JSim Consolidated Model Database
Showing 351 - 400 of 432 models found. [New Search]
NSR0353 (in NSR archive): DISP
Computes the Hurst coefficient for a fractional Gaussian noise series by binning the data (averaging adjacent points) and calculating the standard deviation as a function of bin size.
Computes the Hurst coefficient for a fractional Gaussian noise series by binning the data (averaging adjacent points) and calculating the standard deviation as a function of bin size.
- Key terms: dispersion, fractal, time series, fGn, fractional Gaussian noise, Hurst
- DISP
NSR0359 (in NSR archive): HbOTracer
Oxygen and O-15 tracer content of Blood at 37C (time-dependent/transient oxygen flow), Hill model. import nsrunit; unit conversion on;
Oxygen and O-15 tracer content of Blood at 37C (time-dependent/transient oxygen flow), Hill model. import nsrunit; unit conversion on;
- Key terms: hemoglobin, oxygen, carbon dioxide, saturation, Haldane, Bohr, acidity, pH, blood gases, Hill equation, solubility, cooperativity
- HbOTracer
NSR0360 (in NSR archive): Rideout_PressureFlowNP
CV loop nonpulsatile model ported from Rideout (ACSL program PF-NP). Also in MATLAB.
CV loop nonpulsatile model ported from Rideout (ACSL program PF-NP). Also in MATLAB.
- Key terms: Cardiovascular, CV, Left, Right, Ventricle, Ventricular, Non Pulsatile, Myocardial Infarction, Heart Rate, Systolic, Diastolic, Cardiac Output, Stiffness, Muscle, Atrial, Arterial, Venous, Systemic, Pulmonary, Unstressed, Locus, Pressure-Flow, Ohm's Law, Resistance, Resistive, Conductance, Preload, Afterload, Compliance, Compliant, Stroke Volume, Rideout
- Rideout_PressureFlowNP
NSR0363 (in NSR archive): Heat_Equation
The 2-d heat equation is solved using partial differential equations generated using the Modular Program Constructor (MPC). Heat_Equation_ODE solves the problem using ordinary differential equations.
The 2-d heat equation is solved using partial differential equations generated using the Modular Program Constructor (MPC). Heat_Equation_ODE solves the problem using ordinary differential equations.
- Key terms: Heat equation, 2-D, partial differential equation, PDE, ordinary differential equation, ODE, Modular Program Constructor, MPC
- Heat_Equation
NSR0364 (in NSR archive): Diffusion1DpdeConsumption
Diffusion in one dimension with asymmetrical consumption is modeled using a partial differential equation.
Diffusion in one dimension with asymmetrical consumption is modeled using a partial differential equation.
- Key terms: 1d, 1-d, 1D, 1-D, one dimension, diffusion, PDE, consumption, function generator, optimize, no flux, boundary condition, tutorial
- Diffusion1DpdeConsumption
NSR0366 (in NSR archive): NestedPlots
Models a tissue cylinder consisting of two regions: plasma, and interstitial fluid. Contains nested plots.
Models a tissue cylinder consisting of two regions: plasma, and interstitial fluid. Contains nested plots.
- Key terms: nested, nested plots, world within worlds, BTEX20, PDE, convection, diffusion, permeation, reaction, distributed, capillary, plasma, isf, interstitial fluid
- NestedPlots
NSR0367 (in NSR archive): CerebralBloodFlow_CCT_BS
A lumped parameter model of cerebral blood flow control combining cerebral autoregulation and neurovascular coupling
A lumped parameter model of cerebral blood flow control combining cerebral autoregulation and neurovascular coupling
- Key terms: cerebral blood flow regulation, physiological model, myogenic regulation, neurogenic regulation, visually evoked flow response, publication
- CerebralBloodFlow_CCT_BS
NSR0368 (in NSR archive): CorrelationOfParameters
JSim calculates the correlation between parameters two different ways: Normalizing the inverse of an estimation of the Hessian and a Monte Carlo approach. The results are not necessarily similar.
JSim calculates the correlation between parameters two different ways: Normalizing the inverse of an estimation of the Hessian and a Monte Carlo approach. The results are not necessarily similar.
- Key terms: Monte Carlo, MonteCarlo, Monte-Carlo, Correlation, covariance, normalized covariance, btex10
- CorrelationOfParameters
NSR0369 (in NSR archive): SalicylicAcidClearance
This model is a place-holder for the three separate models, HalfLife, Enzyme, and BriggsHaldane. It is an example of reproducible models leading to reproducible science. Run the SalicylicAcidClearance model first.
This model is a place-holder for the three separate models, HalfLife, Enzyme, and BriggsHaldane. It is an example of reproducible models leading to reproducible science. Run the SalicylicAcidClearance model first.
- Key terms: aspirin, Briggs-Haldane, chemistry, clearance, half-life, JSim, Michaelis-Menten, modeling, pharmacokinetics, physiology, reproducible research, SA, salicylic acid, saturation, simulation
- SalicylicAcidClearance
NSR0370 (in NSR archive): SWV
Scaled Windowed Variance (SWV) Analysis for determining the Hurst coefficient from time series of fractional Brownian motion (fBm). Includes the linearly detrended (LDSWV) and bridge detrended (BDSWV) methods.
Scaled Windowed Variance (SWV) Analysis for determining the Hurst coefficient from time series of fractional Brownian motion (fBm). Includes the linearly detrended (LDSWV) and bridge detrended (BDSWV) methods.
- Key terms: SWV, LDSWV, BDSWV, fractal, time series, fBm, fractional Brownian motion, Hurst, scaled, windowed, variance
- SWV
NSR0371 (in NSR archive): DashRunGasReCirc
Translate original model from Matlab into JSim mml. Four compartment ODE model consisting of Systemic capillary and tissue, Pulmonary capillary, and alveolus compartments. Uses an iterative approach to calculating partial pressures of O2 and CO2 in the capillaries using Dash et al. 2016 simplified calculations for O2 and CO2 binding to Hb.
Translate original model from Matlab into JSim mml. Four compartment ODE model consisting of Systemic capillary and tissue, Pulmonary capillary, and alveolus compartments. Uses an iterative approach to calculating partial pressures of O2 and CO2 in the capillaries using Dash et al. 2016 simplified calculations for O2 and CO2 binding to Hb.
- Key terms: O2-CO2 transport, hemoglobin, oxygen, carbon dioxide, bicarbonate, alveoli, recirculating, HbO2 binding, HbCO2 binding, compartmental modeling, lung, metabolism, myoglobin, matlab
- DashRunGasReCirc
NSR0373 (in NSR archive): SigmaPore
Permeability and reflection coefficient for a hard spherical solute, radius rs,through a cylindrical pore, radius rpore. Minimal code for Sigma and Perm; Hydrodynamic calculation from Bassingthwaighte 2006, corrected 2012
Permeability and reflection coefficient for a hard spherical solute, radius rs,through a cylindrical pore, radius rpore. Minimal code for Sigma and Perm; Hydrodynamic calculation from Bassingthwaighte 2006, corrected 2012
- Key terms: porous transport, hydrodynamic molecular radius, cylindircal pore size, capillary permeability, convection, diffusion, interstitial matrix, Publication, molecular exclusion, osmotic water and solute fluxes, particle flow in fluids, steric hindrance, Spiegler frictional coefficients, Kedem Katchalsky, Data, Tutorial, module, MPC
- SigmaPore
NSR0374 (in NSR archive): FractionalBrownianMotionWalk
Generate a 2-D fractional Brownian motion walk using the the Davies-Harte algorithm. (see FGP, model 346 for details).
Generate a 2-D fractional Brownian motion walk using the the Davies-Harte algorithm. (see FGP, model 346 for details).
- Key terms: fractional Gaussian noise, fractional Brownian motion, fGn, fBm, Davies and Harte, fractal, time series, Fourier transform, spectra, autocovariance, 2-d, random walk
- FractionalBrownianMotionWalk
NSR0375 (in NSR archive): MicroCircIllusoryCooperativity_1
A spatially distributed blood tissue exchange model which incorporates the regulation of coronary blood flow by adenosine acting through adenosine A2A receptors on the surface of vascular smooth muscle cells. This simplified version of the model lumps all interstitial adenosine consuming/transporting processes into a single process with Michaelis Menten kinetics.
A spatially distributed blood tissue exchange model which incorporates the regulation of coronary blood flow by adenosine acting through adenosine A2A receptors on the surface of vascular smooth muscle cells. This simplified version of the model lumps all interstitial adenosine consuming/transporting processes into a single process with Michaelis Menten kinetics.
- Key terms: illusory, cooperativity, adenosine, receptor, transport, PDE
- MicroCircIllusoryCooperativity_1
NSR0376 (in NSR archive): MicroCircIllusoryCooperativity_2
A spatially distributed blood tissue exchange model which incorporates the regulation of coronary bood flow by adenosine acting through adenosine A2A receptors on the surface of vascular smooth muscle cells.
A spatially distributed blood tissue exchange model which incorporates the regulation of coronary bood flow by adenosine acting through adenosine A2A receptors on the surface of vascular smooth muscle cells.
- Key terms: illusory, cooperativity, adenosine, receptor, transport, PDE, Data
- MicroCircIllusoryCooperativity_2
NSR0377 (in NSR archive): SalicylateBodyMito
Aspirin and Salicylate circulate in the plasma and are converted to salicylurate in liver mitochondria prior to clearance, mainly as salicylurate.
Aspirin and Salicylate circulate in the plasma and are converted to salicylurate in liver mitochondria prior to clearance, mainly as salicylurate.
- Key terms: aspirin, Briggs-Haldane, chemistry, clearance, half-life, JSim, Michaelis-Menten, modeling, pharmacokinetics, physiology, reproducible research, SA, salicylic acid, saturation, simulation
- SalicylateBodyMito
NSR0380 (in NSR archive): MPC, the semi-automated Modular Program Constructor
MPC is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML), JSim website, that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models.
MPC is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML), JSim website, that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models.
- Key terms:
- MPC, the semi-automated Modular Program Constructor
NSR0381 (in NSR archive): Rxn_A_plus_B_to_C
Two solutes, A and B, reversibly react to form C. A + B C reaches equilibrium at the ratio A*B/C = Kd.
Two solutes, A and B, reversibly react to form C. A + B C reaches equilibrium at the ratio A*B/C = Kd.
- Key terms: reaction, rxn, biochemistry, dissociation, Kd, equilibrium, reversible, ODEs, implicit, steady state, analytic, A+B, A+B<->C
- Rxn_A_plus_B_to_C
NSR0382 (in NSR archive): Osm.coupledKK.1sol
Transport across a membrane between 2 stirred tanks, V1 and V2 of solute 1 and solvent water. Water fluxes induce volume changes and pressure changes. Solute 1 can also permeate the membrane independently of the pore, Pmemb11, and so can water PmembW. This uses linearized thermodynamics of irreversible processes from Kedem and Katchalsky 1958.
Transport across a membrane between 2 stirred tanks, V1 and V2 of solute 1 and solvent water. Water fluxes induce volume changes and pressure changes. Solute 1 can also permeate the membrane independently of the pore, Pmemb11, and so can water PmembW. This uses linearized thermodynamics of irreversible processes from Kedem and Katchalsky 1958.
- Key terms: One ideal solute, compartment, water and solute exchange coupled, passive transmembrane exchanges, steric hindrance, irreversible thermodynamics, Kedem Katchalsky, reflection coefficients, Staverman, osmosis
- Osm.coupledKK.1sol
NSR0383 (in NSR archive): FEV_Maxwell
Models Forced Expiratory Volume procedure using the Maxwell one chamber viscoelastic compartment model taken from Bates (ch. 7)
Models Forced Expiratory Volume procedure using the Maxwell one chamber viscoelastic compartment model taken from Bates (ch. 7)
- Key terms: FEV, forced, expiratory, volume, VISCOE, ODE, compartment, viscoelastic, Maxwell, lung, linear, compliance, resistance, positive pressure, ventilation, passive, exhalation, data
- FEV_Maxwell
NSR0384 (in NSR archive): FEV_simple
Models Forced Expiratory Volume procedure using the linear one chamber compartment model taken from Bates (ch. 3)
Models Forced Expiratory Volume procedure using the linear one chamber compartment model taken from Bates (ch. 3)
- Key terms: FEV, forced, expiratory, volume, single, compartment, simple, lung, linear, compliance, resistance, positive pressure, ventilation, passive, exhalation, data
- FEV_simple
NSR0385 (in NSR archive): fgen
Java function call. Given y(n) and x(n) (both monotonic). They can be regarded as y(x) and x(y), and given YY, find XX such that y(XX)=YY using binary search.
Java function call. Given y(n) and x(n) (both monotonic). They can be regarded as y(x) and x(y), and given YY, find XX such that y(XX)=YY using binary search.
- Key terms: fgen, interpolate, interpolation, y(x), x(y), real function, Java function, function, binary search
- fgen
NSR0386 (in NSR archive): AccessingJSimArrays
A 3 dimensional array is copied by a JSim procedure illustrating how array elements are addressed between JSim and Java.
A 3 dimensional array is copied by a JSim procedure illustrating how array elements are addressed between JSim and Java.
- Key terms: Java, MML, arrays, accessing, realVal, grid, set, JSim, API, RegularGridData, regular, grid, data, procedures, functions, source
- AccessingJSimArrays
NSR0387 (in NSR archive): primes
A range of numbers is submitted. If a number in the range is prime, it is multiplied by 1, otherwise multipliedby zero. Illustrates the topcode, maincode, and bottomcode in JSim function and procedure calls.
A range of numbers is submitted. If a number in the range is prime, it is multiplied by 1, otherwise multipliedby zero. Illustrates the topcode, maincode, and bottomcode in JSim function and procedure calls.
- Key terms: Java, source, real, function, procedure, F&P, topcode, maincode, bottomcode, method, primes, MML, tips, programming
- primes
NSR0388 (in NSR archive): BR77pkDetect
Demonstrate peak detection using model of Cardiac Action Potential with Ca, K, and Na currents. Model from Beeler-Reuter 1977 paper.
Demonstrate peak detection using model of Cardiac Action Potential with Ca, K, and Na currents. Model from Beeler-Reuter 1977 paper.
- Key terms: Electrophysiology, ionic currents, voltage clamp, fiber action potential, cardiomyocyte, Nernst potential, time and voltage-dependent time constants, cell physiology, peak detection, java procedure, JSim tutorial
- BR77pkDetect
NSR0393 (in NSR archive): Comp1FlowReactionXa2Ua
In a single compartment with flow, substrates Xa (Xanthine) and Ua (Uric acid convert to each other.
In a single compartment with flow, substrates Xa (Xanthine) and Ua (Uric acid convert to each other.
- Key terms: Course, compartment, compartmental, tutorial, flow, decay, clearance, Comp1FlowDecay, Comp1FlowReaction, Xanthine, Uric acid
- Comp1FlowReactionXa2Ua
NSR0395 (in NSR archive): BarrerDiffusion
Models diffusion through one dimensional slab with a constant diffusion coefficient, D, with flux into recipient chamber on right used to estimate the diffusion coefficient. Model includes partition coefficient.
Models diffusion through one dimensional slab with a constant diffusion coefficient, D, with flux into recipient chamber on right used to estimate the diffusion coefficient. Model includes partition coefficient.
- Key terms: Diffusion, Constant diffusion coefficient, PDE, Concentration, One slab, Transport physiology RELATED MODELS: #202: Safford 1977 Dead end pore model for Calciium diffusion in muscle #205: Safford 1978 Water diffusion in heart #193: Suenson 1974 Diffusion in heart tissue, sucrose and water #135: Two slab model: Facil_Diffusion_2Region #184: RandomWalk1D #212: TwoSlab Diffusion: different diffusion coeffs in adjacent slabs require special boundary condition
- BarrerDiffusion
NSR0396 (in NSR archive): Hund_Rudy_2004
Rate Dependence and Regulation of Action Potential and Calcium Transient in a Ventricular Cell Model. Based on the Hund-Rudy 2004 model. Imported from the CellML version of the model.
Rate Dependence and Regulation of Action Potential and Calcium Transient in a Ventricular Cell Model. Based on the Hund-Rudy 2004 model. Imported from the CellML version of the model.
- Key terms: Action potential, LCC, calcium buffer, troponin, calmodulin, myocyte, CICR, electrophysiology, sodium, potassium, Calsequestrin, Calcium induced calcium release, Publication
- Hund_Rudy_2004
NSR0397 (in NSR archive): GasSoly2017
Equations and Data for O2 and CO2 solubility in water, normal saline, human & Ox plasma. This model uses individual fit data to express the O2 and CO2 solubility in various biological solutions. Please refer to the Notes tab for further details on the model and files.
Equations and Data for O2 and CO2 solubility in water, normal saline, human & Ox plasma. This model uses individual fit data to express the O2 and CO2 solubility in various biological solutions. Please refer to the Notes tab for further details on the model and files.
- Key terms: Oxygen, CO2, solubility, plasma, saline, Publication, Data, Cardiac grid, MPC
- GasSoly2017
NSR0398 (in NSR archive): Stabenau93_pKa
Calculation of the apparent pKa for the CO2 hydration reaction in turtle blood. Empirical equations relating pKa to pH, Temperature, Na+, protein conc, and ionic strength and CO2 solubility coefficient to temperature.
Calculation of the apparent pKa for the CO2 hydration reaction in turtle blood. Empirical equations relating pKa to pH, Temperature, Na+, protein conc, and ionic strength and CO2 solubility coefficient to temperature.
- Key terms: CO2 solubility coefficient, CO2 hydration reaction, buffer, blood plasma, Publication, pH, temperature dependence, carbonic acid, bicarbonate, pKa, Data
- Stabenau93_pKa
NSR0399 (in NSR archive): SHbO2CO2_Dash2016
Simulation of oxyhemoglobin (HbO2) and carbaminohemoglobin (HbCO2) dissociation curves and computation of total O2 and CO2 contents in RBCs, Modified from Dash's original 2016 Matlab version. Annotated for use with MPC.
Simulation of oxyhemoglobin (HbO2) and carbaminohemoglobin (HbCO2) dissociation curves and computation of total O2 and CO2 contents in RBCs, Modified from Dash's original 2016 Matlab version. Annotated for use with MPC.
- Key terms: oxygen, O2, carbon dioxide, CO2, Hb, hemoglobin, oxyhemoglobin, carbamino-hemoglobin, dissociation curves, pH, 2,3-diphosphoglycerate, 2,3-DPG, 2,3-bisphosphoglycerate, 2,3-BPG, temperature effects, O2-CO2 interactions, Bohr effects, Haldane effects, MPC, Publication
- SHbO2CO2_Dash2016
NSR0400 (in NSR archive): Tewari2016
(Matlab) Dynamics of cross-bridge cycling, ATP hydrolysis, force generation, and deformation in cardiac muscle.
(Matlab) Dynamics of cross-bridge cycling, ATP hydrolysis, force generation, and deformation in cardiac muscle.
- Key terms: Cross-bridge cycle, Viscoelasticity, Cardiac muscle, Force generation, Metabolites, Sinusoidal perturbation analysis, matlab, ODE, magnesium, ATP, strain, stress, Cardiac Grid, Data, Publication
- Tewari2016
NSR0401 (in NSR archive): Pradhan2016
(Matlab) Model of open-loop (feed-forward) and feedback control of coronary blood flow during exercise, cardiac pacing, and pressure changes.
(Matlab) Model of open-loop (feed-forward) and feedback control of coronary blood flow during exercise, cardiac pacing, and pressure changes.
- Key terms: coronary blood flow, open-loop (feed-forward) control, feedback control, myogenic control, oxygen mass balance, autoregulation, cardiac pacing, Publication, ATP, norepinephrine, Cardiac grid, matlab
- Pradhan2016