Computational Bioengineering Group
Computing Tools and Computational Models

1. Whole-Body:
      Physiologically Based Pharmacokinetics

    A Pediatric PBPK Model for Methadone
  • Brief Description
    Age-dependent physiologically based pharmacokinetic model was used to perform population-based analysis of methadone distribution and metabolism.
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2. Cardiac Tissue Transport and Metabolism

    1D Oxygen Transport and Oxidative
      Phosphorylation in Cardiac Tissue
  • Brief Description
    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
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3. Skeletal Muscle Transport and Metabolism

    Oxidative Phosphorylation in Skeletal Muscle
  • Brief Description
    This model analyzes 31P-NMR spectroscopy data from human skeletal muscle as work rates vary from rest to maximal exercise. It generates reasonable predictions for observed ADP and inorganic phosphate (Pi) concentrations in cytoplasm, which verifies the hypothesis that oxidative ATP synthesis is primarily controlled by substrate (ADP and Pi) levels in skeletal muscle.
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4. Liver Transport and Metabolism

5. Mitochondrial Metabolism

    Mitochondrial Inner Membrane
   Electrophysiology Assessed by
   Rhodamine-123 Transport and Fluorescence
  • Brief Description
    This model was developed to quantitatively analyze the kinetics of the mitochondrial inner membrane potential. It accounts for dye transport, including electrogenic transport across the mitochondrial inner membrane and partition into the membrane, as well as experimentally measured dye self-quenching, and was integrated into a previously developed model of mitochondrial electrophysiology in order to estimate transients in mitochondrial membrane potential from kinetic measurements of fluorescence intensity.
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    A Biophysical Model of the Mitochondrial
   Respiratory System and Oxidative
   Phosphorylation
  • Brief Description
    A computational model for the mitochondrial respiratory chain that appropriately balances mass, charge, and free energy transduction is introduced and analyzed based on a previously published set of data meas-ured on isolated cardiac mitochondria.
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    Computer Modeling of Mitochondrial
   Tricarboxylic Acid Cycle, Oxidative
   Phosphorylation, Metabolite Transport, and
   Electrophysiology
  • Brief Description
    A computational model of mitochondrial metabolism and electrophysiology is introduced and applied to analysis of data from isolated cardiac mitochondria and data on phosphate metabolites in striated muscle in vivo. This model is constructed based on detailed kinetics and thermodynamically balanced reaction mechanisms and a strict accounting of rapidly equilibrating biochemical species.
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6. Other Computational Analysis Tools

    BISEN (Biochemical Simulation Environment)
  • Brief Description
    The Biochemical Simulation Environment (BISEN) software package is a suite of tools for generating equations and associated computer prograss for simulating biochemical systems.
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    King & Altman Pattern Tool for Systematic
   Method for Deriving Steasy-State Equation
   in Enzyme Systems
  • Brief Description
    A Matlab based suite of tools for deriving enzyme kinetic flux expressions using topological theory of linear graphs for systematic generation of valid King and Altman patterns.
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    Tool for Calculation A Solution Ionic
    Composition
  • Brief Description
    A Matlab-based suite of tools for calculation of the free cation in physiological buffer.
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    Microvascular MassTransport
  • Brief Description
    A Matlab-based suite of tools for building models of microvascular transport and exchange from 3D structural information.
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    Minimal Basic Cycle Calculation
  • Brief Description
    MATLAB code for the NP-complete exhaustive calculation of the minimal cycle basis (MCB) for a biochemical network is given here. A MATLAB script demonstrating calculation of the MCB for a few example networks is also included.
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    Thermodynamic-based computational
   profiling of cellular regulatory control in
   hepatocyte metabolism
  • Brief Description
    Thermodynamic-based constraints on biochemical fluxes and concentrations are applied in concert with mass balance of fluxes in glycogenesis and glycogenolysis in a model of hepatic cell metabolism.
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    Ab Initio prediction of thermodynamically
   feasible reaction directions from network
   stoichiometric matrix
  • Brief Description
    Based on the network stoichiometry and sign constraints imposed on the boundary fluxes, this Matlab-based package is used to predict thermodynamically feasible reaction directions.
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7. Mitochondrial Calcium Handling

    Analysis of Cardiac Mitochondrial Na+/Ca2+
    Exchanger Kinetics with a Biophysical Model of
    Mitochondrial Ca2+ Handing Suggests a 3:1
    Stoichiometr
  • Brief Description
    The paper first characterizes the kinetics of mitochondrial Ca2+ uniporter, Na+/Ca2+ exchanger, and Na+/H+ exchanger (i.e., the kinetics of mitochondrial Na+- Ca2+ cycle), and then integrates these kinetic models into our existing biophysical model of mitochondrial respiratory system and oxidative phosphorylation. The integrated model is used to analyze data on the Na+ dose-dependent dynamics of mitochondrial Ca2+ to determine the stoichiometry of mitochondrial Na+/Ca2+ exchanger, as a 3Na+/Ca2+ exchanger
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Computational Bioengineering Group, Biotechnology & Bioengineering Center
Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226