Original code for "Engineered probiotics that block arsenite absorption in the gastrointestinal tract"

Instructions for Using the MATLAB Model

This MATLAB script simulates the time-dependent distribution of arsenite (As(III)) in the gastrointestinal tract, accounting for uptake by gut bacteria and absorption by gastrointestinal epithelial cells. The model is deterministic and based on first-order kinetics with two parallel removal pathways.

Purpose of the Code

The code computes and plots the following parameters as a function of time:

• Total arsenite remaining in the gastrointestinal tract
• Arsenite associated with bacteria
• Arsenite absorbed by gastrointestinal tract cells

How to Run the Code

1. Open MATLAB.
2. Use MATLAB Editor and run the script directly. No external toolboxes are required.

Model Inputs

All parameters are defined at the beginning of the script and may be adjusted to explore different physiological or experimental conditions.

• t: Time vector (hours)
• C0: Initial arsenite concentration in the GI tract (µM)
• V: Volume term associated with bacteria
• nb: Bacterial number density
• k1: Rate constant for bacterial interaction with arsenite
• A: Effective surface area of GI tract cells
• Ne: Number of epithelial cells
• k2: Rate constant for cellular arsenite uptake

The model assumes that arsenite is removed from the GI tract by bacteria and cells simultaneously, and that both processes follow first-order kinetics.

Notes on Time-Dependent Parameters

If different values of k1 are required for different time intervals, the conditional logic must be applied element-wise over the time vector. MATLAB does not support scalar if statements for vector comparisons.

Model Output

The script produces:

• A plot showing arsenite concentration versus time for:
• Total GI tract arsenite
• Bacterial-associated arsenite
• Cell-absorbed arsenite
• Column vectors (t, C, Bacteria, Cells) suitable for export or further analysis