Physiome NSR models
Number of active models: 433
| Model # | Title | Pub | Data | Model Description |
|---|---|---|---|---|
| 0001 | OneAlvLung.Assist | No | No | A compliant 1 compartment lung with resistance to air flow, driven by external positive pressure ventilator. |
| 0002 | OneAlvLung.Chest | No | No | A compliant 1 compartment lung with resistance to air flow, driven by intrapleural negative pressure (chest or diaphragmatic breathing) or by a positive pressure ventilator or both together, even competing, interfering.. |
| 0003 | OneAlvLung.GasExch | No | No | Exchange of gas in external air into a linearly compliant lung with calculation of inhaled gas concentration in lung over a series of breaths. |
| 0004 | 2CompLung_Air | No | No | Airflow between atmosphere and lung modeled with 2 compartments representing the non-exchanging space (bronchus) and exchanging space (alveolus). |
| 0005 | Lutchen | Yes | No | "A nonlinear model combining Pulmonary Mechanics and Gas Concentration Dynamics." IEEE Trans.,BME-29, 1982, p. 629-641. Lutchen, F.P. Primiano Jr., G.M. Saidel |
| 0006 | BronchBronchiolAlv | No | No | This model represents airway with one bronchus, one bronchiole, and an alveolus. |
| 0007 | Transp1sol.Comp2 | No | No | Models a two compartment, 1 solute, T1-T2 (facilitated 4-state transporter. Includes binding steps and transmembrane flip rates for free and occupied transporters. |
| 0008 | Transp1sol.Comp2F | No | No | A two compartment one solute facilitated transporter model with flow through one compartment. Includes binding steps and transmembrane flip rates for transporter. |
| 0009 | Transp1sol.Distrib2F | No | No | A two region axially-distributed model with flow and a facilitating two-sided transporter (T1-T2) for one solute. |
| 0010 | Transp2sol.Comp2 | No | No | Facilitating Transporter for 2 competing solutes including binding steps. Shows countertransport facilitation/inhibition Enymatic conversion in V2. |
| 0011 | Transp2sol.Comp2F | No | No | Facilitating Transporter for 2 competing solutes including binding steps. Shows countertransport facilitation/inhibition. Substrate A is converted to B in region 2. |
| 0012 | Transp2sol.Distrib2F | No | No | An axially-distributed facilitating transporter for two competing solutes, A and B, including binding steps, with input via flow. Shows countertransport facilitation/inhibition. There is Enzymatic conversion A -> B in V2. |
| 0013 | CircAdapt_TriSeg_2009 | Yes | No | (Matlab) Three-Wall Segment (TriSeg) Model Describing Mechanics and Hemodynamics of Ventricular Interaction. |
| 0014 | TranspMM1sidedComp2 | No | No | A two compartment one-sided Michaelis-Menten transporter. |
| 0015 | TranspMM.1sided.Comp2F | No | No | Model for two compartments with flow, 1 solute, 1 sided Michaelis-Menten transporter. |
| 0016 | TranspMM.1sided.Distrib2F | No | No | An axially distributed two region model with a two-sided passive transporter (PSg) through clefts and a one-sided Michaelis-Menten transporter (PSc) for membrane transport. |
| 0017 | TranspMM.2sided.Comp2 | No | No | Comparison of 1-sided and 2 sided Michaelis-Menten transporters in a two compartment model without flow. |
| 0018 | TranspMM.2sided.Comp2F | No | No | Comparison of 1-sided and 2 sided Michaelis-Menten transporters in a two compartment model with flow. |
| 0019 | TranspMM.2sided.Distrib2F | No | No | An axially distributed two region two-sided Michaelis-Menten transporter model, with permeation across the capillary wall via clefts (PSg) and cell transporters (PSc). |
| 0020 | TranspMM.2sided.Distrib3F.2Ch | No | No | A capillary-ISF-cell convection diffusion model, modified BTEX30 with a Michaelis-Menten saturable transporter on the pc membrane. It is represented by two separated and independent unidirectional transporters, each governed by the fractional saturation in the source compartment, i.e. by the concentration in the ISF to define PSISF2pc, and in the pc, Cpc, to define PSpc2ISF, the conductance via the carrier from pc to ISF. A three region two-side Michaelis-Menten transporter model. |
| 0021 | TranspMM.2sol1sided.Comp2 | No | No | A two compartment one-sided Michaelis-Menten transporter with 2 solutes. Detailed Description |
| 0022 | TranspMM.2sol2sided.BolusSw.MID4 | No | Yes | A two region two-sided Michaelis-Menten transporter with bolus sweep multiple indicator dilutions. |
| 0023 | TranspMM.2sol2sided.Comp2 | No | No | A two compartment two-sided Michaelis-Menten transporter with two solutes. |
| 0024 | TranspMM.2sol2sided.Comp2F | No | No | A two compartment two-sided Michaelis-Menten transporter, with flow. |
| 0025 | TranspMM.2sol2sided.Distrib2F | No | No | Two region capillary-tissue exchange model with both passive and Michaelis-Menton (MM) transport of two solutes with MM reaction of A to B in interstitial fluid region. |
| 0026 | MbO2 | No | Yes | Model for Oxygen binding to myoglobin, single site first order binding. |
| 0027 | HbO.Severinghaus | No | Yes | Severinghaus' Equation for O2 binding to hemoglobin |
| 0028 | HbO.Hill | No | Yes | Hill Equation for O2 binding binding to hemoglobin |
| 0029 | HbIndep | No | Yes | Model for slow ligand binding to 4 independent non-cooperative, identical, sites without reaction. |
| 0030 | HbCoop | No | Yes | Oxygen binding to hemoglobin at 4 cooperative sites. alp > 1 for pos cooperativity, alp |
| 0031 | HbO.Adair | No | Yes | Hemoglobin O2 saturation curve using Adair's 4-site equation. |
| 0032 | HbO.Dash | No | Yes | Hemoglobin O2 saturation curve at varied levels of PCO2 and pH. |
| 0033 | TranspMM.2sol2sided.BolusSw.MMID4 | No | Yes | 4 Region Axially Distributed Multi Path Michaelis-Menten Model applied to analysis of serotonin uptake by lung tissue following injection into pulmonary artery. |
| 0034 | BloodO2 | No | Yes | Oxygen Content of Blood at 37C, Hill model. |
| 0035 | HbO.compare | No | Yes | Compare Models of Hemoglobin O2 saturation curve at varied levels of PCO2 and pH. |
| 0036 | HbO.Hill.slow | No | Yes | Hill Equation modified to allow slow binding to hemoglobin |
| 0037 | HbCO2 | No | No | Hemoglobin CO2 saturation curve at varied levels of PO2 and pH. Temperature and 2,3-DPG concentration are assumed constant. Based on Dash 2010 paper. |
| 0038 | Athanasiades_2000 | Yes | No | This model is based on Athanasiades et al. energy analysis of a nonlinear model of the normal human lung. J Biol Sys. 8(2):115-39, 2000. |
| 0039 | Anderson_JC_2007_fig2 | No | No | Equilibrium conc for increasing kon for two compartment model. Figure 2 of "Tracers in Physiological Systems Modeling". |
| 0040 | Anderson_JC_2007_fig3 | No | No | Volume of Distribution of equilibrium binding and unsteady state. Figure 3 of "Tracers in Physiological Systems Modeling". |
| 0041 | Anderson_JC_2007_fig4 | No | No | Tracer added after tracee and binding site have equilibrated. Figure 4 of "Tracers in Physiological Systems Modeling". |
| 0042 | Anderson_JC_2007_fig5 | No | No | Tracer transients Slow versus fast binding. Figure 5 of "Tracers in Physiological Systems Modeling". |
| 0043 | Anderson_JC_2007_fig6 | No | No | Optimization tracer fit of pseudo two equation fit to three equation fit. Figure 6 of "Tracers in Physiological Systems Modeling". |
| 0044 | Anderson_JC_2007_fig7 | No | No | Two compartment model. Optimization to fit 2-Eq model to 3-Eq model solution assuming the absence of ligand binding in V1 or V2. Figure 2 of "Tracers in Physiological Systems Modeling". |
| 0045 | Anderson_JC_2007_fig11 | No | No | Pulse responses in axially-distributed three region model. Figure 11 of "Tracers in Physiological Systems Modeling". |
| 0046 | Anderson_JC_2007_fig12 | No | No | Pulse responses of Nth order Poisson operator with N tanks varied from 2 to 109 tanks in seried. Figure 12 of "Tracers in Physiological Systems Modeling". |
| 0047 | Anderson_JC_2007_fig13 | Yes | Yes | MID curve data fitted to three region PDE and serial compartment models. Figure 13 of "Tracers in Physiological Systems Modeling". |
| 0048 | Anderson_JC_2007_fig14 | Yes | Yes | Fitting Intravascular reference curve to serial stirred tank model. Figure 14 of "Tracers in Physiological Systems Modeling". |
| 0049 | Anderson_JC_2007_fig15 | No | No | MID data curves fit to stirred tank model - compare 1 tank versus 15 serial tanks. Figure 15 of "Tracers in Physiological Systems Modeling". |
| 0050 | gaussian | No | No | Probability density function described by a Gaussian distrubution. |
| 0051 | expdist | No | No | A probability density function as described by an exponential distribution. |
| 0052 | lndc | No | No | A probability density function as described by a lagged normal density curve. |
| 0053 | gamma_variate | No | No | A probability density function described by a gamma-variate distribution. |
| 0054 | CaATPase | No | Yes | Uptake and transport of calcium from the cytosol across the sarcoplasmic reticulum membrane, aided by ATP. |
| 0055 | NaCaX | No | No | An ion channel, a sodium calcium exchanger in the surface membrane (sarcolemma) of mammalian pacemaker cells. A mathematical model for the electrophysiological responses. |
| 0056 | poisson | No | No | This function generates a Poisson-like PDF using a scaled Poisson equation in which lambda is allowed to vary continuously and n is fixed. This curve represents the transport of a tracer through n identical well mixed compartments. |
| 0057 | randwalk | No | No | A probability density function as described by a random walk distribution. |
| 0058 | BTEX40_MID_heart | No | Yes | Blood tissue exchange model for heart capillaries uses literature values for constants to fit multiple indicator dilution data from tracer data through perfused dog hearts. Estimates for permeability surface areas for each solute are made. |
| 0059 | Compliant_Vessel | No | No | This model describes a flow through a single vessel with fixed resistance to flow, R, compliance, C, and a pressure drop along the vessel of Pin - Pout. |
| 0060 | Myogenic_Compliant_Vessel | No | No | This model simulates the flow through a passive and actively responding vessel driven by a sinusoidal pressure input. |
| 0061 | Nonlinear_Compliant_Vessel | No | No | This model describes the flow characteristics of a single vessel with resistance to flow, R, nonlinear compliance, C, and input flow of Fin. |
| 0062 | OneCompLung | No | No | This is a one compartment lung mechanic model. |
| 0063 | Rigid_Vessel | No | No | The model simulates fluid flow, F, through a rigid vessel of resistance, R, given a pressure drop across the length of the vessel Delta_P. |
| 0064 | OneCompLungO2CO2 | No | No | This is a one compartment lung mechanic model with O2-CO2 exchange. |
| 0065 | OneCompLungO2CO2_Cap | No | No | This is a one compartment lung mechanic model with alveolar O2-CO2 exchange with. |
| 0066 | Thin_Wall_Compliant_Vessel | No | No | This model uses simulates the flow through a single vessel with resistance to flow R and compliance of the vessel, C, derived from a thin walled formulation of vessel wall mechanics. |
| 0067 | Compliant_Element | No | No | The model simulates current flow through a capacitor C and is the electrical analog of fluid flowing into or out of a compliant vessel with no outlet. |
| 0068 | Pressure_Driven_Single_Vessel | No | No | This model simulates the single_vessel model with the addition of a pressure-driven flow input. This is analogous to a compliant, resistive vessel with an inflow on one end and an aperture for outflow on the other end. |
| 0069 | Resistive_Element | No | No | The model simulates current flow through a conductor of resistance R. Current is induced by the energy potential V_i applied across the conductor. |
| 0070 | 4-State_Sarcomere_Energetics | No | No | The 4-State model of sarcomeric contraction created by Landesberg and Sideman is investigated in terms of the energy liberated by the system as a function of the rate of shortening. |
| 0071 | Air_Blood_ExchangeNetwork | No | No | Model represents a network of multilayer segments for pulmonary air-blood exchange. |
| 0072 | Airway_bronchiole_alveolus | No | No | This model represents an inertial flow in a rigid airway, compliant bronchiole, compliant bronchiolus and a compliant alveolus. |
| 0073 | Alveoli_Bronchi_2comp | No | No | Airflow from atmosphere to Bronchi to Alveoli modeled with 2 compartments. |
| 0074 | Arterial_flow_with_O2_CO2_HCO3_H_exch | No | No | Distributed model for the O2-CO2 transport and exchange in the arterial portion of the vasculature. |
| 0075 | Baroreceptor_Lu_et_al_2001 | Yes | Yes | The model simulates baroreceptor function by changing heart rate, ventricular contractility, and arterial resistance in response to an input aortic pressure signal. |
| 0076 | barrier | No | Yes | Barrier-limited model of Goresky, using Finite difference method |
| 0077 | Beard2005_Mito_OxidatPhosphor | Yes | No | A model for the mitochondrial respiratory chain that appropriately balances mass, charge, and free energy transduction and analyzed based on a previously published set of data measured on isolated cardiac mitochondria. |
| 0078 | BeelerReuter77 | No | No | Cardiac Action Potential with Ca, K, and Na currents. Beeler-Reuter 1977 paper. |
| 0079 | BTEX10 | No | No | Flow with axial dispersion through a one-region pipe of uniform cross-section. |
| 0080 | BTEX20 | No | No | Models a tissue cylinder consisting of two regionsand interstitial fluid. |
| 0081 | BTEX30 | No | No | Models a tissue cylinder consisting of three regions: plasma, interstitial fluid, and parenchymal cells. |
| 0082 | BTEX40 | No | No | Models a tissue cylinder consisting of four regions: interstitial fluid, endothelial cells, and parenchymal cells. |
| 0083 | BTEX50 | No | No | Models a tissue cylinder consisting of five regions: plasma, interstitial fluid,endothelial cells, parenchymal cells, and mitochondria. |
| 0084 | gentex | No | No | GENTEX is a whole organ model of the vascular network providing intraorgan flow heterogeneity and accounts for substrate transmembrane transport, binding, and metabolism in erythrocytes, plasma, endothelial cells, interstitial space, and cardiomyocytes. |
| 0085 | Vessel_Resistance_Only | No | No | Model rigid vessel flow with vessels of varying diameter and length in series and in parallel. Model 'Two_Resistors' uses two vessels in series and model 'Four_resistors' has two vessels in parallel and two more in series. |
| 0086 | Goldman | No | No | Model of transmembrane resting potential due to concentration differences in K, Na, and Ca across a membrane with constant conductance for each ion. |
| 0087 | Bronchiole_Brochiolus_Alveolus | No | No | This model represents a compliant bronchiole, compliant bronchiolus and a terminal alveolar sac. |
| 0088 | Vinnakota_2003_MyoDensity | Yes | No | (Matlab) Myocardial density and composition: a basis for calculating intracellular metabolite concentrations |
| 0089 | Myo_Dyn_Resp_wFit | No | Yes | This model describes the dynamic response of a vessel after a step increase in intraluminal pressure. |
| 0090 | CardiacOutput_refHuman | Yes | Yes | Cardiac output estimation in reference human. An open-loop cardiovascular model composed of a four-chamber varying-elastance heart, a systemic circulation, a pulmonary circulation, a coronary circulation, and baroreceptors. |
| 0091 | CardiopulmonaryMechanics | No | No | A closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circulation, a pulmonary circulation, a coronary circulation, airways mechanics, and baroreceptors. |
| 0092 | CardiopulmonMechGasExch | No | No | A closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circulation, a pulmonary circulation, a coronary circulation, airways mechanics, baroreceptors, and gas exchange. |
| 0093 | CardiopulmonMechGasBloodExch | No | No | A closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circulation, a pulmonary circulation, a coronary circulation, airways mechanics, baroreceptors, gas exchange, and blood gas handling. |
| 0094 | Adenosine_mid4 | No | Yes | Four region blood-tissue exchange (BTEX) model used to fit data from Schwartz 1999 MID experiments involving cardiac endothelial transport and metabolism of adenosine and inosine. |
| 0095 | Circ_with_Baroreceptors | No | No | A closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circulation, a pulmonary circulation, a coronary circulation, and baroreceptors. |
| 0096 | One_Enz_Reverse.MM | No | No | First-order reversible enzymatic reaction with binding of either substrate or product to enzyme and allows thermodynamic equilibrium. Uses two methods, the enzyme binding and |
| 0097 | Waniewski2009 | Yes | No | (Matlab) Distributed modeling of osmotically driven fluid transport in peritoneal dialysis: theoretical and computational investigations |
| 0098 | IsotopeDecay | No | Yes | Decay data for two radioactive isotopes: optimization to find the fraction of each. |
| 0099 | EC_SMC_Kapela_Microcirc2009 | No | No | A mathematical model of vasoreactivity in rat mesenteric arterioles: I. Myoendothelial communication |
| 0100 | SMC_Kapela_JTB2008_NitricOxideStimulation | Yes | No | A mathematical model of Ca2+ dynamics in rat mesenteric smooth muscle cell: agonist and NO stimulation. |
| 0101 | EC_Silva_AJP2007 | No | No | A mathematical model of plasma membrane electrophysiology and calcium dynamics in vascular endothelial cells. |
| 0102 | CortisolSecrete | No | No | Two compartment model with feedback control of precursor (pregnenolone) to cortisol and its adrenal secretion. |
| 0103 | Comp4ICG | No | Yes | Four-compartment whole body model with recirculation: repeated injections and first order hepatic clearance of Indocyanine Green dye. |
| 0104 | Nernst | No | No | Model of transmembrane voltage as concentration changes across a membrane with a single channel having a constant conductance. |
| 0105 | Vboltzmann | No | No | Model of Boltzmann gated channel conductance vs. transmembrane voltage for any ion. Valence and # of gating charges are variable. |
| 0106 | VboltzmannLagged | No | No | Model of Boltzmann gated channel conductance vs. transmembrane voltage for any ion. Conductance change has fixed timelag, tau. |
| 0107 | GoldmanNaKPump | No | No | Model of transmembrane resting potential due to concentration differences in K, Na, and Ca across a membrane with constant conductance for each ion. |
| 0108 | GoldmanNaKPump2 | No | No | Model of transmembrane resting potential due to concentration differences in K, Na, and Ca with constant conductances for the ions, plus accounting for the NaKPump current using an implicit calculation of EQ.10.4 from Sperelakis (1979). |
| 0109 | TwoToOneEquil | No | No | Two solutes, A and B, react to form C, reaching equilibrium ratio A*B/C = Kd. reaction: A + B C |
| 0110 | Comp1Flow.TracerBind | No | No | Tracer and Mother solute flow past a binding site. Equilibrium upset by an added pulse of mother solute, dislodging tracer. |
| 0111 | Comp2_LignocainePassage | Yes | Yes | A model of the first pass passage of drugs from i.v. injection site to the heart based on the work of Upton RN, 1996. Models the kinetics and dynamics of induction of anaesthesia (lignocaine) in sheep. |
| 0112 | Transp2sol.Comp2.PS | No | No | Models a two compartment, 2 solute, T1-T2 (facilitated 6-state transporter with effective PS calculation. Directly related to model Transp2sol.Comp2 (model #10). |
| 0113 | Vessel_Mechanics | No | Yes | This model describes how a microvessel responds to changes in intraluminal pressure in the steady state. This change in vessel diameter to pressure is known as the myogenic response. |
| 0114 | VSM_4StateXB | Yes | No | Model of the four-state Vascular Smooth Muscle crossbridge dynamics (Hai and Murphy, 1988). Descr |
| 0115 | Comp2_Osmotic_Solute-Water_Interaction | No | No | Model describing osmotic solute-water interaction in a 2 compartment system. |
| 0116 | Comp2_OsmoticWaterSoluteExch | No | No | Model describing 2 compartments with osmotic water and solute exchange (no solute water interaction) |
| 0117 | VSM_Ephys_NaNSCSCC | Yes | No | Vessel Smooth Muscle Electrophysiology model with stress-controlled Na+ conductance of the NSC channel. |
| 0118 | Comp6_Recirc | No | No | Six compartment model with flow, exchange, and recirculation. |
| 0119 | Competitive_Inhibition | No | No | This model shows the case of an enzyme facilitating the formation of a product from a substrate but an inhibitor exists which also can bind to the enzyme rendering it ineffective. |
| 0120 | Comp_four_gen_weibel_lung | No | No | This model represents four generations of the bipodial human lung or the Weibel lung. The lengths and diameter of the airways are based on the Weibel lung geomtery. The airways are assumed compliant. |
| 0121 | Compliant1Comp | No | No | Simple one compartment model with pressure source and constant compliance. |
| 0122 | Compliant_bifurcating_airway | No | No | This model represents a bifurcating compliant airway that could be used as a building block for constructing a network of airways. You could use the model to simulate flow in rigid airway bifurcation. |
| 0123 | Compliant_bifurcating_bronchiole | No | No | This model represents a bifurcating compliant bronchiole that could be used as a building block for constructing a network of bronchi. |
| 0124 | Compliant_bifurcating_bronchiole_compliant_alveoli | No | No | This model represents a bifurcating compliant bronchiole with two compliant alveoli. |
| 0125 | Compliant_bronchiole_compliant_alveolus | No | No | This model represents a compliant bronchiole with a compliant alveolar sac. The driving force for this model is a pressure gradient which represents the difference in the alveolar and the pleural pressures. |
| 0126 | Kuikka1986_MPBTEX20 | No | Yes | Two region multi-path BTEX model. Used to model D-glucose uptake in the heart. Model fit to Kuikka et al. 1986 rabbit heart data. |
| 0127 | Concen_Polarization | No | No | When flow of solute in a solution under pressure is retarded so that its flux across a membrane is slower than the solvent flux, it accumulates on the upstream side of the membrane. This "polarization" retards solvent flow osmotically. |
| 0128 | Zinemanas1994_CoronaryCirc | Yes | No | A lumped parameter model of the coronary circulation. A resistive-compliant network is used to simulate the following circulatory compartments: epicardial arteries, large coronary arteries, small coronary arteries, coronary capillaries, small coronary veins, large coronary veins, and epicardial veins. |
| 0129 | Co-vsCounter-CurrentExchange | No | No | Steady-state air-blood exchange for two geometric configurations. |
| 0130 | One_Enzyme_Reversible | No | No | First-order reversible enzymatic reaction with binding of either substrate or product to enzyme and allows thermodynamic equilibrium. |
| 0131 | One_Enzyme_Sequestered | No | No | This model simulates a single enzyme reaction which occurs inside a vesicle where the substrate and product diffuse across the vesicle boundary on each end of the reaction. |
| 0132 | Two_Enzyme_Reversible | No | No | This model simulates the competitive binding of two different enzymes which result in a similar product. |
| 0133 | Two_Enzyme_Sequestered | No | No | This model represents a two enzyme reversible reaction where the two enzymes are sequestered inside a vesicle and substrate and product are allowed to diffuse across the vesicle boundary. |
| 0134 | Exchange_O2_CO2_HCO3_and_H | No | No | Four region, distributed model for the O2-CO2 transport, exchange and metabolism. |
| 0135 | Facil_Diffusion_2Region | Yes | No | This theoretical model simulates the diffusional transport of fatty acid from a constant source through two unstirred regions separated by a permeable membrane. |
| 0136 | VSM_Ephys | Yes | No | The vascular smooth muscle cell electrophysiology model as developed by Kapela et al, 2008. |
| 0137 | Renkin2region59 | No | Yes | Models uptake of tracer potassium by skeletal muscle during continuous perfusion, flow constant or varied. Estimates the PS for the single composite barrier between axially distributed plasma and the cell potassium pool. (derived from model 0080) |
| 0138 | Fahraeus_Effect | No | No | This model illustrates the variation in blood hematocrit seen in narrow tubes from the blood hematocrit at the tube outlet. |
| 0139 | Feedback_Inhibition | No | No | This model shows an enzymatic reaction in which the product acts as an inhibitor to reduce the reaction progress. |
| 0140 | Sachse2008_Fibroblast | Yes | No | A model of fibroblast electophysiology developed by Sachse et al. 2008. JSim v1.1 |
| 0141 | goresky63 | No | No | Rapid exchange of solutes between the vascular and the extravascular space in a whole organ. |
| 0142 | FourSeg_wPleuralPress | No | No | Four segment (larynx, trachea, bronchi, alveoli) pressure-flow model represents the respiratory system and it is driven by pleural pressure. |
| 0143 | Gao1998_ARD | Yes | No | The autoregulatory device (ARD) developed by Gao et al. is reproduced here to simulate the autoregulation of cerebral blood flow in the 300 to 50 micron diameter vessels. |
| 0144 | Gas_Exch | No | No | Recirculation of O2 and CO2 between a 2-compartment lung and 2-compartment body. |
| 0145 | GasExch_Lu_2001 | Yes | No | Model for O2, CO2, and N2 in airways and O2, CO2 in blood of circulating system. Lu et al 2001. |
| 0146 | Crone63_BTEX | No | Yes | Models a tissue cylinder consisting of two regions: plasma, and interstitial fluid. Fit to Crone 1963 data. |
| 0147 | Vessels_4RC | No | No | This model describes a flow through vessels with resistance to flow, and compliance. Model 'Vessel_2RC' has two RC vessels in series while 'Vessel4RC has two RC vessels in parallel with two RC vessels in series. |
| 0148 | Lenbury2005.pituitary | Yes | No | A delay-differential equation model of the feedback/feedforward-controlled hypothalamus-pituitary-adrenal axis in humans. Lenbury and Pornsawad, 2005 paper. |
| 0149 | HbO2_HbCO2_diss | Yes | No | Blood HbO2 and HbCO2 Dissociation Curves at Varied O2, CO2, pH, 2,3-DPG and Temperature Levels. Based directly on Dash et al. 2010 errata reprint. |
| 0150 | Shrestha_2010 | Yes | Yes | Short term response of parathyroid gland to changes in plasma Ca(2+) levels. Based on Shrestha et al. 2010 paper. |
| 0151 | EnzLysis | No | No | An enzyme E is synthesized at a constant rate, and degraded in a first order process, -ke*E, only when it is unbound. Input of S is sinusoidal. The system amplifies to give an oscillation in product P. From Reich and Selkov 1981 and really from Selkov 1968. |
| 0152 | VelocityProfiles | No | No | Veloicty profiles in straight cylinders. Poiseuille Flow is parabolic (Model 2). Slip at wall is Roevros (Model 1) Two phase flow model (Wang Model 3) has lower viscosity at wall. |
| 0153 | HighlyIntegHuman | No | No | Highly-integrated human, a closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circ, a pulmonary circ, airways mechanics, baroreceptors, gas exch, blood gas handling, coronary circ, and peripheral chemoreceptors. |
| 0154 | HighlyIntHuman_wIntervention | No | Yes | A closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circulation, a pulmonary circulation, airways mechanics, baroreceptors, gas exchange, blood gas handling, coronary circulation, peripheral chemoreceptors and selectable interventions. |
| 0155 | Hodgkin_Huxley1952 | Yes | No | Hodgkin and Huxley (HH 1952d): Nerve action potential for squid giant axon. Quantitative model of time and voltage-dependent transmembrane currents for Na+, K+, and a leak current, Ileak. Centerpiece for Nobel prize. |
| 0156 | Homogenous_AirBlood_Exch | No | No | Periodic airway transport and alveolus-capillary gas exchange. |
| 0157 | InVivoViscosity | No | No | This model represents changes of blood viscosity due to the Fahraeus-Lindqvist effect as observed by Pries, Secomb et al. for flow in the rat mesentery. |
| 0158 | Yaniv_4-State_2005 | No | No | This is a reproduction of the 4 state model of a cardiac sarcomere originally developed by Landesberg and Sideman. The particular version presented here was used in Yaniv, Sivan and Landesberg Am J Physiol 288:H389-H399, 2005. |
| 0159 | Comp2.Binding | No | No | Models two compartments with a single substance passively exchanging between the two compartments, plus first order binding to solute Z to form ZC, both of which are confined to V1. |
| 0160 | Lumped_parameter_circulation | No | No | A closed loop cardiopulmonary model composed of a four-chamber varying-elastance heart, a pericardium, a systemic circulation, a pulmonary circulation, and a coronary circulation. |
| 0161 | Lumped_Param_Circ_wReg | No | No | A closed loop circulatory model with varying elastance heart, pulmonary, coronary and systemic circulatory loops and actively regulating arterioles in the systemic circulation responding to pressure and shear stress on the vessel walls. |
| 0162 | Lung_RC_P | No | No | Single compliant tank driven by pleural pressure. This is the simplest lung model possible. |
| 0163 | Kuikka1986BTEX30MP | Yes | Yes | Multiple tracer dilution estimates of D- and 2-deoxy-D-glucose uptake by the heart using a three region, 7-path, Blood-Tissue-Exchange (BTEX) model for albumin, L-Glucose, D-Glucose, and deoxy-Glucose. From Kuikka J, Levin M, Bassingthwaighte JB 1986 paper. |
| 0164 | Lung_tumor_2region | No | No | 2-region capillary-tissue exch of iodinated contrast in solid tumor. |
| 0165 | Luo-Rudy | No | No | The Modified Luo-Rudy Dynamic Model of the Mammalian Ventricular Myocyte. |
| 0166 | Sedaghat2002_insulin_signal | Yes | Yes | A mathematical model of metabolic insulin signaling pathways based on the work of Ahmad Sedaghat, Arthur Sherman and Michael Quon [2002, AM J Physiol Endocrinol Metab, 283,E1084-E1101]. |
| 0167 | Michailova_McCulloch2001 | No | No | The Michailova-McCulloch model extends the Winslow Jaffri Rice model by adding the buffering by MgATP and MgADP as well as by calmodulin. |
| 0168 | Myocyte_Fibroblast_Coupling | Yes | No | This model simulates the electophysiological effect of inexcitable cardiac fibroblast when coupled with cardiac myocytes. |
| 0169 | Diffusion1DpdeAdvection | No | No | Diffusion in a single region with advection |
| 0170 | PK_van_Bueren_2006 | No | Yes | Dose dependency of therapeutic monoclonal antibody (mAb), 2F8, binding to epidermal growth factor receptor (EGFR). |
| 0171 | NobleVarghese98 | Yes | No | Noble's 1998 improved guinea-pig ventricular cell model. It incorporates a diadic space, rapid and slow potassium currents and length and tension-dependent processes. |
| 0172 | Non_Competitive_Inhibition | No | No | This model describes the kinetics of an enzymatic reaction where an inhibitor can bind to the enzyme in a non-competitive manner. |
| 0173 | Kuikka1986experiment | No | Yes | Multiple tracer dilution estimates of D- and 2-deoxy-D-glucose uptake by the heart using a three region, 7-path, Blood-Tissue-Exchange (BTEX) model. Model fit to all experiments published in Kuikka et al. 1986 paper (See model #0163 for more detatils). |
| 0174 | nStirredTanks | No | No | N Stirred Tanks in Series |
| 0175 | PKComp1Decay | No | No | One compartment with constant elimination rate of a drug, a first order process, and instantaneous injection of drug dose. |
| 0176 | One_Slab_Diffusion_Partition | No | No | This model simulates the diffusion of a substance through a region with a constant diffusivity and different solubilities inside and outside the region. |
| 0177 | O2_CO2_Recirc_4Comp_Hb | No | No | O2 and CO2 exchange between alveolar air and pulmonary capillary and tissue capillary and metabolic reaction with specified Respiratory Quotient |
| 0178 | Pandit_et_al_2001 | Yes | No | This model reproduces the action potential recorded experimentally for epicardial myocytes isolated from the adult rat left ventricle (Pandit et al. 2001). |
| 0179 | Phase_Separation | Yes | No | This model illustrates the variation in cell distribution from that which would be expected by the division of flow at a microvascular bifurcation. |
| 0180 | Pleural_vs_ExternalPress | No | No | Two different ways of expressing breathing, one as if using a ventilator at the mouth and the other one as human pleural muscle generating pressure gradient against external pressure. Three models used to compare differences. |
| 0181 | Pulmonary_Circulation_Olansen_et_al_2000 | No | No | A model of pulmonary circulation based on Olansen et al. (2000) and Lu et al. (2001). A model of pulmonary circulation in which a right ventricle input pressure pulse drives blood flow through vascular components. |
| 0182 | PulmonMech_andGasConc | No | No | This model is based on Lutchen et al. A nonlinear model combining pulmonary mechanics and gas concentration dynamics. IEEE Trans. Biomed. Eng. 29: 629-641, 1982 |
| 0183 | Radial_Diffusion_in_Muscle_Fiber | No | Yes | Model simulates the diffusion of 11 cytosolic proteins from rabbit muscle fibers in a physiological solution. Several mechanisms which alter protein diffusion are considered including binding and hindrance to the myofilament lattice, binding to the other proteins, and protein crowding. |
| 0184 | RandomWalk1D | No | No | 20,000 1-D random walks are taken, the summation of Gaussian distributed steps with mean of 0 and variance = 1 or uniformly distributed steps from -1 to 1. The positions at a specific step number are |
| 0185 | redcell_carriage | No | Yes | Model effect of erythrocyte membrane on exchange of solutes between erythrocytes (red blood cells) and plasma water. |
| 0186 | Regulatory_Vessel | Yes | Yes | This model describes the steady state regulatory vessel response to changes in pressure across and shear stress on the vessel wall. |
| 0187 | Rigid_four_gen_weibel_lung | No | No | This model represents four generations of the bipodial human lung. The lengths and diameter of the airways are based on the weibel model. The compliance of the airway was considered to be negligible to represent rigid airways. |
| 0188 | Rigid_bifurcating_bronchiole_compliant_alveolus | No | No | This model represents a bifurcating rigid bronchiole with two compliant alveoli. |
| 0189 | Rigid_bronchiole_compliant_alveolus | No | No | Mechanics of a rigid resistive bronchiole with compliant alveolar sac. The driving pressure is at entrance to the bronchiole; the reference extrathoracic pressure is constant at zero. |
| 0190 | BTEX20simple | No | No | Simple Model of an axially distributed two-region capillary Blood-Tissue EXchange unit with consumption in interstitium |
| 0191 | Sanshe | Yes | No | The Sangren-Sheppard model (Bull Math Biophys 15: 387-394, 1953) for the exchange of a labeled substance between a liquid flowing in a vessel and an external compartment. Similar to BTEX20 with no diffusion |
| 0192 | nobarrier | No | Yes | Simple elimination with flow-limited distribution |
| 0193 | Suenson1974 | Yes | Yes | Single and Multi-path models of diffusion of sucrose, sodium, and water across a sheet of ventricular myocardium. Suenson et al. 1974 paper. Variation on Crank, 1956, solution for diffusion in a plane sheet with constant surface concentrations. |
| 0194 | Kumagai_2000 | Yes | Yes | Simple compartmental model including soluble gas transport in the alveoli, transfer between the bronchial circulation and the conducting airways, and metabolism. |
| 0195 | OneAlvLung.IronLung | No | No | A compliant 1 compartment lung with resistance to air flow can be driven by an external negative pressure surrrounding the chest (Pexhaust) or by intrapleural negative pressure (chest or diaphragmatic breathing (Pchest)) or a positive pressure ventilator (P or all three together). |
| 0196 | Styrene_Inhalation | Yes | Yes | A model for a physiological based description of the inhalation pharmacokinetics of styrene in rats and humans based on the work of J.C. Ramsey and M.E. Andersen [(1984). Toxicol Appl Pharm. 73(1), 159-175.], developed by Neil Geisler (2006) as a final project for BIOEN 589, University of Washington. |
| 0197 | Surfactant | No | No | Surfactant effect on single bubble dynamics: This models the dynamic adsorption, desorption, and squeeze-out phenomena of surfactant |
| 0198 | JardineSerotonin_FourRegion | Yes | Yes | Four region BTEX model used to describe serotonin uptake in the pulmonary endothelium and beyond. From Jardine et al. 2013 paper. |
| 0199 | JardineSerotonin_TwoRegion | Yes | Yes | Two Region BTEX Model describing serotonin uptake by lung tissue. From Jardine et al. 2013 paper based on model by Linehan et al, 1998. |
| 0200 | JardineSerotonin_OnePathCompare | Yes | Yes | Four and two region BTEX models without heterogeniety used to compare serotonin uptake in the pulmonary endothelium and beyond. From Jardine et al. 2013 paper. |
| 0201 | ten_Tusscher_Noble_Panfilov2004 | Yes | No | This model simulates the action potential for a human ventricular myocyte accounting for Na, K and Ca transport and dynamics. |
| 0202 | Safford1977 | Yes | Yes | Parallel pathway, dead-end pore model that accounts for sequestration or binding of calcium within heart muscle sheet. From Safford and Bassingthwaighte, 1977. Also contains an implementation of Suenson et al. 1974 diffusion model to validate new model with sucrose data. |
| 0203 | Pawlowski2007 | Yes | No | A theoretical model dealing with endocytosis, exocytosis and caveolae invagination, describing plasmalemma homeostasis during cell growth and division, was proposed. It considers transmembrane pressure, membrane tension and mechanosensitivity of membrane processes. |
| 0204 | thick_wall_vessel_tangential_stress | No | No | This model simulates the pressure and geometry resulting from changes in the internal radius of a thick-walled, distensible, isotropic, cylindrical vessel. |
| 0205 | Safford1978 | Yes | Yes | Calculates the bulk diffusion coefficient, Db, for water through a matrix of cells surrounded by ECF, influenced by cell membrane permeability. This is contrasted with results obtained from homogeneous sheet and dead-end pore models. From Safford et al. 1978 paper. |
| 0206 | OneAlvLung.ExchBody | No | No | Exchange of gas in external air into a non-linearly compliant lung with calculation of concentration of material in lung over a series of breaths and transport into the pulmonary capillary blood and subsequent loss into a "body" composed of blood in exchange with a tissue region where consumption occurs. |
| 0207 | ErupakaBruce2010 | Yes | Yes | Circulating, multicompartment O2-CO uptake and Hb/Mb binding model based on Erupaka et al. 2010. All table and eq. references are to 2010 paper unless noted. Figures and data referenced here are from Erupaka et al. 2010 paper. |
| 0208 | LungBtexCO2exch | No | No | Distributed model for O2-CO2 transport and exchange between a three compartment lung and the pulmonary circulation, modeled as a blood tissue exchange (BTEX) unit. |
| 0209 | Tidal_Human | No | No | A single chamber model of the lung pressure and volume with airway resistance and lung compliance. |
| 0210 | 4-State_Sarcomere_inSeries | No | No | A two element model incorporating two 4-state sarcomeres in series. This model is based on the 4 state model of a cardiac sarcomere originally developed by Landesberg and Sideman (Am J Physiol 267:H779-H795, 1994) and has been further developed to describe two sarcomeres. |
| 0211 | Two-barrier model | No | Yes | Two-barrier Model. If a tracer is transformed within the cells, or if its distribution is heterogeneous, two intracellular regions have to be considered, with a second barrier between them. |
| 0212 | TwoSlabDiffusion | No | No | Diffusion through two adjoining slabs with different diffusion coefficients. |
| 0213 | Two_Compartment_Lung | No | No | Airway is one tank, alveolus a second. Both are elastic. Flow direction governs solute flux. |
| 0214 | Ventilation_Response_to_CO | Yes | No | A mathematical model of ventilation response to inhaled carbon monoxide, based on the work of James H. Stuhmiller and Louise M. Stuhmiller [2005, JAP, 98, 2033-2044] and developed by Raymond Yakura as a final project for BIOEN 589, University of Washington. |
| 0215 | Ventricle_three_vessel_loop | No | No | This model simulates a closed loop resistor-capacitor network driven by a pressure generator (Pv). Volumes flow through a varying-elastance pressure generator component (simulating a contracting ventricle) and three compliant vessels in series. |
| 0216 | Weight_Cycling | Yes | No | A model for the dynamics of human weight cycling based on the work of Albert Goldbeter [J. Biosci, 31, 129-136] and presented by Lauren Shepherd as a final project for BIOEN 589, University of Washington. |
| 0217 | Winslow_Rice_Jafri1999 | Yes | No | This model analyzes the influence of voltage-dependent calcium (Ca2+)-independent transient current (Ito1) on the action potential duration (APD) in normal vs failing canine and human cardiac myocytes. |
| 0218 | Single_Vessel | No | No | Fluid flow from an open, compliant vessel, driven only by the energy stored inthe compliant vesel wall. |
| 0219 | Stergiopulos_4_Element_Windkessel | Yes | Yes | Lumped parameter peripheral circulation model from Stergiopulos et al. (1999) Am J Physiol 276: H81-H88. |
| 0220 | Thick_Wall_Vessel_Tangential_Stress | No | No | This model simulates the pressure and geometry resulting from changes in the internal radius of a thick-walled, distensible, isotropic, cylindrical vessel. |
| 0221 | Thick_Wall_Cylinder_Variable_E | Yes | Yes | This model simulates the pressure and geometry resulting from changes in the internal radius of a thick-walled, |
| 0222 | Ventricle_Driven_Two_Vessel | No | No | This model simulates a closed loop resistor-capacitor circulatory network driven by a pressure generator (PV). |
| 0223 | OneCompLungO2CO2H2ON2 | No | No | This is a one compartment lung mechanic model with O2,CO2,H2O,N2 pressure changes. |
| 0224 | Systemic_Circulation_Olansen_et_al_2000 | Yes | No | A lumped-parameter model of the systemic circulation. A chopped-sine left ventricle pressure signal drives flow through the system. |
| 0225 | BTEX20_Augmented | No | No | Models a tissue cylinder consisting of two regions: plasma and interstitial fluid. Model augmented with additional calculations. |
| 0226 | Vinnakota_Kemp_2006 | Yes | Yes | Dynamics of Muscle Glycogenolysis Modeled with pH Time-Course Computation and pH Dependent Reaction Equilibria and Enzyme Kinetics |
| 0227 | Vinnakota_Kemp_2006_Figs1_2 | Yes | Yes | Dynamics of Muscle Glycogenolysis Modeled with pH Time-Course Computation and pH Dependent Reaction Equilibria and Enzyme Kinetics. Reproduce figures 1 and 2. |
| 0228 | Vinnakota_Kemp_2006_Figs12_13 | Yes | Yes | Dynamics of Muscle Glycogenolysis Modeled with pH Time-Course Computation and pH Dependent Reaction Equilibria and Enzyme Kinetics. Scopes 1974 postmortem data. |
| 0229 | Vinnakota_Kemp_2006_Fig15 | Yes | Yes | Dynamics of Muscle Glycogenolysis Modeled with pH Time-Course Computation and pH Dependent Reaction Equilibria and Enzyme Kinetics. Reproduce Fig 15. |
| 0230 | CompDecayTutorial | No | No | Models single compartment with decay, no change, or synthesis of substrate. |
| 0231 | CompReactionTutorial | No | No | Models single compartment with substance A irreversibly becoming substance B. |
| 0232 | CompFlowTutorial | No | No | Models single compartment with inflowing and outflowing concentration of a single substance. |
| 0233 | CompExchangeTutorial | No | No | Models two compartments with substance in one compartment passively fluxing into and out of another compartment. |
| 0234 | CTEX20 | No | No | Computes N compartmental two region CTEX20. |
| 0235 | HbCO | No | Yes | Binding kinetics of carbon monoxide to hemoglobin using Adair's four site model. Two-way binding for carbon monoxide and no interactions between binding sites. |
| 0236 | Comp1FlowReactions2 | No | No | Single Compartment with flow and irreversible conversion of C to D and D to E. |
| 0237 | Comp1FlowReaction | No | No | In a single compartment with flow, substrates C and D convert to each other using an equilibrium constraint. |
| 0238 | shbo2_adair | No | Yes | Adair's hemoglobin-oxygen dissociation equation expressed in terms of P50 for sheep blood. Compare to two other variations of Adair's equation. |
| 0239 | HbO.WCM2state | Yes | Yes | The Monod-Wyman-Changeux model is used to describe the saturation of hemoglobin with oxygen. Accounts for homotropic cooperative effects on each of the four binding sites. |
| 0240 | Comp1Decay | No | No | One compartment with decay of substance, a first order process. |
| 0241 | Comp1Flow | No | No | Models single compartment with inflowing and outflowing concentration of a single substance. |
| 0242 | Comp1FlowDecay | No | No | Models single compartment with inflowing and outflowing concentration of a single substance which undergoes decay. Does not use physiological units. |
| 0243 | Comp1Reaction | No | No | Models single compartment with reversible reaction C becoming D and D becoming C with rate constants Gc2d and Gd2c. Uses non-physiological units. |
| 0244 | Comp1FlowDecayPhysiologicalVersion | No | No | Models single compartment with inflowing and outflowing concentration of a single substance which undergoes decay. |
| 0245 | Comp2Exchange | No | No | Models two compartments with a single substance passively exchanging between the two compartments. |
| 0246 | Comp2ExchangeReaction | No | No | Two comparment model with two substances, irreversibly converting A to B. |
| 0247 | Comp2FlowExchange | No | Yes | Two compartments, plasma and interstitial fluid (ISF), with flow and exchange using physiological names and units for parameters and variables. The model is |
| 0248 | Comp2FlowExchangeReaction | No | No | Model with two species A and B, with flow in a plasma compartment and exchange with an interstitial fluid compartment with A converting to B reversibly. |
| 0249 | Comp2FlowMMExchangeReaction | No | No | Two compartment model with flow, Michaelis-Menten type exchanger, and a reversible reaction in non-flowing compartment converting C to B. |
| 0250 | CompNFlowDelay | No | No | Computes N compartment models in series, each with volume = Vp/N, and with an added delay. |
| 0251 | SIMVOL | No | No | Two organ model recirculating system with shunt. Has separate three region compartmental exchange (CTEX) and blood tissue exchange (BTEX). |
| 0252 | NaKATPase | Yes | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. |
| 0253 | NaKpump2B | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 2B of NaKATPase tutorial. |
| 0254 | NaKpump2C | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 2C of NaKATPase tutorial. |
| 0255 | NaKpump3A | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 3A of NaKATPase tutorial. |
| 0256 | NaKpump3B | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 3B of NaKATPase tutorial. |
| 0257 | NaKpump3C | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 3C of NaKATPase tutorial. |
| 0258 | NaKpump4A | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 4A of NaKATPase tutorial. |
| 0259 | NaKpump4B | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 4B of NaKATPase tutorial. |
| 0260 | NaKpump4C | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 4C of NaKATPase tutorial. |
| 0261 | NaKpump5 | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 5 of NaKATPase tutorial. |
| 0262 | NaKpump6AB | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 6AB of NaKATPase tutorial. |
| 0263 | NaKpump8 | No | No | The exchange of sodium ions for potassium ions across the plasma membrane, via an ATP aided pump. Fig 8 of NaKATPase tutorial. |
| 0264 | CTEX20b | No | No | Capillary-tissue unit using serial stirred tanks with passive exchange via both a passive linear and a saturable transporter |
| 0265 | Comp2FlowMRIContrast | No | No | Model for analysis of NMR contrast agents from MRI signal from an organ region of interest (ROI) |
| 0266 | Comp6Propofol | Yes | Yes | A physiological model of induction of anaesthesia with propofol in sheep. |
| 0267 | Comp3FlowExch | No | No | Three compartment model for plasma (p), interstitial fluid (ISF) and parenchymal cell (pc) |
| 0268 | Progress3.Enz | No | No | Three substrates converted by two 1st order reversible enzymatic reactions. |
| 0269 | Progress3.React | No | No | Sequence of three uncatalyzed 1st order irreversible reactions. |
| 0270 | Progress3.MM | No | No | Sequence of two catalyzed 1st order Michaelis Menten-type irreversible reactions. |
| 0271 | PG_Isomerase | No | No | Single substrate single product reversible enzymatic reaction with parameters for phospho-gluco isomerase in erythrocytes (Ref 1) |
| 0272 | CTEX10 | No | No | Models a capillary consisting of N compartments. Explores sensitivity analysis and optimization and details the Monte-Carlo GUI for robust estimates of parameters, confidence limits and covariance. |
| 0273 | Osm.Uncoupled1 | No | No | Uncoupled, independent fluxes of water and of 2 solutes, across a membrane separating 2 stirred tanks of equal elasticity. |
| 0274 | Osm.Uncoupled2 | No | No | Uncoupled, independent fluxes of water and of 2 solutes, across a membrane separating 2 stirred tanks equipped with columns above each to provide observable column heights as measures of their pressures. |
| 0275 | Comp1EnzReact4 | No | No | Four sequential, first-order enzymatic reactions S P with substrates binding to enzymes, and reversible product formation. |
| 0276 | ThreeEXPdecay | No | Yes | Washout curve simulation by sum of three decaying exponentials: analysis using two or three exponentials. |
| 0277 | CTEX20_5path | No | No | Multipath Capillary-tissue exchange unit accounting for intra-organ flow heterogeneity. |
| 0278 | shbo2_buerk | No | Yes | Oxyhemoglobin dissociation curve calculated using Buerk's equation. The equation contains a term dependent on Temp, CO2, DPG, and pH. |
| 0279 | PoreTransport | Yes | Yes | Permeability and reflection coefficient for a hard spherical solute, radius rs,through a cylindrical pore, radius rpore. Hydrodynamic calculation from Bassingthwaighte 2006, corrected 2012 |
| 0280 | Aspirin | No | Yes | Salicylic acid (SA) clearance for three different dose ranges is modeled as an enzyme reaction. Model parameters are optimized and Monte-Carlo analysis is performed to robustly quantify parameter estimation, variance and covariance with other parameters in the presence of noisy data.. |
| 0281 | Comp1DecayPlus | No | No | One compartment model with decay of substance |
| 0282 | Comp1FlowPlus | No | No | Models single compartment with inflowing and outflowing concentration of a single substance. |
| 0283 | Comp1FlowDecayPlus | No | No | Models single compartment with inflowing and outflowing concentration of a single substance which undergoes decay. |
| 0284 | AllProcessesTutorial | No | No | A two compartmental model with flow, exchange, reaction and decay for two species, A and B. |
| 0285 | Comp2x2Recirc | No | No | Dual comp2 flow-exchange models in series with recirculation and clearance. |
| 0286 | Exchange.Dash.tracer | No | No | Tracer model of distributed model for the O2-CO2 transport, exchange and metabolism. |
| 0287 | BTEX40_Augmented | No | No | Models a tissue cylinder consisting of four regions: plasma, interstitial fluid, endothelial cells, and parenchymal cells. |
| 0288 | MID4ode | No | No | A model for triple-labeled indicator dilution experiments in a four compartment model. |
| 0289 | LongTailFractal | No | No | Fit the long tailed vascular output curves using N decaying exponentials where the ratio of the decay rates is constant and the ratio of the amplitudes is also constant. |
| 0290 | LongTail | No | No | Two, three, or four decaying exponentials are used to fit the long tails on indicator dilution curves for vascular tracers, e.g. albumin, by joining a multi-exponential function to a probability density curve representing a bolus injection. |
| 0291 | LongTailPowerLaw | No | No | Fit the long tailed vascular output curves using N decaying exponentials where the ratio of the decay rates is constant and the ratio of the amplitudes is also constant. |
| 0292 | MID4pde | No | No | A model for triple-labeled indicator dilution experiments in a four region tissue exchange model. |
| 0293 | MID4ctex | No | No | A model for triple-labeled indicator dilution experiments in a CTEX (distributed compartment) model with 4*N compartments. |
| 0294 | shbo2_hill_kelman | No | Yes | Oxyhemoglobin dissociation curve calculated using a simple Hill equation and Kelman's equation which is a modified Adair equation to take into account temperature, CO2 and pH. |
| 0295 | Circ.Windkessel3 | No | No | Three-element windkessel model with a connecting inductor in parallel (W4P), in series (W4S), and with a low-resistance Rc, in series with a viscoelastic windkessel (IVW). |
| 0296 | VascularOperator | No | No | Vascular operator consists of a pure delay operator plus two second order operators, all in series to simulate the mean transit time and dispersion in arteries and veins. |
| 0297 | FourierTransforms | No | No | Select a portion of an input file, smoothly interpolate it, calculate the forward Fourier Transform and the back Fourier Transform. |
| 0298 | LinearRegression | No | Yes | One program generates noisy data and another program calculates the linear regression using the Y fractional error. |
| 0299 | Btex20_comp2 | No | No | Axially distributed 2-region capillary-tissue exchange operator and analogous 2 compartment model. |
| 0300 | Weinstein2000_Fig2 | No | No | Model adapted from cellml repository for "A mathematical model of the outer medullary collecting duct of the rat" by Alan M. Weinstein. |
| 0301 | Weinstein2000_Fig3 | No | No | Model adapted from cellml repository for "A mathematical model of the outer medullary collecting duct of the rat" by Alan M. Weinstein. |
| 0302 | vanBeek2007 | Yes | No | 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. |
| 0303 | vanBeek2011 | Yes | Yes | 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. |
| 0304 | TransComp2 | No | No | 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). |
| 0305 | MMID4 | No | No | A FORTRAN based model for triple-labeled indicator dilution experiments in a four region tissue exchange model with 20 flow paths. WILL NOT RUN ON PC (MS Windows) COMPUTERS IF DOWNLOADED, BUT CAN BE RUN OVER THE WEB AS AN APPLET. |
| 0306 | Tyson1991cycle | Yes | No | 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). |
| 0307 | Lian_Mussig_2009_IDHP | No | No | (C language) Integrated dual-chamber heart and pacer (IDHP) model |
| 0308 | BTEX10_OscillatingFlow | No | No | Two single compartments use an oscillating flow through a pipe (BTEX10) to exchange material and volume. |
| 0309 | BTEX10x2CircularFlow | No | No | Two single compartments use a circular flow through a two pipes (BTEX10s) to exchange material. Pipe 1 has flow to the right, pipe 2 has flow to the left. |
| 0310 | WeightPredictor | No | No | 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. |
| 0311 | PanitchobPlacentaComp2015 | No | No | (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. |
| 0312 | PermeabilityToPotassium | Yes | Yes | 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. |
| 0313 | Botijo | No | No | Water cooling by evaporation from an earthenware jug |
| 0314 | Demir99 | Yes | No | Single Cell action potential of rabbit sinoatrial node modulated by acetyl choline by Demir, Clark, Giles 1999 from CellML source |
| 0315 | Demir94 | Yes | No | 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. |
| 0316 | ConcurrentFlow | Yes | No | Concurrent flow model for extraction during transcapilary passage. J.B. Bassingthwaighte: Circ Res 35:483-503, 1974. |
| 0317 | Transp2sol_Distrib2_F_tracer | No | No | 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. |
| 0318 | MultiCircSystem | No | No | 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., |
| 0319 | btex20_PSx | No | No | Axially-distributed 2-region capillary-tissue exchange operator with permeability varying along the capillary length. |
| 0320 | MM2Substrate_irrevers | No | No | 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 |
| 0321 | MM2Substrate_product_Inhibited | Yes | Yes | 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). |
| 0322 | Vfnet_MM2substrate_reversible | Yes | Yes | 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). |
| 0323 | FullXO | Yes | Yes | 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. |
| 0324 | FourXO | Yes | Yes | Contains four xanthine oxidase models: MM2Substrate_irreversible (Model #0320), MM2substrate_product_inhibited (Model #0321), Vfnet_MM2substrate_reversible (Model #0322), FullXO (Model #0323) |
| 0325 | DiffusionLimitedProfiles | Yes | No | 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. |
| 0326 | RelativeDispersion | Yes | No | Relative dispersion: A characterizing feature of specific vascular beds. Anesth Analg 56: 72-77, 1977. |
| 0327 | BTEX20radialDiffusion | No | No | 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. |
| 0328 | StochasticReaction | No | No | A reaction, A -> B with rate constant k is modeled using an ordinary differential equation and Gillespie's stochastic method. |
| 0329 | Brusselator | No | No | The Brusselator (combination of Brussels and Oscillator) equations of I. Prigogine and R. Lefever are solved both continuously and stochastically. |
| 0330 | Diffusion1Dpde | No | No | Diffusion in one dimension is modeled using a partial differential equation. |
| 0331 | BTEX10stat | No | No | Flow with axial dispersion through a one-region pipe of uniform cross-section. Statistics on inflow and outflow concentration curves */ |
| 0332 | CTEX10stat | No | No | Models a capillary consisting of N compartments. Explores sensitivity analysis and optimization. Includes curve statistics. |
| 0333 | BTEX10_Terminology | No | No | Uses a single capillary convection diffusion model to generate functions of linear stationary systems: h(t), H(t), R(t), eta(t). |
| 0334 | Rideout_IndicatorDilution | No | No | Compartmental cardiovascular indicator dilution model ported from Rideout (ACSL programs IND-DIL). Also in MATLAB. |
| 0335 | Rideout_IndicatorDilution_Modified | No | No | Compartmental cardiovascular indicator dilution model based on Rideout_IndicatorDilution with systemic flow used as constant reference. Also in MATLAB. |
| 0336 | Rideout_PressureFlowLH | No | No | Left heart and systemic arteries pressure-flow model ported from Rideout (ACSL programs LH-PF). Also in MATLAB. |
| 0337 | BronchTwoAlv | No | No | 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. |
| 0338 | Rideout_PressureFlow0 | No | No | Uncontrolled CV loop pressure-flow model ported from Rideout (ACSL program PF-0). Also in MATLAB. |
| 0339 | Logistic | No | No | A n iterative procedure is used to draw the Logistic Map. |
| 0340 | Logistic2 | No | No | Modified Logistic Map shows the fractal nature of the Logistic equation when smaller and smaller ranges of the "R" parameter are used. |
| 0341 | Selkov | No | No | 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. |
| 0342 | Cooperativity | No | No | This cooperativity binding model exhibits bistable bifurcation. |
| 0343 | Rideout_PressureFlow1 | No | No | Uncontrolled CV loop pressure-flow model ported from Rideout (ACSL program PF-1). Also in MATLAB. |
| 0344 | Rideout_PressureFlowReg | No | No | CV loop with baroreceptor regulation ported from Rideout (ACSL program PF-1-REG). Also in MATLAB. |
| 0345 | TwoCompExampMPC | No | No | 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. |
| 0346 | FGP | No | No | Generate both fractional Gaussian noise (fGn) and fractional Brownian motion (fBm) series using the Davies-Harte algorithm. |
| 0347 | wu_2007 | Yes | Yes | Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology. |
| 0348 | threeExponentials | No | No | 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. |
| 0349 | MonteCarlo | No | No | Fitting an equation for a quadratic with added noise is used to illustrate the MonteCarlo Graphical User Interface. |
| 0350 | AutoCovariance | No | No | Compute the autocorrelation for an external time Series and the autocorrelation for the same series filtered by a first order process. |
| 0351 | NyquistFreq | No | No | A continuous function, a sum of 4 cosines, is sampled at delta-t =1/2 and undersampled at delta-t=1 illustrating the folding of frequencies around the Nyquist frequency. |
| 0352 | TimeSeriesFilters | No | No | Simple low pass, high pass, and bandpass filters are illustrated by four examples. |
| 0353 | DISP | No | No | 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. |
| 0354 | No | No | Compute the PDF for a time series. | |
| 0355 | ResolvingFreq | No | No | Spill over of energy into adjacent frequencies is illustrated. |
| 0356 | CrossCovariance | No | No | Compute the crosscovariance for the output of two similar first order operators whose input is the same random variable. |
| 0357 | OperatorsAsFilters | No | No | A series consisting of uniformly distributed random numbers between -1 and 1 is passed through a 1st order operator. |
| 0358 | BloodO2_Transient | No | Yes | Oxygen content of Blood at 37C (time-dependent/transient oxygen flow), Hill model. |
| 0359 | HbOTracer | No | No | Oxygen and O-15 tracer content of Blood at 37C (time-dependent/transient oxygen flow), Hill model. import nsrunit; unit conversion on; |
| 0360 | Rideout_PressureFlowNP | No | No | CV loop nonpulsatile model ported from Rideout (ACSL program PF-NP). Also in MATLAB. |
| 0361 | ActinCycle1 | No | No | ODE model of actin polymerization and depolymerization with tracking of bound nucleotide |
| 0362 | YonXregression | No | No | Compute Y on X regression. Assumes y(i) = slope*x(i) +error(i) (all the error is in y.) Descripti |
| 0363 | Heat_Equation | No | No | 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. |
| 0364 | Diffusion1DpdeConsumption | No | No | Diffusion in one dimension with asymmetrical consumption is modeled using a partial differential equation. |
| 0365 | VISCOE | No | No | Models four different viscoelastic compartments with one or two chambers for modeling lungs. |
| 0366 | NestedPlots | No | No | Models a tissue cylinder consisting of two regions: plasma, and interstitial fluid. Contains nested plots. |
| 0367 | CerebralBloodFlow_CCT_BS | Yes | No | A lumped parameter model of cerebral blood flow control combining cerebral autoregulation and neurovascular coupling |
| 0368 | CorrelationOfParameters | No | No | 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. |
| 0369 | SalicylicAcidClearance | No | No | 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. |
| 0370 | SWV | No | No | 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. |
| 0371 | DashRunGasReCirc | No | No | 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. |
| 0372 | RandomWalk2D | No | No | Random walk diffusion in two dimensions with choice of fixed step size, random step size, random direction and step size. |
| 0373 | SigmaPore | Yes | Yes | 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 |
| 0374 | FractionalBrownianMotionWalk | No | No | Generate a 2-D fractional Brownian motion walk using the the Davies-Harte algorithm. (see FGP, model 346 for details). |
| 0375 | MicroCircIllusoryCooperativity_1 | No | No | 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. |
| 0376 | MicroCircIllusoryCooperativity_2 | No | No | 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. |
| 0377 | SalicylateBodyMito | No | No | Aspirin and Salicylate circulate in the plasma and are converted to salicylurate in liver mitochondria prior to clearance, mainly as salicylurate. |
| 0379 | Baroreflex_SB_CT | No | No | Physiological model of the full baroreflex heart control system based on experimental measurements |
| 0380 | MPC, the semi-automated Modular Program Constructor | Yes | No | 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. |
| 0381 | Rxn_A_plus_B_to_C | No | No | Two solutes, A and B, reversibly react to form C. A + B C reaches equilibrium at the ratio A*B/C = Kd. |
| 0382 | Osm.coupledKK.1sol | No | No | 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. |
| 0383 | FEV_Maxwell | No | Yes | Models Forced Expiratory Volume procedure using the Maxwell one chamber viscoelastic compartment model taken from Bates (ch. 7) |
| 0384 | FEV_simple | No | Yes | Models Forced Expiratory Volume procedure using the linear one chamber compartment model taken from Bates (ch. 3) |
| 0385 | fgen | No | No | 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. |
| 0386 | AccessingJSimArrays | No | Yes | A 3 dimensional array is copied by a JSim procedure illustrating how array elements are addressed between JSim and Java. |
| 0387 | primes | No | No | 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. |
| 0388 | BR77pkDetect | No | No | Demonstrate peak detection using model of Cardiac Action Potential with Ca, K, and Na currents. Model from Beeler-Reuter 1977 paper. |
| 0389 | BinomialRandomNumbers | No | No | Generate Binomial random numbers. |
| 0390 | GeneralizedDistRandomNumbers | No | No | Generate random numbers using a general probability density function. |
| 0391 | BaroreceptorNeuron | No | No | A model of baroreceptor transduction of blood pressure |
| 0392 | FattyAcidBinding | No | No | Long chain fatty acid binding to human plasma albumin |
| 0393 | Comp1FlowReactionXa2Ua | No | No | In a single compartment with flow, substrates Xa (Xanthine) and Ua (Uric acid convert to each other. |
| 0394 | Comp1DecaySalicylicAcid | No | No | The half-life for ingestion of low, middle, and high concentrations of Salicylic acid are computed for three separate experiments. |
| 0395 | BarrerDiffusion | No | No | 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. |
| 0396 | Hund_Rudy_2004 | Yes | No | 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. |
| 0397 | GasSoly2017 | Yes | Yes | 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. |
| 0398 | Stabenau93_pKa | Yes | Yes | 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. |
| 0399 | SHbO2CO2_Dash2016 | Yes | No | 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. |
| 0400 | Tewari2016 | Yes | Yes | (Matlab) Dynamics of cross-bridge cycling, ATP hydrolysis, force generation, and deformation in cardiac muscle. |
| 0401 | Pradhan2016 | Yes | No | (Matlab) Model of open-loop (feed-forward) and feedback control of coronary blood flow during exercise, cardiac pacing, and pressure changes. |
| 0402 | Bazil2016 | Yes | No | (Matlab) Catalytic Coupling of Oxidative Phosphorylation, ATP Demand, and Reactive Oxygen Species Generation. |
| 0403 | Dash2008 | Yes | Yes | (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. |
| 0404 | Li2012 | Yes | Yes | (Matlab) Computational Model of Cellular Metabolic Dynamics in Skeletal Muscle Fibers during Moderate Intensity Exercise. |
| 0405 | RecircO2CO2BTEX_3CompLung | No | No | 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. |
| 0406 | OneEnzRandomBiBi | No | No | 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. |
| 0407 | ATPase_BISEN | No | No | Modeling ATP hydrolysis. |
| 0408 | ANT_BISEN | No | No | (Matlab) Adenine nucleotide translocator (ANT) |
| 0409 | Myokinase_BISEN | No | No | Adenylate Kinase reaction. Translated from BISEN generated model. |
| 0410 | AspartateTransferase_BISEN | No | No | Aspartate Aminotransferase reaction. Translated from BISEN generated model. |
| 0411 | MalateDehydrogenase_BISEN | No | No | Modeling the Malate dehydrogenase reaction. Translated from BISEN generated model. |
| 0412 | Fumarase_BISEN | No | No | Modeling the Fumarase reaction. Translated from BISEN generated model. |
| 0413 | SuccinateDehydrogenase_BISEN | No | No | Modeling the Succinate Dehydrogenase reaction. Translated from BISEN generated model. |
| 0414 | SuccinylCoaSynthetase_BISEN | No | No | Modeling the Succinyl-CoA Synthetase reaction. Translated from BISEN generated Matlab model. |
| 0415 | AlphaKetogluterateDehydrogenase_BISEN | No | No | Modeling the Alpha-Ketogluterate Dehydrogenase reaction. Translated from BISEN generated Matlab model. |
| 0416 | IsocitrateDehydrogenase_BISEN | No | No | Modeling the Isocitrate Dehydrogenase reaction. Translated from BISEN generated Matlab model. |
| 0417 | Aconitase_BISEN | No | No | Modeling the Aconitase reaction. Translated from BISEN generated Matlab model. |
| 0418 | CitrateSynthase_BISEN | No | No | Modeling the Citrate Synthase reaction. Translated from BISEN generated Matlab model. |
| 0419 | PyruvateDehydrogenase_BISEN | No | No | Modeling the Pyruvate Dehydrogenase reaction. Translated from BISEN generated Matlab model. |
| 0420 | HoogAntink2017 | Yes | No | (Matlab) A synthesizer framework for multimodal cardiorespiratory signals. Model from Hoog Antink et. al. 2017 paper. |
| 0421 | RationalExp | No | No | 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. |
| 0422 | Xa_Gentex_MID | No | Yes | 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). |
| 0423 | Linear.Reaction.Sequence | No | No | 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. |
| 0424 | MM.Reaction.Sequence | No | No | 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). |
| 0425 | MM.Lag.Reaction.Sequence | No | No | 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). |
| 0426 | React.Seq.FullEnzKinetics | No | No | 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. |
| 0428 | Hexokinase_KA | No | No | 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. |
| 0429 | AlvCapExch | No | No | 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. |
| 0430 | Equil2bind | No | No | 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. |
| 0431 | FAbt20.1site | No | No | Axially distributed 2-region capillary-tissue exchange operator for Albumin binding fatty acid at a particular binding site. |
| 0432 | AlvCapExchBind | No | No | 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. |
| 0433 | AlvCapExchBuff | No | No | 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. |
| 0434 | BTEX2006_Updated | No | No | 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. |
| 0435 | Transdermal ethanol transport, Ethanol diffusion through the skin | Yes | No | Describes the diffusion of ethanol from the skin capillaries, through the epidermis and stratum corneum and into the supradermal space of the detector. Ethanol enters the capillary bed at a rate Qdot (ml/s) and blood alcohol concentration (BAC(t)). Based directly on paper “A New Approach to Modeling Transdermal Ethanol Kinetics”, Joseph C Anderson, 2024. |