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.
This repository contains codes developed in 2022 to simulate the biofilm formation with the proposed stochastic model based on quorum sensing and chemical reactions.
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.
This repository contains codes developed in 2022 to simulate the bacterial biofilm formation with the proposed stochastic biofilm disruption model based on quorum sensing mimickers and chemical reactions.
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