL.pUCa UCa state probability for Ca2+-dependent gate
Node	INaCa.T absolute temperature [K]
Node	INaCa.Vm membrane potential [mV]
Node	ICaL.Vm membrane potential (mV)

Uses of Node in org.simBio.bio.takeuchi_et_al_2006.function

Classes in org.simBio.bio.takeuchi_et_al_2006.function that implement Node

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.

Fields in org.simBio.bio.takeuchi_et_al_2006.function declared as Node

Node	Electroneutrality.aCa amount of intracellular Ca2+ [pEq]
Node	Electroneutrality.aCl amount of intracellular Cl- [pEq]
Node	Electroneutrality.aK amount of intracellular K+ [pEq]
Node	Electroneutrality.aLA amount of intracellular LA [pEq]
Node	Electroneutrality.aNa amount of intracellular Na+ [pEq]
Node	Electroneutrality.Ca concentration of intracellular Ca2+ [mM]
Node	Electroneutrality.Cl concentration of intracellular Cl- [mM]
Node	ENaCa.ECa equilibrium potential for Ca2+ [mV]
Node	ENaCa.ENa equilibrium potential for Na+ [mV]
Node	Electroneutrality.K concentration of intracellular K+ [mM]
Node	Electroneutrality.LA concentration of intracellular LA [mM]
Node	Ouabain.max maximum amplitude [A/F]
Node	Electroneutrality.Na concentration of intracellular Na+ [mM]
Node	Ouabain.ouabain concentration of extracellular ouabain [mM]
Node	Electroneutrality.totalanion amount of intracellular total anions [pEq]
Node	Electroneutrality.totalcation amount of intracellular total cations [pEq]
Node	Electroneutrality.volume intracellular actuve volume [um^3]

Uses of Node in org.simBio.bio.tenTusscher_et_al_2004.complex

Fields in org.simBio.bio.tenTusscher_et_al_2004.complex declared as Node

Node	SR.Cai
Node	SR.CaTotal
Node	SR.Ileak
Node	SR.Irel
Node	SR.Iup

Uses of Node in org.simBio.bio.tenTusscher_et_al_2004.current

Classes in org.simBio.bio.tenTusscher_et_al_2004.current that implement Node

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.

Fields in org.simBio.bio.tenTusscher_et_al_2004.current declared as Node

Node	IpCa.Cai
Node	ICa.Cai
Node	ICa.Cao
Node	Ito_endo.conductance
Node	Ito.conductance
Node	INa.conductance
Node	IKs.conductance
Node	IKr.conductance
Node	IK1.conductance
Node	ICa.conductance
Node	ICa.d
Node	ICa.dinfi
Node	Ito_endo.dt
Node	Ito.dt
Node	INa.dt
Node	IKs.dt
Node	IKr.dt
Node	ICa.dt
Node	ICa.dtau
Node	ICa.eCa
Node	IbCa.eCa
Node	Ito_endo.eK
Node	Ito.eK
Node	IpK.eK
Node	IKr.eK
Node	IK1.eK
Node	IKs.eKs
Node	INa.eNa
Node	IbNa.eNa
Node	ICa.f
Node	ICa.fCa
Node	ICa.fCainfi
Node	ICa.finfi
Node	ICa.ftau
Node	IK1.gate
Node	INa.h
Node	INa.hinfi
Node	INa.htau
Node	INa.j
Node	INa.jinfi
Node	INa.jtau
Node	IKr.Ko
Node	IK1.Ko
Node	INa.m
Node	INa.minfi
Node	INa.mtau
Node	Ito_endo.r
Node	Ito.r
Node	Ito_endo.rinfi
Node	Ito.rinfi
Node	Ito_endo.rtau
Node	Ito.rtau
Node	Ito_endo.s
Node	Ito.s
Node	Ito_endo.sinfi
Node	Ito.sinfi
Node	INa.ssActivation
Node	INa.ssInactivation
Node	Ito_endo.stau
Node	Ito.stau
Node	Ito_endo.Vm
Node	Ito.Vm
Node	IpK.Vm
Node	INa.Vm
Node	IKs.Vm
Node	IKr.Vm
Node	IK1.Vm
Node	ICa.Vm
Node	IbNa.Vm
Node	IbCa.Vm
Node	IKr.xr1
Node	IKr.xr1infi
Node	IKr.xr1tau
Node	IKr.xr2
Node	IKr.xr2infi
Node	IKr.xr2tau
Node	IKs.xs
Node	IKs.xsinfi
Node	IKs.xstau

Uses of Node in org.simBio.bio.tenTusscher_et_al_2004.current.carrier

Fields in org.simBio.bio.tenTusscher_et_al_2004.current.carrier declared as Node

Node	INaCa.alfa
Node	INaK.amplitude
Node	INaCa.amplitude
Node	INaCa.Cai
Node	INaCa.Cao
Node	INaK.F
Node	INaCa.gamma
Node	INaCa.KmCa
Node	INaK.KmK
Node	INaK.KmNa
Node	INaCa.KmNai
Node	INaK.Ko
Node	INaCa.ksat
Node	INaK.Nai
Node	INaCa.Nai
Node	INaCa.Nao
Node	INaK.R
Node	INaK.T
Node	INaK.Vm
Node	INaCa.Vm

Uses of Node in org.simBio.bio.tenTusscher_et_al_2004.flux

Classes in org.simBio.bio.tenTusscher_et_al_2004.flux that implement Node

class

UpTake Pump current taking up calcium into SR.

Fields in org.simBio.bio.tenTusscher_et_al_2004.flux declared as Node

Node	UpTake.Cai
Node	Release.Cai
Node	Leak.Cai
Node	Release.Casr
Node	Leak.Casr
Node	Release.d
Node	Release.dt
Node	Release.g
Node	Release.ginfi
Node	Release.Vm

Uses of Node in org.simBio.bio.tenTusscher_et_al_2004.function

Classes in org.simBio.bio.tenTusscher_et_al_2004.function that implement Node

class

ReversalPotential2 calculate reversal potential of the specific Ion.

Fields in org.simBio.bio.tenTusscher_et_al_2004.function declared as Node

Node	Current.in
Node	ReversalPotential2.Ki
Node	ReversalPotential2.Ko
Node	ReversalPotential2.Nai
Node	ReversalPotential2.Nao
Node	Charge.Vm

Uses of Node in org.simBio.bio.terashima_et_al_2006.complex

Classes in org.simBio.bio.terashima_et_al_2006.complex that implement Node

class

WaterFlux Water flux across the cell membrane [um3/ms].

Fields in org.simBio.bio.terashima_et_al_2006.complex declared as Node

Node	WaterFlux.Caext concentration of extracellular Ca2+ [mM]
Node	WaterFlux.Caint concentration of intracellular Ca2+ [mM]
Node	WaterFlux.Clext concentration of extracellular Cl- [mM]
Node	WaterFlux.Clint concentration of intracellular Cl- [mM]
Node	WaterFlux.Kext concentration of extracellular K+ [mM]
Node	WaterFlux.Kint concentration of intracellular K+ [mM]
Node	WaterFlux.LAext concentration of extracellular large anionic compound [mM]
Node	WaterFlux.LAint concentration of intracellular large anionic compound [mM]
Node	WaterFlux.Naext concentration of extracellular Na+ [mM]
Node	WaterFlux.Naint concentration of intracellular Na+ [mM]
Node	WaterFlux.TotalIonext sum of extracellular ionic concentration [mM]
Node	WaterFlux.TotalIonint sum of intracellular ionic concentration [mM]
Node	WaterFlux.volumeext extracellular volume [um3]
Node	WaterFlux.volumeint intracellular volume [um3]

Uses of Node in org.simBio.bio.terashima_et_al_2006.current

Fields in org.simBio.bio.terashima_et_al_2006.current declared as Node

Node	Diffusion.Cai concentration of intracellular Ca2+ [mM]
Node	Diffusion.Cao concentration of extracellular Ca2+ [mM]
Node	MembraneTransporter.CCl to see Cl current component
Node	Diffusion.Cli concentration of intracellular Cl- [mM]
Node	Diffusion.Clo concentration of extracellular Cl- [mM]
Node	MembraneTransporter.currentCl link to the Cl component (pA) of compartment
Node	Diffusion.Ki concentration of intracellular K+ [mM]
Node	Diffusion.Ko concentration of extracellular K+ [mM]
Node	Diffusion.Nai concentration of intracellular Na+ [mM]
Node	Diffusion.Nao concentration of extracellular Na+ [mM]

Uses of Node in org.simBio.bio.terashima_et_al_2006.current.carrier

Classes in org.simBio.bio.terashima_et_al_2006.current.carrier that implement Node

class

NKCC Flux via Na+-K+-2Cl- cotransporter [amol/msec].

Fields in org.simBio.bio.terashima_et_al_2006.current.carrier declared as Node

Node	NKCC.ClFlux Cl- current carried by NKCC1 [pA]
Node	NKCC.Cli concentration of intracellular Cl- [mM]
Node	NKCC.Clo concentration of extracellular Cl- [mM]
Node	NKCC.Ki concentration of intracellular K+ [mM]
Node	NKCC.Ko concentration of extracellular K+ [mM]
Node	NKCC.Nai concentration of intracellular Na+ [mM]
Node	NKCC.Nao concentration of extracellular Na+ [mM]
Node	NKCC.P factor to define the maximum flux via NKCC1 [amol]
Node	NKCC.pE1S probability of pE1S

Uses of Node in org.simBio.bio.terashima_et_al_2006.current.cf

Classes in org.simBio.bio.terashima_et_al_2006.current.cf that implement Node

class	CfChannel calculate current component of Na, K, Ca, and Cl ion according to the constant field theory.
class	IClb
class	IVRCC volume-regulated Cl- current.

Fields in org.simBio.bio.terashima_et_al_2006.current.cf declared as Node

Node	Ist.activation
Node	ICaT.activation open probability of activation gate
Node	ICFTR.ATP concentration of intracellular ATP [mM]
Node	ICaL.ATP intracellular ATP concentration (mM)
Node	Iha.C1
Node	Iha.C2
Node	ICaL.CaDiadic local Ca2+ concentration near the mouth of L-type Ca channel (mM)
Node	Ist.Cai
Node	ILCCa.Cai intracellular calcium concentration (mM)
Node	ICaL.Cai intracellular Ca2+ concentration (mM)
Node	ICFTR.cAMP concentration of intracellular cAMP [mM]
Node	CfChannel.constantFieldCa Ca2+ flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldCl Cl- flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldK K+ flux calculated by constant field theory [mM]
Node	CfChannel.constantFieldNa Na+ flux calculated by constant field theory [mM]
Node	ICFTR.cPKA fraction of cAMP-activated PKA
Node	INa.gate ultra-slow gate
Node	ICaL.gate ultra-slow gate probability
Node	Ito.gate1 activation gating variable
Node	Ito.gate2 inactivation gating variable
Node	IKpl.GK channel conductance
Node	Ist.inactivation
Node	ICaT.inactivation open probability of inactivation gate
Node	ICFTR.Isoprenaline concentration of extracellular isoprenaline [uM]
Node	Iha.O1
Node	Iha.O2
Node	Iha.O3
Node	INa.pAI AI state probability for voltage-dependent gate
Node	ICaL.pAI AI state probability for voltage-dependent gate
Node	INa.pAP AP state probability for voltage-dependent gate
Node	ICaL.pAP AP state probability for voltage-dependent gate
Node	ICaL.pC C state probability for calcium-dependent gate
Node	IVRCC.permeabilityCl converting factor for IVRCC [pA/pF/mM]
Node	INab.permeabilityK converting factor (conductance) for K+ background current [pA/pF/mM]
Node	IClb.permeabilityK converting factor (conductance) for K+ background current [pA/pF/mM]
Node	ICFTR.POpen open probability
Node	INa.pRP RP state probability for voltage-dependent gate
Node	ICaL.pRP PR state probability for voltage-dependent gate
Node	ICaL.pU U state probability for calcium-dependent gate
Node	ICaL.pUCa UCa state probability for calcium-dependent gate
Node	Ist.slowInact
Node	IVRCC.Vm membrane potential [mV]
Node	Ito.Vm membrane potential (mV)
Node	Ist.Vm
Node	INa.Vm membrane potential (mV)
Node	IKpl.Vm membrane potential (mV)
Node	Iha.Vm
Node	ICaT.Vm membrane potential
Node	ICaL.Vm membrane potential (mV)
Node	IVRCC.Vt intracellular volume [um^3]

Uses of Node in org.simBio.bio.terashima_et_al_2006.current.potassium

Classes in org.simBio.bio.terashima_et_al_2006.current.potassium that implement Node

class

PureKchannel calculate pure potassium channel current.

Fields in org.simBio.bio.terashima_et_al_2006.current.potassium declared as Node

Node	IK1.alfa rate constant
Node	IKATP.ATPi concentration of intracellular ATP[mM]
Node	IKs.Ca intracellular Ca2+ concentration
Node	IK1.gate gate, blocked by polyamine (time dependent compornent)
Node	IKs.gate1 the open probability of voltage-dependent gate
Node	IKr.gate1 activation gating variable (the rapid component)
Node	IKs.gate2 the open probability of [Ca2+]i-dependent gate
Node	IKr.gate2 activation gating variable (the slow component)
Node	IKr.gate3 inactivation gating variable
Node	PureKchannel.permeabilityK channel permeability for potassium
Node	IKr.POpen
Node	PureKchannel.reversalPotential reversal potential
Node	PureKchannel.Vm membrane potential (mV)
Node	IKs.Vm Membrane Potential(mV)

Uses of Node in org.simBio.bio.terashima_et_al_2006.experiment

Classes in org.simBio.bio.terashima_et_al_2006.experiment that implement Node

class	StepChanger2 step change
class	TonicityChange Change extracellular fluid tonicity

Fields in org.simBio.bio.terashima_et_al_2006.experiment declared as Node

Node	TonicityChange.Caext concentration of extracellular Ca2+ [mM]
Node	TonicityChange.Cainitial concentration of initial extracellular Ca2+ [mM]
Node	TonicityChange.Clext concentration of extracellular Cl- [mM]
Node	TonicityChange.Clinitial concentration of initial extracellular Cl- [mM]
Node	TonicityChange.elapsedTime
Node	TonicityChange.Kext concentration of extracellular K+ [mM]
Node	TonicityChange.Kinitial concentration of initial extracellular K+ [mM]
Node	TonicityChange.LAext concentration of extracellular large anionic compound [mM]
Node	TonicityChange.LAinitial concentration of initial extracellular large anionic compound [mM]
Node	TonicityChange.Naext concentration of extracellular Na+ [mM]
Node	TonicityChange.Nainitial concentration of initial extracellular Na+ [mM]
Node	VolumeRatio.Vt total cell volume (um^3)

Uses of Node in org.simBio.bio.terashima_et_al_2006.function

Classes in org.simBio.bio.terashima_et_al_2006.function that implement Node

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.

Fields in org.simBio.bio.terashima_et_al_2006.function declared as Node

Node	Tonicity.Caext concentration of extracellular Ca2+ [mM]
Node	Tonicity.Clext concentration of extracellular Cl- [mM]
Node	Tonicity.Kext concentration of extracellular K+ [mM]
Node	KoDependency2.Ko out side Potassium concentration
Node	KoDependency.Ko concentration of extracellular Potassium (mM)
Node	Tonicity.LAext concentration of extracellular large anionic compound [mM]
Node	Tonicity.Naext concentration of extracellular Na+ [mM]
Node	Volume.ratio ratio
Node	Tonicity.T extracellular fluid tonicity
Node	Volume.total total value
Node	TotalVolume.Vi the osmotically active cell volume (um^3)
Node	AmplitudeNaK.Vt total cell volume [um^3]

Uses of Node in org.simBio.core

Subinterfaces of Node in org.simBio.core

interface

Variable

Classes in org.simBio.core that implement Node

class	Analyzer Please inherit this Class to manipulate every Node.
class	Component super class of the core package, similar to public String, Component of the Composite Pattern.
class	Composite Composite Pattern.
class	Conductor root instance to conduct integration.
class	Link making Link
class	Parameter labeled public double, Component of the Composite Pattern.
class	Reactor set of equations.

Fields in org.simBio.core declared as Node

Node	Conductor.duration duration of integration
Node	Conductor.elapsedTime elapsed time
Node	Conductor.timeStep time step of integration

Methods in org.simBio.core that return Node

protected Node	Composite.getLink(java.lang.String name) 引数のnameで指定されたxmlのlinkが指し示す対象への参照を返す。
Node	Composite.getNode(java.lang.String name) serch the Node of the same name, 受け取った文字列と同じ名前の最初に見つかったNodeを返す。

Uses of Node in org.simBio.core.integrator

Classes in org.simBio.core.integrator that implement Node

class	Concentration The amount of ion (or molecule) is hold as value.
class	Euler the variable calculated by euler method オイラー法で計算される変数
class	Positive keep the value positive.
class	PositiveRK Keep the value positive, for Runge-Kutta.
class	Probability Keep the value between 0 and 1.
class	RungeKutta RungeKutta法で計算される変数 the variable calculated by RungeKutta method

Uses of Node in org.simBio.sim.analyzer

Classes in org.simBio.sim.analyzer that implement Node

class	StopWatch
class	VisualizeAnalyzer base class for visualized Node(Viewer, Graph, Axis).

Fields in org.simBio.sim.analyzer declared as Node

Node	StopWatch.elapsedTime
Node	StopWatch.lapTime
Node	StopWatch.totalTime

Methods in org.simBio.sim.analyzer that return Node

protected Node	VisualizeAnalyzer.getNodeHierarchically(java.lang.String name) serch the Node of the same name(or upper level node).
Node	VisualizeAnalyzer.getNodeRecursive(java.lang.String name) serch the Node of the same name.

Methods in org.simBio.sim.analyzer with parameters of type Node

protected double

VisualizeAnalyzer.getDouble(Node node) get value from node.

Uses of Node in org.simBio.sim.analyzer.csv

Classes in org.simBio.sim.analyzer.csv that implement Node

class	ALaCarte Writes a numerical value of selected nodes to csv file.
class	CsvMaker Writes values to a file in csv format. If a directory which does not exist is included in the file path, the directory is created.
class	Siblings should be placed into the xml file of the parent node from which one wants to get the childrens' parameters 親Reactorの持つ全てのVariableとReactorの値をcsv形式で書き出す
class	Total writes values of all parameters, variables and nodes to csv file 親Reactor以下のTreeに存在する全てのReactorとParameterの値をcsv fileに書き出す

Fields in org.simBio.sim.analyzer.csv declared as Node

Node	CsvMaker.elapsedTime

Uses of Node in org.simBio.sim.analyzer.csv.keep

Classes in org.simBio.sim.analyzer.csv.keep that implement Node

class	ParamEvalKeeper Keep changing parameters and evaluaion values and write to csv.
class	TimeSeriesKeeper Keep time series data and write to csv.

Fields in org.simBio.sim.analyzer.csv.keep declared as Node

Node	TimeSeriesKeeper.elapsedTime

Uses of Node in org.simBio.sim.analyzer.csv.result

Classes in org.simBio.sim.analyzer.csv.result that implement Node

class

AbstractAppender append the parameters to CSV file at the end of calculation.

Fields in org.simBio.sim.analyzer.csv.result declared as Node

Node	AbstractAppender.fileName file name to write result data.

Uses of Node in org.simBio.sim.analyzer.graph

Classes in org.simBio.sim.analyzer.graph that implement Node

class	AbstractGraph Provides a Graph framework. Constructs a framework in this class so that the Graph class which inherits from it can be implemented simply, without providing redrawing functions etc.
class	Axis Coordinate axis base class
class	AxisX x axis
class	AxisXFix x axis (do not scroll) for RelationGraph.
class	AxisXLog x axis by log scale.
class	AxisY y axis
class	AxisYLog y axis by log scale.
class	BasicGraph Graph which displays time series data.
class	Graph Graph (optimised) which displays 2D graph data in chronological order.
class	Graph4State Draws the target as a surface. Overrides the line/point drawing methods in order to draw the surface.
class	RelationGraph 2D graph of relation between two parameters.
class	StepChart Shifts and displays the target. Overrides the line/point drawing method, and shifts the drawing position.
class	Viewer Graph viewer.

Fields in org.simBio.sim.analyzer.graph declared as Node

protected Node[]

AbstractGraph.target Nodes which become the drawing target (target X)

Uses of Node in org.simBio.sim.analyzer.graph.simple

Classes in org.simBio.sim.analyzer.graph.simple that implement Node

class	RateGraph sample graph for bio.function
class	RateGraph_KA sample graph for bio.function
class	RelationGraph_LP 2D graph of relation between two parameters for org.simBio.sim.analyzer.measure.LeadPotential.

Fields in org.simBio.sim.analyzer.graph.simple declared as Node

Node	RateGraph_KA.iv
Node	RateGraph_KA.max
Node	RateGraph_KA.min
Node	RateGraph_KA.step
Node	Axis.units
Node	RelationGraph_LP.Vm

Uses of Node in org.simBio.sim.analyzer.measure

Classes in org.simBio.sim.analyzer.measure that implement Node

class	AbstractMeasure Measuring.
class	Amplitude get the difference between the maximum and minimum value of the target.
class	AmplitudeInCycle get the difference between the maximum and minimum value of the target in a cycle.
class	APD Measuring Action Potential Duration.
class	APDforSA ペースメーカモデルの活動電位持続時間を計測する。 閾値はmVで指定する。
class	APDforSA2 ペースメーカモデルの活動電位持続時間を計測する。 閾値はAPAのパーセントで指定する。
class	HR 心拍数を計測する。
class	LeadPotential Calculate Lead Potential.
class	Limitter targetの値が設定値を超えたら計算を終了する。
class	PeakDetect
class	Sum targetsの和を求める。
class	Vmax Measuring dV/dt max.
class	VmaxTime measure Vmax and timing of Vmax.

Fields in org.simBio.sim.analyzer.measure declared as Node

Node	APDforSA2.APA 活動電位の大きさ (mV)
Node	APD.APA
Node	LeadPotential.CCa
Node	LeadPotential.CCl
Node	LeadPotential.CK
Node	VmaxTime.Cm membrane capacitance (pS)
Node	Vmax.Cm
Node	LeadPotential.CNa
Node	LeadPotential.currentCa
Node	LeadPotential.currentCl
Node	LeadPotential.currentK
Node	LeadPotential.currentNa
Node	LeadPotential.ECa
Node	LeadPotential.ECl
Node	LeadPotential.EK
Node	LeadPotential.ENa
Node	LeadPotential.INaK
Node	LeadPotential.IPMCA_CCa
Node	Vmax.It
Node	APD.It
Node	HR.iTotal 総電流 (pA)
Node	APDforSA2.iTotal 総電流 (pA)
Node	VmaxTime.Itotal total membrane current (pA)
Node	AmplitudeInCycle.maximum maximum value of the target
Node	Amplitude.maximum maximum value of the target
Node	APDforSA2.MDP 最大分極電位 (mV)
Node	AmplitudeInCycle.minimum minimum value of the target
Node	Amplitude.minimum minimum value of the target
Node	APDforSA2.OverShoot 活動電位のピーク (mV)
Node	APD.peak
Node	APD.percent
Node	APD.resting
Node	PeakDetect.target
Node	Limitter.target 計測対象
Node	AmplitudeInCycle.target to analyze
Node	Amplitude.target to analyze
Node	LeadPotential.Vm
Node	APDforSA.Vm 膜電位 (mV)
Node	APD.Vm
Node	VmaxTime.Vmax Vmax: maximum rate of rise (mV/ms)

Uses of Node in org.simBio.util.numerical

Classes in org.simBio.util.numerical that implement Node

class	MathFunction This abstract class represents a mathematical function on a simBio model tree.
class	MathMultivariableFunction This abstract class represents a mathematical function on a simBio model tree (light-weight version).
class	MathUnivariableFunction This abstract class represents a mathematical function on a simBio model tree (light-weight version).

Uses of Node in org.simBio.util.numerical.methods

Methods in org.simBio.util.numerical.methods with parameters of type Node

static double	BroydenMethod.solve(MathFunction[] functions, Node[] nodes) Solves the specified nonlinear equations for the specified variables.
static double	BroydenMethod.solve(MathFunction[] functions, Node[] nodes, double epsilon, int iteration) Solves the specified nonlinear equations for the specified variables.
static double	SecantMethod.solve(MathFunction function, Node node) Solve the specified nonlinear equation.
static double	SecantMethod.solve(MathFunction function, Node node, double epsilon) Solve the specified nonlinear equation.
static double	BroydenMethod.solve(MathMultivariableFunction[] functions, Node[] nodes) Solves the specified nonlinear equations for the specified variables.
static double	BroydenMethod.solve(MathMultivariableFunction[] functions, Node[] nodes, double epsilon, int iteration) Solves the specified nonlinear equations for the specified variables.
static double	SecantMethod.solve(MathUnivariableFunction function, Node node) Solve the specified nonlinear equation.
static double	SecantMethod.solve(MathUnivariableFunction function, Node node, double epsilon) Solve the specified nonlinear equation.