Computational Models

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Metabolism and Transport

This resource provides a set of of mechanistic models of functional components to use as building blocks to construct computational models of biological systems. Models of biochemical systems—including signaling pathways, electrophysiological systems, and cellular metabolism—are built from models of individual components such as enzymes, transporters, and ion channels. This databank of open source of component models uses a consistent notation, obeying a common set of criteria, with clear documentation and links to the primary literature. Code modules for enzymes and transporters can be downloaded in CellML or MATLAB, for use with the BISEN package.

This integrated model on oxygen transport and ox-phos is able to reproduce experimental observations on ATP, ADP, CrP, and inorganic phosphate (Pi) levels in canine hearts over a range of workload and during coronary hypoperfusion, and predicts that cytoplasmic inorganic phosphate level is a key regulator of the rate of mitochondrial respiration.

Integrated Computational Modeling of Oxygen Transport and Cellular Energetics

Population-Based Analysis of Methadone Distribution and Metabolism Using an Age-Dependent Physiologically Based Pharmacokinetic Model

Analysis of Cardiac Mitochondrial Na+/Ca2+ Exchanger Kinetics with a Biophysical Model of Mitochondrial Ca2+ Handing  Suggests a 3:1 Stoichiometry

Thermodynamic-Based Computational Profiling of Cellular Regulatory Control in Hepatocyte Metabolism

Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology

Model for Mitochondrial Inner Membrane Electrophysiology Assessed by Rhodamine Transport and Fluorescence

Simulates cytoplasmic ADP and inorganic phosphate Pi concentrations in human skeletal muscle.

The presented work proposes specific roles for the two mitochondrial Ca2+ uptake pathways: CU in Ca2+buffering, and RTC in cardiac metabolism.

This model integrates the biophysical processes of oxidative phosphorylation and ROS generation. 

Cardiovascular Dynamics

A mathematical model of the muscle cross-bridge (XB) cycle based on Huxley's sliding filament theory that explicitly accounts for the chemical transformation events and the influence of strain on state transitions. The model is identified based on elastic and viscous moduli data from mouse and rat myocardial strips over a range of perturbation frequencies, and MgATP and inorganic phosphate (Pi) concentrations.

We present a phenomenological ODE model of baroreflex open-loop control of heart rate.

The integrated cardiovascular model combines a simple model of the cardiovascular system (Smith, 2004) and a model describing baroreflex control of the heart (Bugenhagen, 2010). 

Computer model capturing chronic adaptation of acute renal function in blood pressure control

Heart

This package contains MATLAB codes for simulating in vivo cardiac energetics in normal and left ventricular hypertrophy (LVH) hearts as reported in “Wu F, Zhang J, & Beard DA (2009).

A mathematical model of the muscle cross-bridge (XB) cycle based on Huxley’s sliding filament theory which explicitly accounts for the chemical transformation events and the influence of strain on state transitions.

Kidney

The mathematical model of renal blood flow, glomerular filtration, and mass transport in nephrons.

A demonstration renal nephron model interface.