JSim Consolidated Model Database
Showing 301 - 350 of 432 models found. [New Search]
NSR0302 (in NSR archive): vanBeek2007
Models the adaptation of ATP production by the mitochondria to ATP hydrolysis. This model contains only diffusion, mitochondrial outer membrane (MOM) permeation, and two isoforms of creatine kinase (CK), in cytosol and mitochondrial intermembrane space (IMS), respectively.
Models the adaptation of ATP production by the mitochondria to ATP hydrolysis. This model contains only diffusion, mitochondrial outer membrane (MOM) permeation, and two isoforms of creatine kinase (CK), in cytosol and mitochondrial intermembrane space (IMS), respectively.
- Key terms: systems biology, computational model, creatine kinase, phosphocreatine shuttle, regulatory module, mitochondrial membrane permeability, oxygen consumption, publication
- vanBeek2007
NSR0303 (in NSR archive): vanBeek2011
Whole body model of human energy conversion and heat transport. Used to simulate a mountain time trial for the Tour de France. Model transposed directly from 'R' model written for van Beek et al., 2011 paper.
Whole body model of human energy conversion and heat transport. Used to simulate a mountain time trial for the Tour de France. Model transposed directly from 'R' model written for van Beek et al., 2011 paper.
- Key terms: whole body modelling, metabolic pathways, heat transport, muscle power, skeletal muscle metabolism, ODE, publication, Data
- vanBeek2011
NSR0304 (in NSR archive): TransComp2
Two compartment master transporter model with choices: Flow: yes or no, Solutes: A only, A and B; Conversion A to B: none, linear, Michaelis-Menten (MM); Transporters: Passive, MM A1 1-sided, MM A1,A2 two 1-sided,MM A1,A2 one 2-sided, MM A,B 2-sided, and T1&T2 (facilitated).
Two compartment master transporter model with choices: Flow: yes or no, Solutes: A only, A and B; Conversion A to B: none, linear, Michaelis-Menten (MM); Transporters: Passive, MM A1 1-sided, MM A1,A2 two 1-sided,MM A1,A2 one 2-sided, MM A,B 2-sided, and T1&T2 (facilitated).
- Key terms: Two compartments, compartmental, flow, no flow, one solute, two solutes, transporters, 1 sided, 2 sided, passive, Michaelis-Menten, facilitated, MM, reaction, conversion, linear, enzyme, statistics, area, mean transit time, relative dispersion
- TransComp2
NSR0306 (in NSR archive): Tyson1991cycle
Model the interactions of proteins cdc2 and cyclin which form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. Tyson 1991 model imported from Biomodels (www.ebi.ac.uk).
Model the interactions of proteins cdc2 and cyclin which form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. Tyson 1991 model imported from Biomodels (www.ebi.ac.uk).
- Key terms: Cell cycle, proteins, cdc2, cyclin, MPF, cell division, metaphase, midblastula transition, maturation promoting factor, enzyme, embryos, SBML, Publication
- Tyson1991cycle
NSR0310 (in NSR archive): WeightPredictor
Program predicts how many calories you are consuming to maintain your current weight based on sex, lifestyle, age, height, number of hours of exercise per week. Projections of weight based on modification of life style, calories, and exercise.
Program predicts how many calories you are consuming to maintain your current weight based on sex, lifestyle, age, height, number of hours of exercise per week. Projections of weight based on modification of life style, calories, and exercise.
- Key terms:
- WeightPredictor
NSR0311 (in NSR archive): PanitchobPlacentaComp2015
(Matlab) Integrated compartmental model of amino acid transport in the placenta. Model describes amino acid interactions between three placental compartments, which are regulated by three transport mechanisms.
(Matlab) Integrated compartmental model of amino acid transport in the placenta. Model describes amino acid interactions between three placental compartments, which are regulated by three transport mechanisms.
- Key terms: Placenta, compartmental model, transporter, membrane transport, matlab
- PanitchobPlacentaComp2015
NSR0312 (in NSR archive): PermeabilityToPotassium
Tancredi RG, Yipintsoi T, and Bassingthwaighte JB. Capillary and cell wall permeability to potassium in isolated dog hearts. Am J Physiol 229: 537-544, 1975.
Tancredi RG, Yipintsoi T, and Bassingthwaighte JB. Capillary and cell wall permeability to potassium in isolated dog hearts. Am J Physiol 229: 537-544, 1975.
- Key terms: diffusion across membranes, emergence function, fractional escape rates, indicator-dilution techniques, permeability surface area product, potassium reside function, data, publication
- PermeabilityToPotassium
NSR0314 (in NSR archive): Demir99
Single Cell action potential of rabbit sinoatrial node modulated by acetyl choline by Demir, Clark, Giles 1999 from CellML source
Single Cell action potential of rabbit sinoatrial node modulated by acetyl choline by Demir, Clark, Giles 1999 from CellML source
- Key terms: action potential simulation, isoprenaline, muscarinic receptors, junctional receptor, extrajunctional receptor, phase sensitivity, phase-response curve, steady-state entrainment, cardiac pacemaker cell, whole cell voltage clamp, Hodgkin-Huxley model, Publication, Demir
- Demir99
NSR0315 (in NSR archive): Demir94
A mathematical model of a rabbit sinoatrial node cell. Demir, S., J. Clark, C. Murphey, and W. Giles. Am. J. Physiol. Cell Physiol. 266: C832-C852, 1994.
A mathematical model of a rabbit sinoatrial node cell. Demir, S., J. Clark, C. Murphey, and W. Giles. Am. J. Physiol. Cell Physiol. 266: C832-C852, 1994.
- Key terms: action potential simulation, isoprenaline, muscarinic receptors, junctional receptor, extrajunctional receptor, phase sensitivity, phase-response curve, steady-state entrainment, cardiac pacemaker cell, whole cell voltage clamp, Hodgkin-Huxley model, Publication, Demir
- Demir94
NSR0316 (in NSR archive): ConcurrentFlow
Concurrent flow model for extraction during transcapilary passage. J.B. Bassingthwaighte: Circ Res 35:483-503, 1974.
Concurrent flow model for extraction during transcapilary passage. J.B. Bassingthwaighte: Circ Res 35:483-503, 1974.
- Key terms: indicator dilution, capillary membrane permeability, mathematical analysis, blood flow, coronary artery, myocardial metabolism, isotope, compartmental analysis, blood-tissue exchange, transport mechanisms, publication
- ConcurrentFlow
NSR0317 (in NSR archive): Transp2sol_Distrib2_F_tracer
Model for two regions, one with flow, one without, for two species A and B, both tracer (h) and non-tracer (c) with full T1T2 transporter on membrane and MM conversion of A to B in non-flowing region.
Model for two regions, one with flow, one without, for two species A and B, both tracer (h) and non-tracer (c) with full T1T2 transporter on membrane and MM conversion of A to B in non-flowing region.
- Key terms: transporter, T1T2, Michaelis-Menten, flow, convection, diffusion, reaction, permeability, surface area
- Transp2sol_Distrib2_F_tracer
NSR0318 (in NSR archive): MultiCircSystem
The MultiCompartment Circulatory System is based on pages 450-452 from J. Keener and J. Sneyd, Mathematical Physiology, Vol. 8 in series Interdisciplinary Applied Mathematics, Springer-Verlag New York Inc.,
The MultiCompartment Circulatory System is based on pages 450-452 from J. Keener and J. Sneyd, Mathematical Physiology, Vol. 8 in series Interdisciplinary Applied Mathematics, Springer-Verlag New York Inc.,
- Key terms: Multicompartment, circulatory, linear, systemic, pulmonary, resistance, compliance, circulation, heart, two chambers
- MultiCircSystem
NSR0320 (in NSR archive): MM2Substrate_irrevers
Single enzyme irreversible Michaelis-Menten Eqs for Hx->Xa->Ua: Progress curves for xanthine oxidase reactions to oxidize hypoxanthine, Hx, to xanthine, Xa, to uric acid, Ua
Single enzyme irreversible Michaelis-Menten Eqs for Hx->Xa->Ua: Progress curves for xanthine oxidase reactions to oxidize hypoxanthine, Hx, to xanthine, Xa, to uric acid, Ua
- Key terms: purine nucleosides, xanthine oxidase, simple Michaelis-Menten equations, double reaction, serial reactions, progress curves, unidirectional, bovine milk, XO, Hx, Xa, Ua, hypoxanthine, xanthine, uric acid, saturable binding
- MM2Substrate_irrevers
NSR0321 (in NSR archive): MM2Substrate_product_Inhibited
Single enzyme irreversible Michaelis-Menten Eqs for Hx->Xa->Ua: Progress curves for xanthine oxidase reactions to oxidize hypoxanthine, Hx, to xanthine, Xa, to uric acid, Ua, and invokes inhibition by second product.(Data and equations from Escribano 1988).
Single enzyme irreversible Michaelis-Menten Eqs for Hx->Xa->Ua: Progress curves for xanthine oxidase reactions to oxidize hypoxanthine, Hx, to xanthine, Xa, to uric acid, Ua, and invokes inhibition by second product.(Data and equations from Escribano 1988).
- Key terms: purine nucleosides, xanthine oxidase, simple Michaelis-Menten equations, double reaction, serial reactions, progress curves, unidirectional, bovine milk, XO, Hx, Xa, Ua, hypoxanthine, xanthine, uric acid, saturable binding, data, publication
- MM2Substrate_product_Inhibited
NSR0322 (in NSR archive): Vfnet_MM2substrate_reversible
Single enzyme reversible Michaelis-Menten Eqs for Hx->Xa->Ua, that is, two reactions on one enzyme. Data are progress curves for xanthine oxidase reactions to oxidize hypoxanthine, Hx, to xanthine, Xa, to uric acid, Ua, without inhibition by product.(Data from Escribano 1988).
Single enzyme reversible Michaelis-Menten Eqs for Hx->Xa->Ua, that is, two reactions on one enzyme. Data are progress curves for xanthine oxidase reactions to oxidize hypoxanthine, Hx, to xanthine, Xa, to uric acid, Ua, without inhibition by product.(Data from Escribano 1988).
- Key terms: purine nucleosides, xanthine oxidase, simple Michaelis-Menten equations, double reaction, serial reactions, progress curves, unidirectional, bovine milk, XO, Hx, Xa, Ua, hypoxanthine, xanthine, uric acid, saturable binding, Data, publication
- Vfnet_MM2substrate_reversible
NSR0323 (in NSR archive): FullXO
Two sequential, first-order enzymatic reactions S P with substrates binding to enzymes, and reversible product formation. Reactions facilitated by a single enzyme, Xanthine Oxidase.
Two sequential, first-order enzymatic reactions S P with substrates binding to enzymes, and reversible product formation. Reactions facilitated by a single enzyme, Xanthine Oxidase.
- Key terms: Transport Physiology, Chemical Reaction Enzymes, Enzymatic Reaction, Single Enzyme, Reversible, Michaelis-Menten Kinetics, Briggs-Haldane Kinetics, Publication, Data, reproducible, matlab
- FullXO
NSR0324 (in NSR archive): FourXO
Contains four xanthine oxidase models: MM2Substrate_irreversible (Model #0320), MM2substrate_product_inhibited (Model #0321), Vfnet_MM2substrate_reversible (Model #0322), FullXO (Model #0323)
Contains four xanthine oxidase models: MM2Substrate_irreversible (Model #0320), MM2substrate_product_inhibited (Model #0321), Vfnet_MM2substrate_reversible (Model #0322), FullXO (Model #0323)
- Key terms: purine nucleosides, xanthine oxidase, simple Michaelis-Menten equations, double reaction, serial reactions, progress curves, unidirectional, bovine milk, XO, Hx, Xa, Ua, hypoxanthine, xanthine, uric acid, saturable binding, publication, Data
- FourXO
NSR0325 (in NSR archive): DiffusionLimitedProfiles
Concentration profiles in capillary and tissue when exchange is diffusion limited. Includes axial and radial diffusion in a 2-D (x,r,t) partial differential equation problem.
Concentration profiles in capillary and tissue when exchange is diffusion limited. Includes axial and radial diffusion in a 2-D (x,r,t) partial differential equation problem.
- Key terms: diffusion limited, btex20, radial diffusion, wire mesh, contour, 2-d, 2D, partial differential equation, PDE, Modular Program Constructor, MPC, publication
- DiffusionLimitedProfiles
NSR0327 (in NSR archive): BTEX20radialDiffusion
A two region model of capillary and cell with cell subdivided into 20 subregions with axial and radial diffusion. Time-dependent plots of contours and center-of-mass of material are calculated using MATLAB.
A two region model of capillary and cell with cell subdivided into 20 subregions with axial and radial diffusion. Time-dependent plots of contours and center-of-mass of material are calculated using MATLAB.
- Key terms: plasma, cell, 2-d, radial diffusion, axial diffusion, center of mass, Java interface, Matlab movie, avi, statistics, MPC
- BTEX20radialDiffusion
NSR0331 (in NSR archive): BTEX10stat
Flow with axial dispersion through a one-region pipe of uniform cross-section. Statistics on inflow and outflow concentration curves */
Flow with axial dispersion through a one-region pipe of uniform cross-section. Statistics on inflow and outflow concentration curves */
- Key terms: BTEX10, PDE, convection, diffusion, permeation, reaction, distributed, capillary, plasma, piston flow or plug flow, statistics, mean transit time, RD, relative dispersion, skewness, kurtosis
- BTEX10stat
NSR0332 (in NSR archive): CTEX10stat
Models a capillary consisting of N compartments. Explores sensitivity analysis and optimization. Includes curve statistics.
Models a capillary consisting of N compartments. Explores sensitivity analysis and optimization. Includes curve statistics.
- Key terms: CTEX, CTEX10, convection, diffusion, capillary, compartment, plasma, sensitivity, optimization, Tutorial, statistics, mean transit time, RD, relative dispersion, skewness, kurtosis
- CTEX10stat
NSR0333 (in NSR archive): BTEX10_Terminology
Uses a single capillary convection diffusion model to generate functions of linear stationary systems: h(t), H(t), R(t), eta(t).
Uses a single capillary convection diffusion model to generate functions of linear stationary systems: h(t), H(t), R(t), eta(t).
- Key terms: BTEX10, PDE, convection, diffusion, reaction, distributed, capillary, plasma, terminology, Tutorial
- BTEX10_Terminology
NSR0334 (in NSR archive): Rideout_IndicatorDilution
Compartmental cardiovascular indicator dilution model ported from Rideout (ACSL programs IND-DIL). Also in MATLAB.
Compartmental cardiovascular indicator dilution model ported from Rideout (ACSL programs IND-DIL). Also in MATLAB.
- Key terms: compartment, compartmental, flow, first order process, recirculation, circulation, closed loop, open loop, clearance, cardiovascular, indicator, dilution, defect, septal, VSD, ASD, PDA, Rideout
- Rideout_IndicatorDilution
NSR0335 (in NSR archive): Rideout_IndicatorDilution_Modified
Compartmental cardiovascular indicator dilution model based on Rideout_IndicatorDilution with systemic flow used as constant reference. Also in MATLAB.
Compartmental cardiovascular indicator dilution model based on Rideout_IndicatorDilution with systemic flow used as constant reference. Also in MATLAB.
- Key terms: compartment, compartmental, flow, first order process, recirculation, circulation, closed loop, cardiovascular, indicator, dilution, defect, atrial, atrium, ventricle, ventricular, septal, VSD, ASD, Rideout
- Rideout_IndicatorDilution_Modified
NSR0336 (in NSR archive): Rideout_PressureFlowLH
Left heart and systemic arteries pressure-flow model ported from Rideout (ACSL programs LH-PF). Also in MATLAB.
Left heart and systemic arteries pressure-flow model ported from Rideout (ACSL programs LH-PF). Also in MATLAB.
- Key terms: Cardiovascular System, Left Heart, Ventricle, Systemic Arteries, Valve, Mitral, Aortic, RC, RLC, RC circuit, RLC circuit, RC model, RLC model, Ohm's Law, Resistance, Resistive, Capacitance, Compliance, Compliant, Stiffness, Varying Elastance, Inertance, Pressure, Flow, Pressure-Flow, Pressure-Flow-Volume, Rideout
- Rideout_PressureFlowLH
NSR0337 (in NSR archive): BronchTwoAlv
This model represents a bifurcating bronchiole with two alveolar compartments. The resistance to air flow is represented by resistors, and the compliance is repsented by a capacitor. It compares this model to Lutchen's model.
This model represents a bifurcating bronchiole with two alveolar compartments. The resistance to air flow is represented by resistors, and the compliance is repsented by a capacitor. It compares this model to Lutchen's model.
- Key terms: lung compliance, resistance, RC circuit, lung mechanics, airflow in trachea, tidal volume, positive pressure ventilation
- BronchTwoAlv
NSR0338 (in NSR archive): Rideout_PressureFlow0
Uncontrolled CV loop pressure-flow model ported from Rideout (ACSL program PF-0). Also in MATLAB.
Uncontrolled CV loop pressure-flow model ported from Rideout (ACSL program PF-0). Also in MATLAB.
- Key terms: Cardiovascular, CV, aorta, Left, Right, Ventricle, Ventricular, VSD, Ventricular Septal Defect, Systemic Circulation, Pulmonary Circulation, Uncontrolled, Heart Rate, Cardiac Output, Varying Elastance, Stiffness, Contraction, Muscle, Pressure-Flow-Volume, Ohm's Law, RLC circuit, Resistance, Resistive, Compliance, Compliant, Inertance, Stroke, End-systolic, End-diastolic, Ejection Fraction, Rideout
- Rideout_PressureFlow0
NSR0341 (in NSR archive): Selkov
The Selkov model for glycolysis exhibits a Hopf bifurcation. As the b parameter increases from 0.25 to 0.95, the model switches from a stable equilibrium point to a limit cycle near b=0.41 and back to a stable equilibrium point near b=0.8.
The Selkov model for glycolysis exhibits a Hopf bifurcation. As the b parameter increases from 0.25 to 0.95, the model switches from a stable equilibrium point to a limit cycle near b=0.41 and back to a stable equilibrium point near b=0.8.
- Key terms: glycolysis, Selkov, Hopf, bifurcation, phase plane, stable steady point, oscillations, limit cycle, nullclines
- Selkov
NSR0343 (in NSR archive): Rideout_PressureFlow1
Uncontrolled CV loop pressure-flow model ported from Rideout (ACSL program PF-1). Also in MATLAB.
Uncontrolled CV loop pressure-flow model ported from Rideout (ACSL program PF-1). Also in MATLAB.
- Key terms: Cardiovascular, CV, Aorta, Left, Right, Ventricle, Ventricular, Systemic Circulation, Pulmonary Circulation, Frank-Starling Mechanism, Uncontrolled, Myocardial Infarction, Blood Infusion, Bleeding, Heart Rate, Cardiac Output, Varying Elastance, Stiffness, Contraction, Muscle, Pressure-Flow-Volume, Ohm's Law, RLC circuit, Resistance, Resistive, Compliance, Compliant, Inertance, Stroke, Rideout
- Rideout_PressureFlow1
NSR0344 (in NSR archive): Rideout_PressureFlowReg
CV loop with baroreceptor regulation ported from Rideout (ACSL program PF-1-REG). Also in MATLAB.
CV loop with baroreceptor regulation ported from Rideout (ACSL program PF-1-REG). Also in MATLAB.
- Key terms: Cardiovascular, CV, Aorta, Carotid, Left, Right, Ventricle, Ventricular, CNS, Central Nervous System, Baroreceptor, Negative Feedback, Regulation Mechanism, Baroreflex, Afferent, Efferent, Nerve Signals, Closed Loop, Controlled, Myocardial Infarction, Blood Infusion, Bleeding, Heart Rate, Cardiac Output, Varying Elastance, Stiffness, Contraction, Muscle, Pressure-Flow-Volume, Ohm's Law, RLC circuit, Resistance, Resistive, Compliance, Compliant, Inertance, Frank-Starling, Stroke, Rideout
- Rideout_PressureFlowReg
NSR0345 (in NSR archive): TwoCompExampMPC
Example JSim model generated from Modular Program Constructor (MPC). Three species (A, B, C), two compartment model with two reactions in compartment two with species concentrations described by ordinary differential equations (ODEs). Taken from 2015 F1000 article.
Example JSim model generated from Modular Program Constructor (MPC). Three species (A, B, C), two compartment model with two reactions in compartment two with species concentrations described by ordinary differential equations (ODEs). Taken from 2015 F1000 article.
- Key terms: modular modeling, JSim, computational biology, compartmental modeling, MPC, enzyme reactions, ODE, two compartment
- TwoCompExampMPC
NSR0346 (in NSR archive): FGP
Generate both fractional Gaussian noise (fGn) and fractional Brownian motion (fBm) series using the Davies-Harte algorithm.
Generate both fractional Gaussian noise (fGn) and fractional Brownian motion (fBm) series using the Davies-Harte algorithm.
- Key terms: Gaussian, noise, fractional Gaussian noise, Brownian, motion, fractional Brownian motion, fGn, fBm, Davies and Harte, fractal, time series, Fourier transform, spectra, autocovariance
- FGP
NSR0347 (in NSR archive): wu_2007
Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology.
Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology.
- Key terms: Mitochondria, Metabolism, Publication, Data, Electrophsyiology, NAD, ADP, TCA cycle, transport, enzyme reaction, redox
- wu_2007
NSR0348 (in NSR archive): threeExponentials
Generate CleanCurve = sum of three exponential curves and NoisyCurve=CleanCurve with 5% proportional Gaussian noise. Fit, the sum of three exponentials with amplitudes and decay rates found by optimization, attempts to fit the NoisyCurve. Parameters and confidence limts are compared with MonteCarlo estimates.
Generate CleanCurve = sum of three exponential curves and NoisyCurve=CleanCurve with 5% proportional Gaussian noise. Fit, the sum of three exponentials with amplitudes and decay rates found by optimization, attempts to fit the NoisyCurve. Parameters and confidence limts are compared with MonteCarlo estimates.
- Key terms: exponential, three exponentials, 3 exponentials, Monte-Carlo, Monte Carlo, MonteCarlo, decay curves, isotope disintegration, washout curves, residue analysis, pharmacokinetics, noise, Gaussian random
- threeExponentials