Implementation of BIO_PORE_EOC model in COMSOL MultiphysicsTM for simulation of emerging organic contaminants in horizontal subsurface flow constructed wetlands

This user manual presents the implementation of the BIO_PORE_EOC model code in COMSOL Multiphysics™ (version 6.3) for simulating the fate and transport of emerging organic contaminants (EOCs) in horizontal subsurface flow constructed wetlands (HFCWs). The BIO_PORE_EOC model developed by Huma Ilyas and Diederik Rousseau of the Ghent University extends the existing physically based BIO_PORE model by integrating the fate and transport of EOCs. These contaminants are modeled alongside conventional water quality parameters (CWQPs) such as chemical oxygen demand, nitrogen and sulphur, capturing their interactions with microbial communities, uptake by the plants, and sorption dynamics in saturated porous media. The original BIO_PORE model was created by Roger Samsó and Joan García of the Universitat Politècnica de Catalunya · BarcelonaTech for simulating the behavior of CWQPs and to infer the distribution of functional microbial populations. The manual provides software code and a step-by-step methodology for implementing the model using COMSOL’s PDE interfaces and multiphysics coupling capabilities. It includes guidance on geometry definition, meshing strategies, initial and boundary condition assignment, reaction network formulation, and numerical solver configuration. Special attention is given to modelling EOC-specific biodegradation pathways, microbial kinetics, and diffusion-sorption interactions. Practical case studies and simulation examples are provided to illustrate the application of the model in performance assessment and optimization of HFCWs for CWQPs and EOCs removal. Designed for researchers, engineers, and environmental modelers, this manual provides guidance for evaluating and improving nature-based wastewater treatment systems using advanced modelling techniques. The BIO_PORE_EOC implementation enables a deeper understanding of contaminant dynamics and provides a flexible tool for simulating and designing constructed wetlands under varying environmental conditions and contaminant loads.