This repository contains the code for simulating the growth of a Biofilm after attachment using Molecular dynamics simulation methods. The project was build as part of the iGEM 2020 Contest. The BiofilmSimulation software can be installed as A python package, documented under https://pypi.org/project/BiofilmSimulation.
Biofilm-Grazer Model is an agent based model I developed as part of my masters thesis in the marine biology MSc, at University of Bremen, Germany under the suoervision of Dr. Arjun Chennu, the head of Data Science &Technology working group at ZMT. The model predicts how nutrient(phosphorus), light and grazers affects the spatio-temporal developm…
Code corresponding to paper "Robust time-discretisation and linearisation schemes for singular and degenerate evolution systems modelling biofilm growth" implemented in python using FEniCSx. It covers the biofilm model and the porous medium equation.
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