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Cardiovascular Models

All models posted from www.physiome.org can be run over the web, or downloaded and run on on your own computers. Source code is open and free.

Electrophysiology Models

Hodgkin_Huxley1952. Model # 0155. Nerve action potential for squid giant axon. (Open source code) Quantitative model of time- and voltage-dependent transmembrane currents for Na+, K+, and a leak current, Ileak. Run model at: http://physiome.org/jsim/models/webmodel/NSR/Hodgkin_Huxley1952/. Centerpiece for Nobel prize. One of the few reproducible papers in the published literature. (Hodgkin AL and Huxley AF. A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117: 500-544, 1952.). The classic.

BeelerReuter77. Model # 0078. Cardiac Action Potential with Ca, K, and Na currents. (Open source code) Run model at: http://physiome.org/jsim/models/webmodel/NSR/BeelerReuter77/. (Beeler GW Jr and Reuter H. Reconstruction of the action potential of ventricular myocardial fibres. J Physiol (Lond) 268: 177-210, 1977.) Provides Na, Ca, and K currents for canine cardiac action potential. Predicts responses to ionic currents during voltage clamp of ventricular muscle fibers. Lacks details of other cardiac ionic fluxes.

Luo-Rudy 1994-. Model # 0165. The Modified Luo-Rudy Dynamic Model of the Mammalian Ventricular Myocyte. (Open source code) Run model at: http://physiome.org/jsim/models/webmodel/NSR/Luo-Rudy/. From Luo CH, Rudy Y.; A dynamic model of the cardiac ventricular action potential. II. Afterdepolarizations, triggered activity, and potentiation, Circ Res 1994;74:1097-1113 and improved frequently through 2000 with the publication of Faber GM, Rudy Y.; Action potential and contractility changes in [Na(+)](i) overloaded cardiac myocytes: a simulation study. Biophy J 2000;78:2392-2404. Originating as a guinea pig ventricular myocyte model it has taken on more generality.

Demir99 SA Node. Model # 0314. Single cell action potential of rabbit sinoatrial node modulated by acetyl choline. (Open source code.) Run model at: http://physiome.org/jsim/models/webmodel/NSR/Demir99/ ( Demir, Semahat S., John W. Clark, and Wayne R.Giles. Parasympathetic modulation of sinoatrial node pacemaker activity in rabbit heart: a unifying model. Am J Physiol Heart Circ 276: H2221-H2244, 1999. Channel-based representation of ionic currents and action potential in pacemaker cells.

Winslow_Rice_Jafri1999. Model # 0217. Models 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. (Open source code) Run model at: http://physiome.org/jsim/models/webmodel/NSR/Winslow_Rice_Jafri1999/. Predicts action potential of heart cell under wide range of ionic concentration changes, heart, rate, temperature and serves as test base for pharmacologic interventions. (This model was reproduced in collaboration with the author prior to publication, courtesy of the Am Heart Assoc.)

Modified Michailova_McCulloch2001. Model # 0167. The model extends the Winslow Jaffri Rice model by adding the buffering by MgATP and MgADP as well as by calmodulin (Michailova A. and McCulloch A.; Model study of ATP and ADP buffering, transport of Ca(2+) and Mg(2+), and regulation of ion pumps in ventricular myocyte. Biophys J. 2001 Aug, 81:614-29.) It has been further modified by Bassingthwaighte and Sachs to add a stretch channel, Istr, assuming passive flux of cation with a reversal potential Estr, taken to be between -20 and 0 mV, and a conductance not dependent on time or voltage, but dependent on length of sarcomere. See Vetter and McCulloch 2001. (Open source code.) Run model at: http://physiome.org/jsim/models/webmodel/NSR/Michailova_McCulloch2001/. This model accounts for intracellular ionic buffering, which has a large effect on stabilizing the ionic driving forces.

ten_Tusscher_Noble_Panfilov2004. Model # 0201. This model simulates the action potential for a human ventricular myocyte accounting for Na, K and Ca transport and dynamics. (From ten Tusscher KHWJ, Noble D, Noble PJ and Panfilov AV. A model for human ventricular tissue, Am J Physiol 286:H1573-H1589, 2004.) (Open source code.) Run model at: http://physiome.org/jsim/models/webmodel/NSR/ten_Tusscher_Noble_Panfilov2004/ Based on a modification of the Luo-Rudy model (1994-2002).

Cardiovascular Mechanics

Zinemanas1994_CoronaryCirc. Model # 0128 (Open source code.) Run model at https://www.physiome.org/jsim/models/webmodel/NSR/Zinemanas1994_Coronar…. 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. Model accounts for systolic compression with cardiac contraction. Useful for assessing MRI or ultrasound measures of coronary arterial velocities.

Rideout 1991 PressureFlowLH. Model # 0336 Left ventricle (only) and systemic arteries pressure-flow model ported from Rideout's book, RIdeout VC. Mathematical and computer Modeling of Physiological Systems. Englewood Cliffs, NJ: Prentice Hall 1991. (Open source code.) Run over web at http://physiome.org/jsim/models/webmodel/NSR/Rideout_PressureFlowLH/ using JSim's MML Also available in ACSL programs LH-PF and in MATLAB. Provides varying elastance presentation of cardiac contraction and ejection fraction and evolution of pressures and flows in elastic aorta.

Systemic_Circulation_Olansen_et_al_2000. Model #224. A lumped-parameter model of the systemic circulation. Run model at http://physiome.org/jsim/models/webmodel/NSR/Systemic_Circulation_Olansen_et_al_2000/ A chopped-sine left ventricle pressure signal drives flow through the system. (Open Source code.) Illustrates pulse pressure amplification (increasing peak minus end-diastolic arterial pressure) with increasing distance along the artery.

HighlyIntegHuman, Model # 0153. 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 exchange, blood gas handling, coronary circ, and peripheral chemoreceptors. Run model at http://physiome.org/jsim/models/webmodel/NSR/HighlyIntegHuman/. (From Neal ML and Bassingthwaighte JB. Subject-specific model estimation of cardiac output and blood volume during hemorrhage. Cardiovasc Eng 7: 97-120, 2007). About 240 varaailes, 2600 lines of MML code. Basic cardiorespiratory mechanics model suitable for adding neural and hormonal regulation.

HighlyIntHuman_wIntervention. Model # 0154. 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. Accounts for 9 different structural injuries and 5 other disordered states. Run model at http://physiome.org/jsim/models/webmodel/NSR/HighlyIntHuman_wIntervention/. Predicts responses to 14 acute changes in structure or physical interventions.

Cardiovascular Transport

HbO2_HbCO2_dissociation. Model # 0149. Blood HbO2 and HbCO2 Dissociation Curves at Varied O2, CO2, pH, 2,3-DPG and Temperature Levels. Run model at http://physiome.org/jsim/models/webmodel/NSR/HbO2_HbCO2_diss/ (From Dash RK and Bassingthwaighte JB. Erratum to: Blood HbO] and HbCO2 dissociation curves at varied O2, CO2, pH, 2,3-DPG and Temperature Levels. Ann Biomed Eng 38(4): 1683-1701, 2010.) Provides state of blood oxygenation over widest physiological ranges of conditions using computationally efficient code centered on an invertible Hill-type equation. Used to understand gas exchange in anesthesia, altitude and temperature changes in clinic or external environment.

Exchange_O2_CO2_HCO3_and_H. Model # 0134. Four region, distributed model for the O2-CO2 transport, exchange and metabolism. (Open source code) (From Dash RK, Li Z, and Bassingthwaighte JB. Simultaneous blood-tissue exchange of oxygen, carbon dioxide, bicarbonate, and hydrogen ion. Ann Biomed Eng 34: 1129-1148, 2006.) Run model at http://physiome.org/jsim/models/webmodel/NSR/Exchange_O2_CO2_HCO3_and_H. Uses Model 149 for gas equilibration in blood in the context of gas exchanges in alveoli and in body tissues. The speedy computation allows accounting for spatial gradients along capillaries in lung and in tissue. Predicts state of tissue oxygenation, pH, PCO2 and PO2 dependent on ventilation and on cardiac performance.

Cancer Models

Breast

Prostate

Neuro Models

Neocortical

Model of oscillation generation in neocortex

Hippocampal

Oscillations and ketamine effects in a CA3 model

Spinal Cord

Central Pattern Generators

Musculoskeletal Models

Open Knee: A Three-Dimensional Finite Element Representation of the Knee Joint: Project Site: https://simtk.org/home/openknee; Download: Please follow the Downloads link at the project site to access openknee_v1-0-1.zip, login will be required for tracking of download statistics. SimTk registration is available to anyone through https://simtk.org/account/register.php.; Package Contents: Data files (geometry, IGES; MRI, DICOM; mesh, text based), Documentation, Source files (Python scripts, FEBio model, XML), Solution files (sample simulation of passive knee flexion); Documentation: https://simtk.org/websvn/wsvn/openknee/doc/guide.pdf; Additional Requirements: Updating the model requires free and open source Python programming language (http://www.python.org), running finite element analysis requires academic free and open source FEBio (http://mrl.sci.utah.edu/software).; Notes:; ErdemirA 08:40, 4 February 2013 (EST) This is an example model from our research program. Simulations using this model have predictive capacity of tibiofemoral joint response (kinematic-kinetic) and tissue stress-strains. Credibility is questionable, i.e., validity of the model to represent population or subject-specific kinematics-kinetics response of the tibiofemoral joint and tissue deformation metrics is not established. Yet, the model is a unique example of organ scale finite element representations in terms of its accessibility.

Template for Model Indexing

The Model and Data Sharing Working Group proposes this template for new contributions to this index. Our goal is to collect searchable, useful information for many more models from MSM members. We have kept the template simple in order to encourage its use. Your suggestions are welcome. --MoodyG 11:36, 2 May 2013 (EDT)

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