Generic SimBiology PBPK model

SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies.
Updated 1 Apr 2021

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SimBiology project file and associated MATLAB files that contain a generic and adaptable PBPK model. Human fasted, Human fed and Rat physiologies are included as variants.

Once you download the folder, either change your current folder in MATLAB to be this folder or add the folder to the MATLAB path. You can add/remove a folder to/from the path by right-clicking on it in the 'Current Folder' panel in the main MATLAB window and selecting "Add/Remove from path".
This folder includes helper functions for the SimBiology model, calculateParacellularAbsorption.m and calculateTissuePartition.m, and for SimBiology to find those functions their containing folder must be on the path or the current folder.

Tested on R2019a and R2018a but will likely work on earlier versions. Does not contain tasks or the Renin-Angiotensin model as used in the June 2012 webinar. Please see for the project used in that webinar.

Model Structure:
Peters, S. A. (2008). Evaluation of a generic physiologically based pharmacokinetic model for lineshape analysis. Clinical pharmacokinetics, 47(4), 261-75.
Tissue Partition Coefficients:
Rodgers, T., & Rowland, M. (2006). Physiologically Based Pharmacokinetic Modelling 2 : Predicting the Tissue Distribution of Acids , Very Weak Bases , Neutrals and Zwitterions. Journal of pharmaceutical sciences, 95(6), 1238-1257.
Rodgers, T., Leahy, D., & Rowland, M. (2005). Physiologically based pharmacokinetic modeling 1: predicting the tissue distribution of moderate-to-strong bases. Journal of pharmaceutical sciences, 94(6), 1259-76.

Cite As

MathWorks SimBiology Team (2024). Generic SimBiology PBPK model (, MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2019a
Compatible with any release
Platform Compatibility
Windows macOS Linux
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Version Published Release Notes

Updated description to include instructions to add the folder to MATLAB path.

Included Plasma and Blood concentrations
Changed Ktransit = 0.693/TransitTime to Ktransit = 1/TransitTime
Changed transit rate normalizations small intestine from Ktransit_i = Ktransit*length_i/length_tot to Ktransit_i = Ktransit*length_tot/length_i

Correct modeling errors associated with volume corrections.

Updated license

Updated Screenshot