BISEN

BISEN generates systems of differential equations to simulate multi-compartment biochemical models that include enzymes, transporters, biochemical thermodynamics, rapid equilibria among biochemical species, and dynamic buffering by protons and metal ions within the MATLAB computing environment.

Key Features:

• Differential equation generation: Automatically constructs systems of differential equations tailored to user-specified multi-compartment models.
• Enzyme and transporter representation: Includes explicit modeling of enzymes and transporters within compartments and across membranes.
• Biochemical thermodynamics: Incorporates detailed biochemical thermodynamic constraints into simulations.
• Rapid equilibria handling: Accounts for rapid equilibria among multiple biochemical species.
• Dynamic buffering: Models dynamic buffering mechanisms involving protons and metal ions.
• MATLAB integration: Operates within the MATLAB computing environment for computation and analysis.
• Computational efficiency: Implements approaches intended to enable extensive analyses with manageable computational cost.

Scientific Applications:

• Metabolic pathway simulation: Simulates dynamics of metabolic networks across multiple compartments incorporating enzyme kinetics and transport.
• Enzyme kinetics analysis: Analyzes enzyme-mediated reaction dynamics with thermodynamic constraints and rapid equilibria.
• Cellular transport modeling: Models transport processes and their impact on compartmental concentrations and system behavior.
• Buffering and ion speciation studies: Investigates proton buffering and metal ion interactions affecting biochemical states.
• Hypothesis testing and data validation: Supports theoretical scenario exploration and comparison with experimental data using thermodynamically informed models.

Methodology:

Generation of systems of differential equations for user-specified multi-compartment models implemented in MATLAB, incorporating biochemical thermodynamics, rapid equilibria among species, and dynamic proton and metal ion buffering.