JSim Consolidated Model Database
Showing 401 - 432 of 432 models found. [New Search]
NSR0402 (in NSR archive): Bazil2016
(Matlab) Catalytic Coupling of Oxidative Phosphorylation, ATP Demand, and Reactive Oxygen Species Generation.
(Matlab) Catalytic Coupling of Oxidative Phosphorylation, ATP Demand, and Reactive Oxygen Species Generation.
- Key terms: mitochondria, ROS, ATP, phosphate, metabolism, Cardiac grid, Publication, matlab, NADH, oxygen, redox, thermodynamics, respiratory, BISEN, quinone pool, ANT, UQH2, TCA cycle
- Bazil2016
NSR0403 (in NSR archive): Dash2008
(Matlab) Metabolic Dynamics in Skeletal Muscle during Acute Reduction in Blood Flow and Oxygen Supply to Mitochondria: In-Silico Studies Using a Multi-Scale, Top-Down Integrated Model.
(Matlab) Metabolic Dynamics in Skeletal Muscle during Acute Reduction in Blood Flow and Oxygen Supply to Mitochondria: In-Silico Studies Using a Multi-Scale, Top-Down Integrated Model.
- Key terms: TCA, ATP, NADH, Publication, matlab, Cardiac grid, compartmental model, cytosol, mitochondria, Michaelis-Menten, ischemia, exercise, metabolism, skeletal muscle, data, blood, oxygen, ACoA, citrate, creatine, phospate
- Dash2008
NSR0404 (in NSR archive): Li2012
(Matlab) Computational Model of Cellular Metabolic Dynamics in Skeletal Muscle Fibers during Moderate Intensity Exercise.
(Matlab) Computational Model of Cellular Metabolic Dynamics in Skeletal Muscle Fibers during Moderate Intensity Exercise.
- Key terms: computational modeling, skeletal muscle, fiber types, metabolism, exercise, Publication, Data, Cardiac grid, Matlab, cytosol, mitochondria, glycogen, creatine, phospate, TCA, ATP
- Li2012
NSR0405 (in NSR archive): RecircO2CO2BTEX_3CompLung
Four region, recirculating model for the O2-CO2 transport, exchange and metabolism. Based on Dash 2006 paper. Computes dissolved O2 and CO2 from total O2 and CO2 (TO2 and TCO2) through numerical inversion method using SHbO2CO2_EJAP2016 routine and Christmas 2017 O2/CO2 solubility algorithm. Gas exchange with 3 comp lung is used. Incorporates Calculations for temperature changes based on consumption of O2 in parenchymal region.
Four region, recirculating model for the O2-CO2 transport, exchange and metabolism. Based on Dash 2006 paper. Computes dissolved O2 and CO2 from total O2 and CO2 (TO2 and TCO2) through numerical inversion method using SHbO2CO2_EJAP2016 routine and Christmas 2017 O2/CO2 solubility algorithm. Gas exchange with 3 comp lung is used. Incorporates Calculations for temperature changes based on consumption of O2 in parenchymal region.
- Key terms: BTEX, PDE, Cardiac grid, Oxygen, CO2, pH, Solubility, tissue exchange, gas exchange, Haldane Hemoglobin binding, MPC
- RecircO2CO2BTEX_3CompLung
NSR0406 (in NSR archive): OneEnzRandomBiBi
One Enzyme 2 Substrates, A and B, to 2 Products, C and D, Reversible Second-order enzyme kinetic model with capacitance and reversible enzymatic reaction with binding and release kinetics for two substrates givng two products, thermodynamically constrained.
One Enzyme 2 Substrates, A and B, to 2 Products, C and D, Reversible Second-order enzyme kinetic model with capacitance and reversible enzymatic reaction with binding and release kinetics for two substrates givng two products, thermodynamically constrained.
- Key terms: Transport Physiology, Chemical Reaction Enzymes, Enzymatic Reaction, Single Enzyme, Reversible, Michaelis-Menten Kinetics, Briggs-Haldane Kinetics, Cardiac grid RELATED MODELS: PGIsomerase Model 130 Single Substrate -->product, using biinding and release kinetics, with capacitance
- OneEnzRandomBiBi
NSR0408 (in NSR archive): ANT_BISEN
(Matlab) Adenine nucleotide translocator (ANT)
(Matlab) Adenine nucleotide translocator (ANT)
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, ANT, creatine, Phosphocreatine, ATP Hydrolysis, Creatine Kinase
- ANT_BISEN
NSR0409 (in NSR archive): Myokinase_BISEN
Adenylate Kinase reaction. Translated from BISEN generated model.
Adenylate Kinase reaction. Translated from BISEN generated model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Myokinase, ATP, ADP, AMP, Adenylate Kinase
- Myokinase_BISEN
NSR0410 (in NSR archive): AspartateTransferase_BISEN
Aspartate Aminotransferase reaction. Translated from BISEN generated model.
Aspartate Aminotransferase reaction. Translated from BISEN generated model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, ketogluterate, Aspartate, glutamate, aspartate transferase, oxaloacetate
- AspartateTransferase_BISEN
NSR0411 (in NSR archive): MalateDehydrogenase_BISEN
Modeling the Malate dehydrogenase reaction. Translated from BISEN generated model.
Modeling the Malate dehydrogenase reaction. Translated from BISEN generated model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, ATP, Malate, NADH, NAD, Oxaloacetate, Malate dehydrogenase (EC 1.1.1.37)
- MalateDehydrogenase_BISEN
NSR0412 (in NSR archive): Fumarase_BISEN
Modeling the Fumarase reaction. Translated from BISEN generated model.
Modeling the Fumarase reaction. Translated from BISEN generated model.
- Key terms: Fumarase (EC 4.2.1.2), TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Malate
- Fumarase_BISEN
NSR0413 (in NSR archive): SuccinateDehydrogenase_BISEN
Modeling the Succinate Dehydrogenase reaction. Translated from BISEN generated model.
Modeling the Succinate Dehydrogenase reaction. Translated from BISEN generated model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Fumarate, Oxaloacetate, Succinate, coenzyme Q, CoQ
- SuccinateDehydrogenase_BISEN
NSR0414 (in NSR archive): SuccinylCoaSynthetase_BISEN
Modeling the Succinyl-CoA Synthetase reaction. Translated from BISEN generated Matlab model.
Modeling the Succinyl-CoA Synthetase reaction. Translated from BISEN generated Matlab model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Succinyl-CoA Synthetase (EC 6.2.1.4), GTP, COAS, Succinate
- SuccinylCoaSynthetase_BISEN
NSR0415 (in NSR archive): AlphaKetogluterateDehydrogenase_BISEN
Modeling the Alpha-Ketogluterate Dehydrogenase reaction. Translated from BISEN generated Matlab model.
Modeling the Alpha-Ketogluterate Dehydrogenase reaction. Translated from BISEN generated Matlab model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, SuccinateCoA, Ketogluterate, NAD, CO2, carbon dioxide
- AlphaKetogluterateDehydrogenase_BISEN
NSR0416 (in NSR archive): IsocitrateDehydrogenase_BISEN
Modeling the Isocitrate Dehydrogenase reaction. Translated from BISEN generated Matlab model.
Modeling the Isocitrate Dehydrogenase reaction. Translated from BISEN generated Matlab model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, CO2, Isocitrate, Ketogluterate, NAD, carbon dioxide
- IsocitrateDehydrogenase_BISEN
NSR0417 (in NSR archive): Aconitase_BISEN
Modeling the Aconitase reaction. Translated from BISEN generated Matlab model.
Modeling the Aconitase reaction. Translated from BISEN generated Matlab model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Citrate, Isocitrate, aconitase
- Aconitase_BISEN
NSR0418 (in NSR archive): CitrateSynthase_BISEN
Modeling the Citrate Synthase reaction. Translated from BISEN generated Matlab model.
Modeling the Citrate Synthase reaction. Translated from BISEN generated Matlab model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Citrate, AcetylcoA, Oxaloacetate
- CitrateSynthase_BISEN
NSR0419 (in NSR archive): PyruvateDehydrogenase_BISEN
Modeling the Pyruvate Dehydrogenase reaction. Translated from BISEN generated Matlab model.
Modeling the Pyruvate Dehydrogenase reaction. Translated from BISEN generated Matlab model.
- Key terms: TCA, enzyme, BISEN, Cardiac grid, proton, inorganic phosphate, hydrolysis, magnesium, potassium, Gibbs free energy, thermodynamics, Matlab, Pyruvate, NADH, AcetylcoA, CO2, carbon dioxide
- PyruvateDehydrogenase_BISEN
NSR0420 (in NSR archive): HoogAntink2017
(Matlab) A synthesizer framework for multimodal cardiorespiratory signals. Model from Hoog Antink et. al. 2017 paper.
(Matlab) A synthesizer framework for multimodal cardiorespiratory signals. Model from Hoog Antink et. al. 2017 paper.
- Key terms: signal synthesis, multimodal biosignals, dynamic systems, heart rate variability, respiratory sinus arrhythmia, Mayer waves, sensor fusion, matlab, publication
- HoogAntink2017
NSR0421 (in NSR archive): RationalExp
A rational exponential function, R(x)= exp(-P(x)/Q(x)), where P and Q are polynomial in x expressed p1 + p2*x + p3*x^2 +.. pn*x^(n-1) and 1 + q1*x + q2*x^2 + ....+ qn*x^m, where n is not necessarily = m.
A rational exponential function, R(x)= exp(-P(x)/Q(x)), where P and Q are polynomial in x expressed p1 + p2*x + p3*x^2 +.. pn*x^(n-1) and 1 + q1*x + q2*x^2 + ....+ qn*x^m, where n is not necessarily = m.
- Key terms: compartment, compartmental, decay, first order process, Tutorial, exponential, probability density function, pdf
- RationalExp
NSR0422 (in NSR archive): Xa_Gentex_MID
This Gentex-based model simulates the transport and metabolism processes of exogenous Xa in the isolated, perfused non-working guinea pig heart, based on data from the multiple-indicator dilution technqiue (MID).
This Gentex-based model simulates the transport and metabolism processes of exogenous Xa in the isolated, perfused non-working guinea pig heart, based on data from the multiple-indicator dilution technqiue (MID).
- Key terms: purine nucleoside metabolism, convection diffusion reaction model, GENTEX, transporter, xanthane, uric acid, xanthine oxidase, axially distributed blood tissue exchange processes, constrained parameter estimation, simultaneous optimization, data, PDE, BTEX, Cardiac Grid
- Xa_Gentex_MID
NSR0423 (in NSR archive): Linear.Reaction.Sequence
First Order Reaction Sequence for solutes A to E in a stirred tank flowing reactor with constant volume, Vol, and step jumps in flow and in reaction rates. This is the basis for a series of models to account for substrate capacitance in enzymatic networks.
First Order Reaction Sequence for solutes A to E in a stirred tank flowing reactor with constant volume, Vol, and step jumps in flow and in reaction rates. This is the basis for a series of models to account for substrate capacitance in enzymatic networks.
- Key terms: first order, unidirectional reactions, substrate capacitance, enzymatic networks, compartmental, Cardiac Grid
- Linear.Reaction.Sequence
NSR0424 (in NSR archive): MM.Reaction.Sequence
Michaelis-Menten Reaction Sequence for solutes A to E in a stirred tank flowing reactor with constant volume, Vol, and step jumps in flow and in reaction rates. This is the second in a series of four models to account for substrate capacitance in enzymatic networks. The first model is Linear.Reaction.Sequence (Model #0423).
Michaelis-Menten Reaction Sequence for solutes A to E in a stirred tank flowing reactor with constant volume, Vol, and step jumps in flow and in reaction rates. This is the second in a series of four models to account for substrate capacitance in enzymatic networks. The first model is Linear.Reaction.Sequence (Model #0423).
- Key terms: unidirectional reactions, substrate capacitance, enzymatic networks, compartmental, Michaelis-Menten, Cardiac Grid
- MM.Reaction.Sequence
NSR0425 (in NSR archive): MM.Lag.Reaction.Sequence
Michaelis-Menten Reaction Sequence for solutes A to E in a stirred tank, with lagged input into flowing reactor with constant volume, Vol, and step jumps in flow and in reaction rates. This is the third in a series of four models to account for substrate capacitance in enzymatic networks. The first model is Linear.Reaction.Sequence (Model #0423).
Michaelis-Menten Reaction Sequence for solutes A to E in a stirred tank, with lagged input into flowing reactor with constant volume, Vol, and step jumps in flow and in reaction rates. This is the third in a series of four models to account for substrate capacitance in enzymatic networks. The first model is Linear.Reaction.Sequence (Model #0423).
- Key terms: first order, unidirectional reactions, substrate capacitance, enzymatic networks, compartmental, Michaelis-Menten time lag
- MM.Lag.Reaction.Sequence
NSR0426 (in NSR archive): React.Seq.FullEnzKinetics
React.Seq.FullEnz.Kinetics is the fourth and last of a series to illustrate the influences of capacitances on the duration of transients in the reaction series A --> B --> C --> D--> E in a compartment. It includes the on- and off kinetics for enzyme-substrate binding and release for each reaction; the capacitive delay is the dwell time in the ES complex.
React.Seq.FullEnz.Kinetics is the fourth and last of a series to illustrate the influences of capacitances on the duration of transients in the reaction series A --> B --> C --> D--> E in a compartment. It includes the on- and off kinetics for enzyme-substrate binding and release for each reaction; the capacitive delay is the dwell time in the ES complex.
- Key terms: first order, unidirectional reactions, substrate capacitance, enzymatic networks, compartmental on off kinetics, Cardiac Grid, reaction sequence
- React.Seq.FullEnzKinetics
NSR0428 (in NSR archive): Hexokinase_KA
Working file for parameterizing a series of rate constants from King and Altman notation representing Hexokinase (E.C. 2.7.1.1) as a random order Bi-Bi, data from Leuck and Fromm. This model assesses the kinetic equilibrium for multiple representations of hexokinase with varying simulations with a range of pH's.
Working file for parameterizing a series of rate constants from King and Altman notation representing Hexokinase (E.C. 2.7.1.1) as a random order Bi-Bi, data from Leuck and Fromm. This model assesses the kinetic equilibrium for multiple representations of hexokinase with varying simulations with a range of pH's.
- Key terms: Michaelis-Menten, enzyme reactions, King-Altman, skeletal muscle, hexokinase, kinetic modeling, Cardiac grid
- Hexokinase_KA
NSR0429 (in NSR archive): AlvCapExch
Models two compartments, fluid and air, for a soluble gas passively exchanging between the volumes, V1 liquid, V2 air, forming a closed system. Assumes constant volumes, dry air. Simple model of alveolar-capillary gas exchange.
Models two compartments, fluid and air, for a soluble gas passively exchanging between the volumes, V1 liquid, V2 air, forming a closed system. Assumes constant volumes, dry air. Simple model of alveolar-capillary gas exchange.
- Key terms: gas exchange, Compartment model, ODE, carbon dioxide, oxygen, gas solubilty, mass balance, alveolus, lung, Cardiac grid, tutorial
- AlvCapExch
NSR0430 (in NSR archive): Equil2bind
Two solutes, with given total concentrations, Atot and Ftot, bind with an equilibrium dissociation constant of Kd. The result gives the concentrations of A, F, and AF after equilibration. Check affirms totals.
Two solutes, with given total concentrations, Atot and Ftot, bind with an equilibrium dissociation constant of Kd. The result gives the concentrations of A, F, and AF after equilibration. Check affirms totals.
- Key terms: fatty acid binding, Equilibrium dissociation constant, albumin, modeling tools
- Equil2bind
NSR0431 (in NSR archive): FAbt20.1site
Axially distributed 2-region capillary-tissue exchange operator for Albumin binding fatty acid at a particular binding site.
Axially distributed 2-region capillary-tissue exchange operator for Albumin binding fatty acid at a particular binding site.
- Key terms: fatty acid binding, Equilibrium dissociation constant, albumin, modeling tools, Cardiac grid, PDE, two region BTEX, BTEX20, plasma, ISF
- FAbt20.1site
NSR0432 (in NSR archive): AlvCapExchBind
Models two compartments, fluid and air, for a soluble gas passively exchanging between the volumes, V1 liquid, V2 air, with a binding site in V1, forming a closed system. Assumes constant volumes, dry air. Simple model of alveolar-capillary gas exchange.
Models two compartments, fluid and air, for a soluble gas passively exchanging between the volumes, V1 liquid, V2 air, with a binding site in V1, forming a closed system. Assumes constant volumes, dry air. Simple model of alveolar-capillary gas exchange.
- Key terms: gas exchange, Compartment model, ODE, carbon dioxide, oxygen, gas solubilty, mass balance, alveolus, lung, Cardiac grid, binding, tutorial
- AlvCapExchBind
NSR0433 (in NSR archive): AlvCapExchBuff
Models two compartments, fluid and air, for a soluble gas passively exchanging between the volumes, V1 liquid, V2 air, with buffering site in V1, forming a closed system. Assumes constant volumes, dry air. Simple model of alveolar-capillary gas exchange.
Models two compartments, fluid and air, for a soluble gas passively exchanging between the volumes, V1 liquid, V2 air, with buffering site in V1, forming a closed system. Assumes constant volumes, dry air. Simple model of alveolar-capillary gas exchange.
- Key terms: gas exchange, Compartment model, ODE, carbon dioxide, oxygen, gas solubilty, mass balance, alveolus, lung, Cardiac grid, buffering, bicarbonate, pH, tutorial
- AlvCapExchBuff
NSR0434 (in NSR archive): BTEX2006_Updated
Four region, distributed model for the O2-CO2 transport, exchange and metabolism. From Dash 2006 paper. Annotated for use with MPC. Compute dissolved O2 and CO2 from total O2 and CO2 (TO2 and TCO2) through numerical inversion method that uses SHbO2CO2_EJAP2016 routine and Christmas 2017 O2/CO2 solubility algorithm. Incorporates Calculations for temperature changes based on consumption of O2 in parenchymal region.
Four region, distributed model for the O2-CO2 transport, exchange and metabolism. From Dash 2006 paper. Annotated for use with MPC. Compute dissolved O2 and CO2 from total O2 and CO2 (TO2 and TCO2) through numerical inversion method that uses SHbO2CO2_EJAP2016 routine and Christmas 2017 O2/CO2 solubility algorithm. Incorporates Calculations for temperature changes based on consumption of O2 in parenchymal region.
- Key terms: BTEX, PDE, Cardiac grid, Oxygen, CO2, pH, Solubility, tissue exchange, gas exchange, Haldane, Hemoglobin binding, MPC, temperature, metabolism
- BTEX2006_Updated