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NSR Physiome course: August 23-27, 2010, University of Washington

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JSim CellML Models Page

This page allows users to run models from the CellML model archive under JSim. To run these models online, you must have a Java plugin installed in your WWW browser. To run them in JSim on your own computer, download the model code and the JSim application. Either way, see Running JSim for instructions on how to use JSim. Since CellML models do not specify simulation time length or delta, these must be set by the user before running the model.

Users are strongly advised to read Running CellML Models under JSim before running CellML models under JSim. The warning icon indicates that a unit conversion has been turned off because the model does not satisfy JSim unit balance.

Terms of use

Currently available models

A Primer on Modular Mass Action Modelling with CellML

Adrian, Chandler, Hodgkin, 1970
Voltage clamp experiments in striated muscle fibres

Aguda, 1999
A quantitative analysis of the kinetics of the G2 DNA damage checkpoint system

Aguda, Tang, 1999
The kinetic origins of the restriction point in the mammalian cell cycle

Albrecht, Colegrove, Friel, 2002
Differential Regulation of ER Ca2+ Uptake and Release Rates Accounts for Multiple Modes of Ca2+-induced Ca2+ Release

Albrecht, Colegrove, Hongpaisan, Pivovarova, Andrews, Friel, 2001
Multiple Modes of Calcium-induced Calcium Release in Sympathetic Neurons I: Attenuation of Endoplasmic Reticulum Ca2+ Accumulation at Low [Ca2+]i during Weak Depolarisation

Aon, Cortassa, 2002
Coherent and robust modulation of a metabolic network by cytoskeletal organization and dynamics

Aslanidi, Boyett, Dobrzynski, Li, Zhang, 2009
Mechanisms of transition from normal to reentrant electrical activity in a model of rabbit atrial tissue: interaction of tissue heterogeneity and anisotropy

Aslanidi, Stewart, Boyett, Zhang, 2009
Optimal velocity and safety of discontinuous conduction through the heterogeneous Purkinje-ventricular junction

Asthagiri, Lauffenburger, 2001
A Compuational Study of Feedback Effects on Signal Dynamics in a Mitogen-Activated Protein Kinase (MAPK) Pathway Model

Bagci, Vodovotz, Billiar, Ermentrout, Bahar, 2006
Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores

Bagci, Vodovotz, Billiar, Ermentrout, Bahar, 2008
Computational insights on the competing effects of nitric oxide in regulating apoptosis

Bakker, Mensonides, Teusink, van Hoek, Michels, Westerhoff, 2000
Compartmentation protects trypanosomes from the dangerous design of glycolysis

Bakker, Michels, Opperdoes, Westerhoff, 1997
Glycolysis in Bloodstream Form Trypanosoma brucei Can Be Understood in Terms of the Kinetics of the Glycolytic Enzymes

Barberis, Klipp, Vanoni, Alberghina, 2007
Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network

Baylor, Hollingworth, Chandler, 2002
Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog

Beard, 2005
A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation

Beeler, Reuter, 1977
Reconstruction of the action potential of ventricular myocardial fibres

Ben-Tal, 2006
Simplified models for gas exchange in the human lungs

Benson, Aslanidi, Zhang, Holden, 2008
The canine virtual ventricular wall: a platform for dissecting pharmacological effects on propagation and arrhythmogenesis

Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002
A computationally efficient electrophysiological model of human ventricular cells

Bertram, Arnot, Zamponi, 2002
Role for G protein G-beta-gamma isoform specificity in synaptic signal processing: a computational study

Bertram, Pedersen, Luciani, Sherman, 2006
A simplified model for mitochondrial ATP production

Bertram, Previte, Sherman, Kinard, Satin, 2000
The Phantom Burster Model for Pancreatic Beta Cells

Bertram, Satin, Pedersen, Luciani, Sherman, 2007
Intra- and inter-islet synchronization of metabolically driven insulin secretion

Bertram, Satin, Zhang, Smolen, Sherman, 2004
Calcium and Glycolysis Mediate Multiple Bursting Modes in Pancreatic Islets

Bertram, Sherman, 2004
A Calcium-based Phantom Bursting Model for Pancreatic Islets

Bertram, Smolen, Sherman, Mears, Atwater, Martin, Soria, 1995
A role for calcium release-activated current (CRAC) in cholinergic modulation of electrical activity in pancreatic beta-cells

Bhalla, Iyengar, 1999
Emergent Properties of Networks of Biological Signaling Pathways

Bindschadler, Sneyd, 2001
A Bifurcation Analysis of Two Coupled Calcium Oscillators

Bingzheng, Zhenye, Liansong, 1990
A mathematical model of the regulation system of the secretion of glucocorticoids

Bondarenko, Szigeti, Bett, Kim, Rasmusson, 2004
Computer model of action potential of mouse ventricular myocytes

Bonhoeffer, Rembiszewski, Ortiz, Nixon, 2000
Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection

Borghans, Dupont, Goldbeter, 1997
Complex intracellular calcium oscillations. A theoretical exploration of possible mechanisms

Bornheimer, Maurya, Farquhar, Subramaniam, 2004
Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction

Boyett, Zhang, Garny, Holden, 2001
Control of the pacemaker activity of the sinoatrial node by intracellular Ca2+. Experiments and modelling

Brightman, Fell, 2000
Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells.

Brown, Choe, Shanahan, Czeisler, 1997
A mathematical model of diurnal variations in human plasma melatonin levels

Bueno, 2007
Mathematical modeling and spectral simulation of genetic diseases in the human heart

Bugbuster Systems Model

Butera, Rinzel, Smith, 1999
Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. I. Bursting Pacemaker Neurons

Calzone, Thieffry, Tyson, Novak, 2007
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

Campbell, Chandra, 2006
Functions of Stretch Activation in Heart Muscle

Cartwright, Husain, 1986
A model for the control of testosterone secretion

Chang, Fujita, 1999
A numerical model of the renal distal tubule

Chang, Fujita, 1999
A kinetic model of the thiazide-sensitive Na-Cl cotransporter

Chang, Fujita, 2001
A numerical model of acid-base transport in rat distal tubule

Chassagnole, Rais, Quentin, Fell, Mazat, 2001
An integrated study of Threonine-pathway enzyme kinetics in Escherichia coli

Chay, 1997
Effects of extracellular calcium on electrical bursting and intracellular and luminal calcium oscillations in insulin secreting pancreatic beta-cells

Chay, Lee, Fan, 1995
Appearance of Phase-locked Wenchbach-like Rhythms, Devil's Staircase and Universality in Intracellular Calcium Spikes in Non-excitable Cell Models

Chen, Calzone, Csikasz-Nagy, Cross, Novak, Tyson, 2004
Integrative Analysis of Cell Cycle Control in Budding Yeast

Chen, Csikasz-Nagy, Gyorffy, Val, Novak, Tyson, 2000
Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle

Chen, Popel, 2006
Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells

Chen, Popel, 2007
Vascular and perivascular nitric oxide release and transport: biochemical pathways of neuronal nitric oxide synthase (NOS1) and endothelial nitric oxide synthase (NOS3)

Cheng, Brown, Loeb, 2000
Virtual muscle: a computational approach to understanding the effects of muscle properties on motor control

Ciliberto, Novak, Tyson, 2003
Mathematical Model of the Morphogenesis Checkpoint in Budding Yeast

Ciliberto, Petrus, Tyson, Sible, 2003
A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus

Ciliberto, Tyson, 2000
Mathematical Model for Early Development of the Sea Urchin Embryo

Clancy, Rudy, 2001
Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death

Clancy, Rudy, 2002
Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism

Cloutier, Bolger, Lowry, Wellstead, 2009
An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements

Cloutier, Wellstead, 2009
The control systems structures of energy metabolism

Colegrove, Albrecht, Friel, 2000
Quantitive Analysis of Mitochondrial Ca2+ Uptake and Release Pathways in Sympathetic Neurons Reconstruction of the Recovery after Depolarisation-evoked [Ca2+] Elevations

Cooling, Hunter, Crampin, 2008

Cooling, Hunter, Crampin, 2009. Dual Calcium Protocol

Cooling, Hunter, Crampin, 2009. Shen Calcium Protocol

Cooling, Hunter, Crampin, 2009. Tomida Calcium Protocol

Corrias, Buist, 2007
A quantitative model of gastric smooth muscle cellular activation

Corrias, Buist, 2008
Quantitative cellular description of gastric slow wave activity

Cortassa, Aon, Marban, Winslow, O'Rourke, 2003
An Integrated Model of Cardiac Mitrochondrial Energy Metabolism and Calcium Dynamics

Cortassa, Aon, Winslow, O'Rourke, 2004
A mitochondrial oscillator dependent on reactive oxygen species

Costa, Holmes, McCulloch, 2001
Modelling Cardiac Mechanical Properties In Three Dimensions

Courtemanche, Ramirez, Nattel, 1998
Ionic mechanisms underlying human atrial action potential properties: insights from a mathematical model

Creating a Systems Model from SVPs - a Tutorial

Cronwright, Rohwer, Prior, 2002
Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae

Csikasz-Nagy, Battogtokh, Chen, Novak, Tyson, 2006
Analysis of a generic model of eukaryotic cell-cycle regulation: budding yeast taken from the original model code

Cui, Kaandorp, 2006
Mathematical modeling of calcium homeostasis in yeast cells

Cui, Kaandorp, 2008
Simulating Complex Calcium-Calcineurin Signaling Network

Cui, Kaandorp, Lloyd, 2008
Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli

Curien, Ravanel, Dumas, 2003
A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana

Dash, Bassingthwaighte, 2004
Blood HbO2 and HbCO2 dissociation curves at varied O2, CO2, pH, 2,3-DPG and temperature levels

Dawson, Lea, Irvine, 2003
Kinetic model of the inositol trisphosphate receptor that shows both steady-state and quantal patterns of Ca2+ release from intracellular stores

De Paor, Timmons, 1986
A feedback oscillator model for circulatory autoregulation

De Vries, Sherman, 2000
Channel Sharing in Pancreatic Beta-Cells Revisited: Enhancement of Emergent Bursting by Noise

De Vries, Sherman, 2001
From Spikers to Bursters Via Coupling: Help from Heterogeneity

De Young, Keizer, 1992
A single-pool inositol 1,4,5-triphosphate-receptor-based model for agonist-stimulated oscillations in Ca 2+ concentration

Decker, Heijman, Silva, Hund, Rudy, 2009
Properties and ionic mechanisms of action potential adaptation, restitution, and accommodation in canine epicardium

Demir, Clark, Giles, 1999
Parasympathetic modulation of sinoatrial node pacemaker activity in rabbit heart: a unifying model

Demir, Clark, Giles, Murphey, 1994
A Mathematical Model of a Rabbit Sinoatrial Node Cell

Demiray, 1981
Large deformation analysis of some soft biological tissues

Dempsher, Gann, Phair, 1984
A mechanistic model of ACTH-stimulated cortisol secretion

DiFrancesco, Noble, 1985
A Model of Cardiac Electrical Activity Incorporating Ionic Pumps and Concentration Changes

Dixit, Perelson, 2004
Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay

Dokos, Celler, Lovell, 1996
Ion currents underlying sinoatrial node pacemaker activity: a new single cell mathematical model

Dougherty, Wright, Yew, 2005
Computational model of the cAMP-mediated sensory response and calcium-dependent adaptation in vertebrate olfactory receptor neurons

Drouhard, Roberge, 1987
Revised formulation of the Hodgkin-Huxley representation of the sodium current in cardiac cells

Dumaine, Towbin, Brugada, Vatta, Nesterenko, Nesterenko, Brugada, Brugada, Antzelevitch, 1999
Ionic mechanisms responsible for the electrocardiographic phenotype of the Brugada Syndrome are temperature dependent

Dupont, Berridge, Goldbetter, 1991
Signal-induced Ca2+ oscillations: Properties of a model based on (Ca2+)-induced Ca2+ release

Dupont, Goldbeter, 1992
Protein phosphorylation driven by intracellular calcium oscillations: A kinetic analysis

Earm, Noble, 1990
A Model of the Single Atrial Cell: Relation between Calcium Current and Calcium Release

Ebihara, Johnson, 1980
Fast sodium current in cardiac muscle: A quantitative description

Egli, Bertram, Sellix, Freeman, 2004
Rhythmic secretion of prolactin in rats: action of oxytocin coordinated by vasoactive intestinal polypeptide of suprachiasmatic nucleus origin

ElectrEcoBlu Systems Model

Elowitz, Leibler, 2000
A Synthetic Oscillatory Network of Transciptional Regulators

Enciso, Sontag, 2004
On the stability of a model of testosterone dynamics

Endresen, 1996
Chaos in Weakly-coupled Pacemaker Cells

Eskandari, Wright, Loo,
Kinetics of the Reverse Mode of the Na+/Glucose Cotransporter

Espinosa, 1998
L'Echange Na+ /Ca2+ dans l'Hypertrophie Ventriculaire D'Altitude chez le Rat: Etude Electrophysiologique et Utilisation du Modele "Oxsoft Heart"

Evans, Errington, Shelly, Feeney, Chapman, Godfrey, Smith, Chappell, 2004
A mathematical model for the in vitro kinetics of the anti-cancer agent topotecan

Faber, Rudy, 2000
Action potential and contractility changes in [Na(+)](i) overloaded cardiac myocytes: a simulation study.

Fall, Keizer, 2001
Mitochondrial Modulation of Intracellular Ca2+ Signalling

Fallon, Lauffenburger, 2000
Computational Model for Effects of Ligand/Receptor Binding Properties on Interleukin-2 Trafficking Dynamics and T Cell Proliferation Response

Farhy, Bowers, Veldhuis, 2007
Model-projected mechanistic bases for sex differences in growth hormone regulation in humans.

Favile, Pullan, Sanders, Koh, Lloyd, Smith, 2009
Biophysically based mathematical modeling of interstitial cells of Cajal slow wave activity generated from a discrete unitary potential basis

Faville, Pullan, Sanders, Smith, 2008
A Biophysically Based Mathematical Model of Unitary Potential Activity in Interstitial Cells of Cajal

Fenton, Karma, 1998
Vortex dynamics in three-dimensional continuous myocardium with fiber rotation: Filament instability and fibrillation

Fink, Noble, Virag, Varro, Giles, 2008
Contributions of HERG K+ current to repolarization of the human ventricular action potential

Fink, Slepchenko, Loew, 1999
Determination of time-dependent inositol-1,4,5-triphosphate concentrations during calcium release in a smooth muscle cell

Fink, Slepchenko, Moraru, Watras, Schaff, Loew, 2000
An image-based model of calcium waves in differentiated neuroblastoma cells

Fitzhugh, 1961
Impulses and Physiological States in Theoretical Models of Nerve Membrane

Flynn, Green, Pedley, Boxer, Dearling, Watson, Boden, Begent, 2002
A Model-Based Approach for the Optimization of Radioimmunotherapy through Antibody Design and Radionuclide Selection

Fohlmeister, Miller, 1997
Impulse Encoding Mechanisms of Ganglion Cells in the Tiger Salamander Retina

Fox, McHarg, Gilmour, 2002
Ionic mechanism of electrical alternans

Fridlyand, Tamarina, Philipson, 2003
Modeling of Ca2+ flux in pancreatic beta-cells: role of the plasma membrane and intracellular stores

Friel, 1995
[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model

Gall, Susa, 1999
Effect of Na/Ca Exchange on Plateau Fraction and [Ca]i in Models for Bursting in Pancreatic Beta-Cells

Gardner, Dolnik, Collins, 1998
A theory for controlling cell cycle dynamics using a reversibly binding inhibitor

Garny, Kohl, Hunter, Boyett, Noble, 2003
One-dimensional Rabbit Sinoatrial Node Models: Benefits and Limitations

Gasser, Ogden, Holzapfel, 2006
Hyperelastic modelling of arterial layers with distributed collagen fibre orientations

Gilbert, Heiner, Rosser, Fulton, Gu, Trybilo, 2007
A Case Study in Model-driven Synthetic Biology

Goforth, Bertram, Khan, Zhang, Sherman, Satin, 2002
Calcium-activated K+ Channels of Mouse Beta Cells are Controlled by Both Store and Cytoplasmic Ca2+: Experimental and Theoretical Studies

Goldbeter,
A model for the dynamics of human weight cycling

Goldbeter, 1991
A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase

Goldbeter, 1995
A model for circadian oscillations in the Drosophila period protein (PER)

Goldbeter, Dupont, Berridge, 1990
Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation

Goldbeter, Pourquie, 2008
Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways

Gonzalez-Heydrich, Steingard, Kohane, 1994
A computer simulation of the hypothalamic-pituitary-adrenal axis

Goodwin, 1965
Oscillatory behavior in enzymatic control processes

Grandi, Pasqualini, Bers, 2009
A novel computational model of the human ventricular action potential and Ca transient

Grange, Holford, Guentert, 2001
A pharmacokinetic model to predict the PK interaction of L-dopa and benserazide in rats

Greenstein, Wu, Po, Tomaselli, Winslow, 2000
Role of the Calcium-Independent Transient Outward Current Ito1 in Shaping Action Potential Morphology and Duration

Grossman, Feinberg, Kuznetsov, Dimitrov, Paul, 1998
HIV infection: how effective is drug combination treatment?

Guccione, McCulloch, Waldman, 1991
Passive Material Properties of Intact Ventricular Myocardium Determined From a Cylindrical Model

Gupta, Aslakson, Gurbaxani, Vernon, 2007
Inclusion of the glucocorticoid receptor in a hypothalamic pituitary adrenal axis model reveals bistability

Gupta, Maurya, Stephens, Dennis, Subramaniam, 2009
An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis

Guyton, Aldosterone, 2008
Description of Guyton aldosterone module

Guyton, Angiotensin, 2008
Description of Guyton angiotensin module

Guyton, Antidiuretic Hormone, 2008
Description of Guyton antidiuretic hormone module

Guyton, Atrial Natriuretic Peptide, 2008
Description of Guyton atrial natriuretic peptide module

Guyton, Autonomics, 2008
Description of Guyton autonomics module

Guyton, Capillary Dynamics, 2008
Description of Guyton capillary dynamics module

Guyton, Cardiovascular, Circulation, 2008
Description of Guyton 1992 Full Cardiovascular Circulation Model

Guyton, Circulatory Dynamics, 2008
Description of Guyton circulatory dynamics module

Guyton, Electrolytes, 2008
Description of Guyton electrolytes module

Guyton, Heart Hypertrophy or Deterioration, 2008
Description of Guyton heart hypertrophy or deterioration module

Guyton, Heart Rate and Stroke Volume, 2008
Description of Guyton heart rate and stroke volume module

Guyton, Kidney, 2008
Description of Guyton kidney module

Guyton, Muscle Blood Flow Control, 2008
Description of Guyton muscle blood flow control module

Guyton, Muscle Oxygen Delivery, 2008
Description of Guyton muscle oxygen delivery module

Guyton, Non-Muscle Blood Flow, 2008
Description of Guyton non-muscle local blood flow control module

Guyton, Non-Muscle Oxygen Delivery, 2008
Description of Guyton non-muscle oxygen delivery module

Guyton, Pulmonary Fluid Dynamics, 2008
Description of Guyton pulmonary fluid dynamics module

Guyton, Pulmonary Oxygen Uptake, 2008
Description of Guyton pulmonary oxygen uptake module

Guyton, Red Cells and Viscosity, 2008
Description of Guyton red cells and viscosity module

Guyton, Stress Relaxation, 2008
Description of Guyton stress relaxation module

Guyton, Thirst, Drinking and Salt Appetite, 2008
Description of guyton thirst, drinking and salt appetite module

Guyton, Volume Receptors, 2008
Description of Guyton volume receptors module

Halloy, Bernard, Loussouarn, Goldbeter, 2002
The Follicular Automaton Model: Effect of Stochasticity and of Synchronization of Hair Cycles

Hatakeyama, Shirouzu, Yokoyama, Konagaya, Kimura, Naka, Kawasaki, Yumoto, Ichikawa, Kim, Saito, Saeki, 2003
A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling

Hatzimanikatis, Lee, Bailey, 1999
A mathematical description of regulation of the G1-S transition of the mammalian cell cycle

Haugh, 2004
Mathematical model of human growth hormone (hGH)-stimulated cell proliferation explains the efficacy of hGH variants as receptor agonists or antagonists

Heinze, Keener, Midgley, 1998
A mathematical model of luteinizing hormone release from ovine pituitary cells in perifusion

Heldt, Shim, Kamm, Mark, 2002
Computational modeling of cardiovascular response to orthostatic stress

Herz, Bonhoeffer, Anderson, May, Nowak, 1996
Viral Dynamics in vivo: Limitations on estimates of intracellular delay and virus decay

Heyd, Drew, 2003
A mathematical model for elongation of a peptide chain

Hilgemann, Noble, 1987
Excitation-contraction coupling and extracellular calcium transients in rabbit atrium: reconstruction of basic cellular mechanisms

Hinch, Greenstein, Tanskanen, Xu, Winslow, 2004
A Simplified Local Control Model of Calcium-Induced Calcium Release in Cardiac Ventricular Myocytes

Hodgkin, Huxley, 1952
A quantitative description of membrane current and its application to conductance and excitation in nerve

Hoefnagel, Starrenburg, Martens, Hugenholtz, Kleerebezem, Van Swam, Bongers, Westerhoff, Snoep, 2002
Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis

Holmes, 2006
Teaching from classic papers: Hill's model of muscle contraction

Hornberg, Binder, Bruggeman, Schoeberl, Heinrich, Westerhoff, 2005
Control of MAPK signalling: from complexity to what really matters

Huang, Ferrell, 1996
Ultrasensitivity in the mitogen-activated protein kinase cascade

Hund, Rudy, 2004
Rate dependence and regulation of action potential and calcium transient in a canine cardiac ventricular cell model

Hunter, McCulloch, ter Keurs, 1998
Modelling the mechanical properties of cardiac muscle

Hunter, McNaughton, Noble, 1975
Analytical models of propagation in excitable cells

Hunter, Smaill, Hunter, 1995
A pole-zero constitutive law for myocardium

Hynne, Dano, Sorensen, 2001
Full-scale model of glycolysis in Saccharomyces cerevisiae

Iancu, Jones, Harvey, 2007
Compartmentation of cAMP signaling in cardiac myocytes: a computational study

Iber, Maini, 2002
A Mathematical Model for Germinal Centre Kinetics and Affinity Maturation

Inada, Hancox, Zhang, Boyett, 2009
One-dimensional mathematical model of the atrioventricular node including atrio-nodal, nodal, and nodal-his cells

International SI Units, 2006
International SI Units, 2006

Iribe, Kohl, Noble, 2006
Modulatory effect of calmodulin-dependent kinase II (CaMKII) on sarcoplasmic reticulum Ca2+ handling and interval-force relations: a modelling study.

Irvine, Jafri, Winslow, 1999
Cardiac sodium channel Markov model with temperature dependence and recovery from inactivation

Itskov, Ehret, Mavrilas, 2006
A Polyconvex Anisotropic Strain-Energy Function for Soft Collagenous Tissues

Iyer, Hajjar, Armoundas, 2007
Mechanisms of Abnormal Calcium Homeostasis in Mutations Responsible for Catecholaminergic Polymorphic Ventricular Tachycardia

Iyer, Mazhari, Winslow, 2004
A computational model of the human left-ventricular epicardial myocyte

Izakov, Katsnelson, Blyakhman, Markhasin, Shkylar, 1991
Cooperative Effects Due to Calcium Binding by Troponin and Their Consequences for Contraction and Relaxation of Cardiac Muscle Under Various Conditions of Mechanical Loading

Jafri, Rice, Winslow, 1998
Cardiac Ca2+ Dynamics: The Roles of Ryanodine Receptor Adaptation and Sarcoplasmic Reticulum Load

Jelic, Cupic, Kolar-Anic, 2005
A Hypothalamic-Pituitary-Adrenal System Model: Full Model

Joseph, Zavros, Merchant, Kirschner, 2003
A model for integrative study of human gastric acid secretion

Karagiannis, Popel, 2004
A theoretical model of type I collagen proteolysis by matrix metalloproteinase (MMP) 2 and membrane type 1 MMP in the presence of tissue inhibitor of metalloproteinase 2

Karagiannis, Popel, 2006
Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: insights from a computational model

Katsnelson, Nikitina, Chemla, Solovyova, Coirault, Lecarpentier, Markhasin, 2004
Influence of viscosity on myocardium mechanical activity: a mathematical model

Keener, 2001
Diffusion Induced Oscillatory Insulin Secretion

Keizer, Levine, 1996
Ryanodine Receptor Adaptation and Ca2+-Induced Ca2+ Release-Dependent Ca2+ Oscillations

Kesmir, De Boer, 1999
A Mathematical Model on Germinal Center Kinetics and Termination

Kholodenko, Demin, Moehren, Hoek, 1999
Quantification of short term signalling by the epidermal growth

Kirschner, Panetta, 1998
Modeling immunotherapy of the tumor-immune interaction

Kirschner, Webb, 1996
A Model For Treatment Strategy In The Chemotherapy Of AIDS

Kneller, Ramirez, Chartier, Courtemanche, Nattel, 2002
Time-dependent transients in an ionically based mathematical model of the canine atrial action potential

Koivumaki, Takalo, Korhonen, Tavi, Weckstrom, 2009
Modelling Sarcoplasmic Reticulum Calcium APTase and its Regulation in Cardiac Myocytes

Komarova, Wodarz, 2003
Evolutionary Dynamics of Mutator Phenotypes in Cancer: Implications for Chemotherapy

Kongas, van Beek, 2001
Creatine kinase in energy metabolic signaling in muscle

Korzeniewski, Zoladz, 2001
A model of oxidative phosphorylation in mammaliam skeletal muscle

Kroll, 2000
Parathyroid hormone temporal effects on bone formation and resorption

Kurata, Hisatome, Imanishi, Shibamoto, 2002
Dynamical description of sinoatrial node pacemaking: improved mathematical model for primary pacemaker cell

Kyrylov, Severyanova, Vieira, 2005
Modeling robust oscillatory behavior of the hypothalamic-pituitary-adrenal axis

Lambeth, Kushmerick, 2002
A computational model for glycogenolysis in skeletal muscle

Landesberg, Sideman, 1994
Mechanical regulation of cardiac muscle by coupling calcium kinetics with cross-bridge cycling: a dynamic model

LeBeau, Robson, McKinnon, Donald, Sneyd, 1997
Generation of Action Potentials in a Mathematical Model of Corticotrophs

LeBeau, Yule, Groblewski, Sneyd, 1999
Agonist-dependent Phosphorylation of the Inositol 1,4,5-Triphosphate Receptor

Leloup, Goldbeter,
A Model for Circadian Rhythms in Drosophila Incorporating the Formation of a Complex between the PER and TIM Proteins

Leloup, Goldbeter, 2003
Toward a detailed computational model for the mammalian circadian clock

Leloup, Goldbeter, 2004
Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms

Leloup, Gonze, Goldbeter, 1999
Limit Cycle Models for Circadian Rhythms Based on Transcriptional Regulation in Drosophila and Neurospora

Lemaire, Tobin, Greller, Cho, Suva, 2004
Main Model + Adding Osteoblasts

Lemon, Gibson, Bennett, 2003
Metabotropic receptor activation, desensitization and sequestration-I: modelling calcium and inositol 1,4,5-trisphosphate dynamics following receptor activation

Lenbury, Pacheenburawana, 1991
Modelling fluctuation phenomena in the plasma cortisol secretion system in normal man

Lenbury, Pornsawad, 2005
A delay-differential equation model of the feedback-controlled hypothalamus-pituitary-adrenal axis in humans

Lenbury, Ruktamatakul, Amornsamarnkul, 2001
Modeling insulin kinetics: responses to a single oral glucose administration or ambulatory-fed conditions

Li, Bertram, Rinzel, 1996
Modeling N-methyl-D-aspartate-induced bursting in dopamine neurons

Li, Kuang, Mason, 2006
Modeling the glucose-insulin regulatory system and ultradian insulin secretory oscillations with two explicit time delays

Li, Rinzel, 1994
Equations for InsP3 Receptor-mediated [Ca2+]i Oscillations Derived from a Detailed Kinetic Model: A Hodgkin-Huxley Like Formalism

Lindblad, Murphey, Clark, Giles, 1996
A Model of the Action Potential and Underlying Membrane Currents in a Rabbit Atrial Cell

Liu, Hu, Peng, Liu, 1999
A dynamical model for the pulsatile secretion of the hypothalamo-pituitary-adrenal axis

Livshitz, Rudy, 2007
Regulation of Ca2+ and electrical alternans in cardiac myocytes: role of CAMKII and repolarizing currents

Lockwood, Ewy, Hermann, Holford, 2006
Application of clinical trial simulation to compare proof-of-concept study designs for drugs with a slow onset of effect; an example in Alzheimer's disease

Lokta, Volterra,
Predator-prey dynamics

Lovell, Cloherty, Celler, Dokos, 2004
A gradient model of cardiac pacemaker myocytes

Luo, Rudy, 1991
A Model of the Ventricular Cardiac Action Potential. Depolarization, repolarization and their interaction

Luo, Rudy, 1994
A Dynamic Model of the Cardiac Ventricular Action Potential I. Simulations of Ionic Currents and Concentration Changes

MacGregor, Leng, 2005
Modelling the hypothalamic control of growth hormone secretion.

Mackenzie, Loo, Panayotova-Heiermann, Wright,
Biophysical Characteristics of the Pig Kidney Na/Glucose Cotransporter SGLT2 Reveal a Common Mechanism for SGLT1 and SGLT2

Magnus, Keizer, 1997
Minimal Model of beta-cell mitochondrial Ca2+ handling

Magnus, Keizer, 1998
Model of beta_cell mitochondrial calcium handling and electrical activity. I. Cytoplasmic variables

Mahajan, Shiferaw, Sato, Baher, Olcese, Xie, Yang, Chen, Restrepo, Karma, Garfinkel, Qu, Weiss, 2008
Mahajan, Shiferaw, Sato, Baher, Olcese, Xie, Yang, Chen, Restrepo, Karma, Garfinkel, Qu, Weiss, 2008

Maleckar, Greenstein, Trayanova, Giles, 2009
Mathematical simulations of ligand-gated and cell-type specific effects on the action potential of human atrium

Maltsev, Lakatta, 2009
Synergism of coupled subsarcolemmal Ca2+ clocks and sarcolemmal voltage clocks confers robust and flexible pacemaker function in a novel pacemaker cell model.

Maly, Wiley, Lauffenburger, 2004
Self-Organization of Polarized Cell Signaling via Autocrine Circuits: Computational Model Analysis

Margarida Martins, Mendes, Coreiro, Poces Freire, 2001
In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae

Marhl, Haberichter, Brumen, Heinrich, 2000
Complex calcium oscillations and the role of mitochondria and cytosolic proteins

Marhl, Schuster, Brumen, Heinrich, 1997
Modelling the interrelations between calcium oscillations and ER membrane potential oscillations

Martinov, Vitvitsky, Mosharov, Banerjee, Ataullakhanov, 2000
A Substrate Switch: A New Mode of Regulation in the Methionine Metabolic Pathway

Marwan, 2003
Theory of Time-Resolved Somatic Complementation and Its Use to Explore the Sporulation Control Network in Physarum polycephalum

Matsuoka, Sarai, Kuratomi, Ono, Noma, 2003
Role of individual ionic current systems in ventricular cells hypothesized by a model study

Maurya, Bornheimer, Venkatasubramanian, Subramaniam, 2005
Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module

Mazhari, Greenstein, Winslow, Marban, Nuss, 2001
Molecular Interactions Between Two Long-QT Syndrome Gene Products, HERG and KCNE2, Rationalized by In Vitro and In Silico Analysis

McAllister, Noble, Tsien, 1975
Reconstruction of the electrical activity of cardiac Purkinje fibres.

McKenzie, Sneyd, 1998
On the Formation and Breakup of Spiral Waves of Calcium

McLean, Su, van den Bogert, 2003
Development and Validation of a 3-D Model to Predict Knee Joint Loading During Dynamic Movement

Mears, Sheppard, Atwater, Rojas, Bertram, Sherman, 1997
Evidence That Calcium Release-activated Current Mediates the Biphasic Electrical Activity of Mouse Pancreatic Beta-Cells

Michailova, McCulloch, 2001
Model study of ATP and ADP buffering, transport of Ca2+ and Mg2+, and regulation of ion pumps in ventricular myocyte

Michailova, Saucerman, Belik, McCulloch, 2005
Modeling regulation of cardiac KATP and L-type Ca2+ currents by ATP, ADP, and Mg2+

Miftakhov, Abdusheva, Christensen, 1999
Numerical Simulation of Motility Patterns of the Small Bowel. I. Formulation of a Mathematical Model

Mijailovich, Butler, Fredburg, 2000
Perturbed Equilibria of Myosin Binding in Airway Smooth Muscle: Bond-Length Distributions, Mechanics and ATP Metabolism

Mikane, Suga, Araki, Kohno, Nakayama, Suzuki, Shimuzi, Matsubara, Hirakawa, Takaki, 1997
Mechanism of Constant Contractile Efficiency Under Cooling Intropy of Myocardium: Simulation

Mitchell, Schaeffer, 2003
A two-current model for the dynamics of cardiac membrane

Mittler, Sulzer, Neumann, Perelson, 1998
Influence of delayed viral production on viral dynamics in HIV-1 infected patients

Mlcek, Neumann, Kittnar, Novak, 2001
Mathematical Model of the Electromechanical Heart Contractile System - Regulatory Subsystem Physiological Considerations

Modelling Hypertrophic IP3 Transients in the Cardiac Myocyte (Cooling, Hunter, Crampin, 2007)

Mohr, Taylor, Newell, 2008
codata_2006

Moore, Li, 2004
A mathematical model for chronic myelogenous leukemia (CML) and T cell interaction

Mosekilde, Lading, Yanchuk, Maistrenko, 2001
Bifurcation structure of a model of bursting pancreatic cells

Moss, Kazmierczak, Kirley, Harris, 2009
A computational model for emergent dynamics in the kidney

Muller, Obeyesekere, Mills, Ram, 2008
Network topology determines dynamics of the mammalian MAPK1,2 signaling network: bifan motif regulation of C-Raf and B-Raf isoforms by FGFR and MC1R

Nagano, Gerritsen, 2001
Effects of Neuromuscular Strength Training on Vertical Jumping Performance - A Computer Simulation Study

Nagerl, Novo, Mody, Vergara, 2000
Binding Kinetics of Calbindin-D28k Determined by Flash Photolysis of Caged Ca2+

Nash, Panfilov, 2004
Electromechanical model of excitable tissue to study reentrant cardiac arrhythmias

Nelson, Murray, Perelson, 2000
A model of HIV-1 pathogenesis that includes an intracellular delay

Nelson, Perelson, 1995
Modeling defective interfering virus therapy for AIDS: conditions for DIV survival

Neumann, Lam, Dahari, Gretch, Wiley, Layden, Perelson, 1998
Hepatitis C Viral Dynamics in Vivo and the Antiviral Efficacy of Interferon-alpha Therapy

Nevo, Golding, Neumann, Schwartz, Akselrod, 2004
Nevo et al.'s 2004 mathematical model of autoimmunity.

Niederer, Hunter, Smith, 2006
A quantitative analysis of cardiac myocyte relaxation: a simulation study

Niederer, Smith, 2007
A Mathematical Model of the Slow Force Response to Stretch in Rat Ventricular Myocytes

Noble, 1962
A Modification of the Hodgkin-Huxley Equations Applicable to Purkinje Fibre Action and Pace-Maker Potentials

Noble, DiFrancesco, Denyer, 1989
Ionic Mechanisms in Normal and Abnormal Cardiac Pacemaker Activity

Noble, Noble, 1984
A Model of Sino-Atrial Node Electrical Activity Based on a Modification of the DiFrancesco-Noble (1984) Equations

Noble, Noble, 2001
Remodelling of Calcium Dynamics in Guinea-Pig Ventricular Cells

Noble, Noble, Bett, Earm, Ho, So, 1991
The Role of Sodium-Calcium Exchange During the Cardiac Action Potential

Noble, Varghese, Kohl, Noble, 1998
Improved guinea-pig ventricular cell model incorporating a diadic space, IKr and IKs, and length- and tension-dependent processes.

Noble, Varghese, Kohl, Noble, 1998
Improved guinea-pig ventricular cell model incorporating a diadic space, IKr and IKs, and length- and tension-dependent processes.

Novak, Csikasz-Nagy, Gyorffy, Chen, Tyson, 1998
Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions

Novak, Pataki, Ciliberto, Tyson, 2001
Mathematical model of the cell division cycle of fission yeast

Novak, Tyson, 1993
Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos.

Novak, Tyson, 1997
Modeling the control of DNA replication in fission yeast

Novak, Tyson, 2004
A model for restriction point control of the mammalian cell cycle

Nowak, Bangham, 1996
Population dynamics of immune responses to persistent viruses

Nygren, Fiset, Firek, Clark, Lindblad, Clark, Giles, 1998
Mathematical Model of an Adult Human Atrial Cell: The Role of K+ Currents in Repolarization

Obeyesekere, Zimmerman, Tecarro, Auchmuty, 1999
A model of cell cycle behavior dominated by kinetics of a pathway stimulated by growth factors

Olsen, Hauser, Kummer, 2003
Mechanism of protection of peroxidase activity by oscillatory dynamics

Oomens, Maenhout, van Oijen, Drost, Baaijens, 2003
Finite element modelling of contracting skeletal muscle

Ostby, Omholt, Oyehaug, Einevoll, Nagelhus, Plahte, Zeuthen, Voipio, Lloyd, Ottersen, 2008
Astrocytic processes explaining neural-activity-induced shrinkage of extraneuronal space

Overgaard, Holford, Rytved, Madsen, 2007
PKPD model of interleukin-21 effects on thermoregulation in monkeys--application and evaluation of stochastic differential equations

Palecek, Horwitz, Lauffenburger, 1999
Kinetic Model for Integrin-mediated Adhesion Release During Cell Migration

Pandit, Clark, Giles, Demir, 2001
A mathematical model of action potential heterogeneity in adult rat left ventricular myocytes

Pandit, Giles, Demir, 2003
A Mathematical Model of the Electrophysiological Alterations in Rat Ventricular Myocytes in Type-I Diabetes

Panerai, 1980
A Model of Cardiac Muscle Mechanics and Energetics

Parent, Supplisson, Loo, Wright,
Electrogenic Properties of the Cloned Na+/Glucose Cotransporter: II. A Transport Model under Nonrapid Equilibrium Conditions

Pasek, Simurda, Christe, 2006
The functional role of cardiac T-tubules explored in a model of rat ventricular myocytes

Pasek, Simurda, Orchard, Christe, 2008
A model of the guinea-pig ventricular cardiac myocyte incorporating a transverse-axial tubular system

Pedersen, Bertram, Sherman, 2005
Intra- and inter-islet synchronization of metabolically driven insulin secretion

Perelson, Kirschner, de Boer, 1993
Dynamics of HIV infection of CD4+ T cells

Perelson, Neumann, Markowitz, Leonard, Ho, 1996
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time

Phillips, Robinson, 2007
A quantitative model of sleep-wake dynamics based on the physiology of the brainstem ascending arousal system

Phillips, Robinson, 2008
Sleep deprivation in a quantitative physiologically based model of the ascending arousal system

Plant, 1981
Bifurcation and resonance in a model for bursting nerve cells

Potter, Greller, Cho, Nuttall, Stroup, Suva, Tobin, 2005
Response to continuous and pulsatile PTH dosing: a mathematical model for parathyroid hormone receptor kinetics

Potter, Zager, Barton, 2006
Mathematical model for the androgenic regulation of the prostate in intact and castrated adult male rats.

Priebe, Beuckelmann, 1998
Simulation Study of Cellular Electrical Properties in Heart Failure

Proctor, Soti, Boys, Gillespie, Shanley, Wilkinson, Kirkwood, 2005
Modelling the actions of chaperones and their role in ageing.

Proctor, Tsiringotis, Gray, 2007
An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline

Puglisi, Bers, 2001
LabHEART: an interactive computer model of rabbit ventricular myocyte ion channels and Ca transport

Purvis, Butera, 2005
Ionic Current Model of a Hypoglossal Motoneuron

Purvis, Smith, Koizumi, Butera, 2007
Intrinsic Bursters Increase the Robustness of Rythm Generation in an Excitatory Network

Qu, MacLellan, Weiss, 2003
Dynamics of the Cell Cycle: Checkpoints, Sizers, and Timers

Ralser, Lehrach, Krobitsch, Wamelink, Kowald, Gerisch, Heeren, Struys, Klipp, Jakobs, Breitenbach, 2007
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress

Ramirez, Nattel, Courtemanche, 2000
Mathematical analysis of canine atrial action potentials: rate, regional factors, and electrical remodeling

Rangamani, Sirovich, 2007
Survival and apoptotic pathways initiated by TNF-alpha: modeling and predictions

Rattananakul, Lenbury, Krishnamara, Wollkind, 2003
Modeling of bone formation and resorption mediated by parathyroid hormone: response to estrogen/PTH therapy

Razumova, Bukatina, Campbell, 1999
Stiffness-distortion sacromere model for muscle stimulation

Razumova, Bukatina, Campbell, 2000
Different Myofilament Nearest-Neighbor Interactions Have Distinctive Effects on Contractile Behavior

Reed, Nijhout, Sparks, Ulrich, 2004
A mathematical model of the methionine cycle

Reidl, Borowski, Sensse, Starke, Zapotocky, Eiswirth, 2006
Model of Calcium Oscillations Due to Negative Feedback in Olfactory Cilia

Revilla, Garcia-Ramos, 2003
Revilla and Garcia-Ramos's 2003 dynamic model for HIV-1 therapy.

Riccobene, Omann, Linderman, 1999
Modeling Activation and Desensitisation of G-Protein Coupled Receptors Provides Insight into Ligand Efficacy

Rice, Jafri, Winslow, 2000
Modeling short-term interval-force relations in cardiac muscle

Rice, Wang, Bers, de Tombe, 2008
Approximate model of cooperative activation and crossbridge cycling in cardiac muscle using ordinary differential equations

Rice, Winslow, Hunter, 1999
Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses

Rice, Winslow, Jafri, 1999
Modeling Gain and Gradedness of Ca2+ Release in the Functional Unit of the Cardiac Diadic Space

Riemer, Sobie, Tung, 1998
Stretch-induced changes in arrhythmogenesis and excitability in experimentally based heart cell models

Rivlin, Saunders, 1951
Large Elastic Deformations of Isotropic Materials. VII. Experiments on the Deformation of Rubber

Rogers, McCulloch, 1994
A collocation--Galerkin finite element model of cardiac action potential propagation

Romond, Rustici, Gonze, Goldbeter, 1999
Alternating Oscillations and Chaos in a Model of Two Coupled Biochemical Oscillators Driving Successive Phases of the Cell Cycle

Rong, Perelson, 2009
Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy

Roux, Noble, Noble, Marhl, 2006
Modelling of calcium handling in airway myocytes

Sachse, Glanzel, Seemann, 2003
Modeling of Protein Interactions Involved in Cardiac Tension Development

Sachse, Moreno, Abildskov, 2008
Electrophysiological Modeling of Fibroblasts and Their Interaction with Myocytes

Saftenku, Williams, Sitsapesan, 2001
Markovian Models of Low and High Activity Levals of Cardiac Ryanodine Receptors

Sakmann, Spindler, Bryant, Linz, Noble, 2000
Distribution of a persistent sodium current across the ventricular wall in guinea pigs.

Salem, Saidel, Stanley, Cabrera, 2002
Mechanistic Model of Myocardial Energy Metabolism Under Normal and Ischemic Conditions

Sarai, Matsuoka, Kuratomi, Ono, Noma, 2003
Role of individual ionic current systems in the SA node hypothesized by a model study

Sarkar, Lauffenburger, 2003
Cell-Level Pharmacokinetic Model of Granulocyte Colony-Stimulating Factor: Implications for Ligand Lifetime and Potency in Vivo

Saucerman, Bers, 2008
Calmodulin Mediates Differential Sensitivity of CAMKII and Calcineurin to Local Ca2+ in Cardiac Myocytes

Saucerman, Brunton, Michailova, McCulloch, 2003
Modeling beta-adrenergic control of cardiac myocyte contractility in silico

Saucerman, McCulloch, 2004
Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation

Schenzle, 1994
A model for AIDS pathogenesis

Schlosser, Selgrade, 2000
A model of gonadotropin regulation during the menstrual cycle in women: qualitative features

Schmid, Nash, Young, Hunter, 2006
Myocardial Material Parameter Estimation - A Comparative Study for Simple Shear

Schneider, Shimayoshi, Amano, Matsuda, 2006
Mechanism of the Frank-Starling law-- A simulation study with a novel cardiac muscle contraction model that includes titin and tropomyosin

Schoeberl, Eichler-Jonsson, Gilles, Muller, 2002
Computational Modeling of the Dynamics of the MAP Kinase Cascade Activated by Surface and Internalized EGF Receptors.

Schuster, Beny, Meister, 2003
Modelling the electrophysiological endothelial cell response to bradykinin

Sedaghat, Sherman, Quon, 2002
A mathematical model of metabolic insulin signaling pathways

Seemann, Sachse, Weib, Dossel, 2003
Quantitative Reconstruction of Cardiac Electromechanics in Human Myocardium: Regional Heterogeneity

Shannon, Wang, Puglisi, Weber, Bers, 2004
A Mathematical Treatment of Integrated Ca Dynamics within the Ventricular Myocyte

Shaw, Chase, Starfinger, Smith, Hann, Desaive, Ghuysen, 2007
Modeling the Cardiovascular System

Shaw, Rudy, 1997
Electrophysiological effects of acute myocardial ischemia: a theoretical study of altered cell excitability and action potential duration

Shi, Hose, 2009
Zero dimensional (lumped parameter) modelling of native human cardiovascular dynamics

Shiferaw, Watanabe, Garfinkel, Weiss, Karma, 2003
Model of Intracellular Calcium Cycling in Ventricular Myocytes

Shorten, O'Callaghan, Davidson, Soboleva, 2007
A mathematical model of fatigue in skeletal muscle force contraction

Shorten, Robson, McKinnon, Wall, 2000
CRH-induced Electrical Activity and Calcium Signalling in Pituitary Corticotrophs

Shorten, Wall, 2000
A Hodgkin-Huxley Model Exhibiting Bursting Oscillations

Siebert, Rode, Herzog, Till, Blickhan, 2008
Nonlinearities make a difference: comparison of two common Hill-type models with real muscle

Sine-Approximations
Sine-Approximations

Skouibine, Trayanova, Moore, 1999
Anode/cathode make and break phenomena in a model of defibrillation

Smith, 1980
Smith, 1980

Smith, Chase, Nokes, Shaw, Wake, 2004
Minimal haemodynamic system model including ventricular interaction and valve dynamics.

Smith, Crampin, 2004
Development of models of active ion transport for whole-cell modelling: cardiac sodium-potassium pump as a case study

Sneyd, Dufour, 2002
A dynamic model of the type-2 inositol triphosphate receptor

Sneyd, Tsaneva-Atanasova, Bruce, Straub, Giovannucci, Yule, 2003
A Model of Calcium Waves in Pancreatic and Parotid Acinar Cells

Sneyd, Tsaneva-Atanasova, Yule, Thompson, Shuttleworth, 2004
Sneyd et al.'s 2004 mathematical model for Ca2+ oscillations and their control by membrane fluxes.

Sneyd, Wetton, Charles, Sanderson, 1995
Intercellular calcium waves mediated by diffusion of inositol trisphosphate: a two-dimensional model

Snyder, Palmer, Moore, 2000
A Mathematical Model of Cardiocyte Ca2+ Dynamics with a Novel Representation of Sarcoplasmic Reticular Ca2+ Control

Sobie, Dilly, dos Santos Cruz, Lederer, Jafri, 2002
Termination of Cardiac Ca2+ Sparks: An Investigative Mathematical Model of Calcium-Induced Calcium Release

Soboleva, Vetharaniam, Nixon, Montenegro, Pearson, Sneyd, 2005
Mathematical modelling of prolactin-receptor interaction and the corollary for prolactin receptor gene expression in skin

Spiro, Parkinson, Othmer, 1997
A model of excitation and adaptation in bacterial chemotaxis

Sriram, Bernot, Kepes, 2007
A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle

St Hilaire, Gronfier, Zeitzer, Klerman, 2007
A physiologically based mathematical model of melatonin including ocular light suppression and interactions with the circadian pacemaker

Starbuck, Wiley, Lauffenburger, 1990
Epidermal Growth Factor Binding and Trafficking Dynamics in Fibroblasts: Relationship to Cell Proliferation

Stern, Song, Sham, Yang, Boheler, Rios, 1999
Local Control Models of Cardiac Excitation-Contraction Coupling A Possible Role for Allosteric Interactions between Ryanodine Receptors

Stewart, Aslanidi, Noble, Noble, Boyett, Zhang, 2009
Mathematical models of the electrical action potential of Purkinje fibre cells

Stilianakis, Dietz, Schenzle, 1997
Analysis of a Model for the Pathogenesis of AIDS

Surkis, Peskin, Tranchina, Leonard, 1998
Recovery of Cable Properties Through Active and Passive Modeling of Subthreshold Membrane Responses From Laterodorsal Tegmental Neurons

Sveiczer, Csikasz-Nagy, Gyorffy, Tyson, Novak, 2000
Modeling the fission yeast cell cycle: quantized cycle times in wee1- cdc25Delta mutant cells.

Swanson, True, Lin, Buhler, Vessella, Murray, 2001
A Quantitative Model for the Dynamics of Serum Prostate-Specific Antigen as a Marker for Cancerous Growth

Tabak, Mascagni, Bertram, 2010
Mechanism for the Universal Pattern of Activity in Developing Neuronal Networks

Tabak, Toporikova, Freeman, Bertram, 2007
Low dose of dopamine may stimulate prolactin secretion by increasing fast potassium currents

Ten Tusscher, Noble, Noble, Panfilov, 2004
A model for human ventricular tissue

ten Tusscher, Panfilov, 2006
Alternans and spiral breakup in a human ventricular tissue model.

Terkildsen, Niederer, Crampin, Hunter, Smith, 2008
Using Physiome standards to couple cellular functions for rat cardiac excitation-contraction

Teusink, Westerhoff, Snoep, Passarge, Reijenga, Esgalhado, van der Weijden, Schepper, Walsh, Bakker, van Dam, 2000
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.

Tham, Wang, Soo, Lee, Lee, Yong, Goh, Holford, 2008
A pharmacodynamic model for the time course of tumor shrinkage by gemcitabine + carboplatin in non-small cell lung cancer patients

Thomas, 2000
Inner medullary lactate production and accumulation: a vasa recta model

Thomsen, Neubig, 1989
Rapid kinetics of alpha 2-adrenergic inhibition of adenylate cyclase. Evidence for a distal rate-limiting step

Tolic, Mosekilde, Sturis, 2000
Modelling the Insulin-Glucose Feedback System: The Significance of Pulsatile Insulin Secretion

Tomida, Hirose, Takizawa, Shibasaki, Iino, 2003
NFAT functions as a working memory of Ca2+ signals in decoding Ca2+ oscillation

Tomida, Hirose, Takizawa, Shibasaki, Iino, 2003
Tomida, Hirose, Takizawa, Shibasaki, Iino, 2003

Topp, Promislow, de Vries, Miura, Finegood, 2000
A Model of Beta-Cell Mass, Insulin, and Glucose Kinetics: Paythways to Diabetes

Tran, Smith, Loiselle, Crampin, 2009
A metabolite-sensitive, thermodynamically-constrained model of cardiac cross-bridge cycling: Implications for force development during ischemia

Tran, Smith, Loiselle, Crampin, 2009
A Thermodynamic Model of the Cardiac Sarcoplasmic/Endoplasmic Ca(2+) (SERCA) Pump

Tyson, 1991
Modeling the Cell Division Cycle:cdc2 and Cyclin Interactions

Tyson, Hong, Thron, Novak, 1999
A Simple Model of Circadian Rhythms Based on Dimerization and Proteolysis of PER and TIM

Ueda, Hagiwara, Kitano, 2001
Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm

van Beek, 2007
Adenine nucleotide-creatine-phosphate module in myocardial metabolic system explains fast phase of dynamic regulation of oxidative phosphorylation

van Capelle, Durrer, 1980
Computer simulation of arrhythmias in a network of coupled excitable elements

Van der Pol, Van der Mark, 1928
The Heartbeat Considered as a Relaxation Oscillation, and an Electrical Model of the Heart.

Van Goor, LeBeau, Krsmanovic, Sherman, Catt, Stojilkovic, 2000
Amplitude-Dependent Spike-Broadening and Enhanced Ca2+ Signaling in GnRH-Secreting Neurons

Vaseghi, Baumeister, Rizzi, Reuss, 1999
In Vivo Dynamics of the Pentose Phosphate Pathway in Saccharomyces cerevisiae

Vempati, Karagiannis, Popel, 2007
A Biochemical Model of Matrix Metalloproteinase 9 Activation and Inhibition

Vendelin, Kongas, Saks, 2000
Regulation of mitochondrial respiration in heart cells analyzed by reaction-diffusion model of energy transfer

Vilar, Jansen, Sander, 2006
Signal processing in the TGF-beta superfamily ligand-receptor network

Vilar, Kueh, Barkai, Leibler, 2002
Mechanisms of noise-resistance in genetic oscillators

Vinnakota, Kemp, Kushmeric, 2006
Dynamics of Muscle Glycogenolysis Modeled with pH Time Course Computation and pH-Dependent Reaction Equilibria and Enzyme Kinetics

Vinnakota, Rusk, Palmer, Shankland, Kushmeric, 2010
Common Phenotype of Resting Mouse EDL and SOL Muscles: EDL

Viswanathan, Shaw, Rudy, 1999
Effects of IKr and IKs heterogeneity on action potential duration and its rate dependence: a simulation study

Wanant, Quon, 2000
Insulin receptor binding kinetics: modeling and simulation studies

Wang, Huang, Huang, 2006
A quantitative kinetic model for ATP-induced intracellular Ca2+ oscillations

Wang, Li, Kuang, 2007
Mathematical modeling and qualitative analysis of insulin therapies

Wang, Lin, Lin, Wu, 2008
Effect of riluzole on action potential in cultured human skeletal muscle cells

Wang, Sobie, 2008
Mathematical model of the neonatal mouse ventricular action potential

Warashina, Ogura, 2004
Modeling of simulation-secretion coupling in a chromaffin cell

Warren, Tawhai, Crampin, 2009
Mathematical modelling of calcium wave propagation in airway epithelium: evidence for regenerative ATP release

Waugh, Sherratt, 2006
Macrophage Dynamics in Diabetic Wound Healing

Waugh, Sherratt, 2007
Modeling the effects of treating diabetic wounds with engineered skin substitutes

Webb, Sherratt, Fish, 2002
Cells behaving badly: a theoretical model for the Fas/FasL system in tumour immunology

Wein, D'Amato, Perelson, 1998
Mathematical analysis of antiretroviral therapy aimed at HIV-1 eradication or maintenance of low viral loads

Weinstein, 1998
A mathematical model of the inner medullary collecting duct of the rat: acid/base transport

Weinstein, 2000
A mathematical model of the outer medullary collecting duct of the rat

Westermark, Lansner, 2003
A Model of Phosphofructokinase and Glycolytic Oscillations in the Pancreatic Beta-cell

Wierschem, Bertram,
Complex bursting in pancreatic islets: a potential glycolytic mechanism

Wilkins, Sneyd, 1998
Intercellular Spiral Waves of Calcium

Winograd, Destexhe, Sanchez-Vives, 2008
Hyperpolarization-activated graded persistent activity in the prefrontal cortex

Winslow, Rice, Jafri, Marban, O'Rorke, 1999
Mechanisms of Altered Excitation-Contraction Coupling in Canine Tachycardia-Induced Heart Failure, II Model Studies

Wodarz, 2003
Evolution of Immunological Memory and the Regulation of Competition between Pathogens

Wodarz, Hamer, 2007
Infection dynamics in HIV-specific CD4 T cells: Does a CD4 T cell boost benefit the host or the virus?

Wodarz, Jansen, 2003
A dynamical perspective of CTL cross-priming and regulation: implications for cancer immunology

Wodarz, Nowak, 1999
Specific therapy regimes could lead to long-term immunological control of HIV

Wodarz, Sierro, Klenerman, 2007
Dynamics of killer T cell inflation in viral infections

Wolf, Heinrich, 2000
Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation

Wolf, Passarge, Somsen, Snoep, Heinrich, Westerhoff, 2000
Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations

Wolf, Sohn, Heinrich, Kuriyama, 2001
Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisae

Wu, Jeneson, Beard, 2006
Oxidative ATP Synthesis in Skeletal Muscle is Controlled by Substrate Feedback

Wu, Yang, Vinnakota, Beard, 2007
Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology

Yamaguchi, Takaki, Matsubara, Yasuhara, Suga, 1996
Constancy and variability of contractile efficiency as a function of calcium and cross-bridge kinetics: simulation

Yanagihara, Noma, Irisawa, 1980
Reconstruction of sino-atrial node pacemaker potential based on the voltage clamp experiments

Yang, Clark, Bryan, Robertson, 2003
The myogenic response in isolated rat cerebrovascular arteries: smooth muscle cell model

Yang, Tong, McCarver, Hines, Beard, 2006
Population-Based Analysis of Methadone Distribution and Metabolism Using an Age-Dependent Physiologically Based Pharmacokinetic Model

Yasamura, Suga, 1987
Crossbridge Model Compatible with the Linear Relationship between Left Ventricular Oxygen Consumption and Pressure-Volume Area

Yates, Stark, Klein, Antia, Callard, 2007
Understanding the slow depletion of memory CD4+ T cells in HIV infection

Yi, Fogelson, Keener, Peskin, 2003
A Mathematical Study of Volume Shifts and Ionic Concentration Changes during Ischemia and Hypoxia

Youm, Kim, Han, Kim, Joo, Leem, Goto, Noma, Earm, 2006
A mathematical model of pacemaker activity recorded from mouse small intestine

Zager, Schlosser, Tran, 2007
A delayed nonlinear PBPK model for genistein dosimetry in rats

Zeng, Laurita, Rosenbaum, Rudy, 1995
Two Components of the Delayed Rectifier K+ Current in Ventricular Myocytes of the Guinea Pig Type

Zhang, Holden, Kodama, Honjo, Lei, Varghese, Boyett, 2000
Mathematical models of action potentials in the periphery and center of the rabbit sinoatrial node.

Model development and archiving support at physiome.org provided by the following grants: NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.