jianqiuz/cyberneticn

Cybernetic modeling of N biogeochemical cycling

CyberneticN

This repository is archived for manuscript "The cybernetic approach to modeling dynamic regulation of nitrogen biogeochemical transformations ". Nitrogen (N) cycling in the environment is driven by complex networks of microorganisms and enzymatic processes. Competitive and cooperative relationships are often observed among various nitrogen transforming pathways, creating substantial challenges for the development of dynamic models. Here we address this need using a cybernetic approach that captures dynamic interplay among nitrogen transformation reactions without prescribing the nature of these interactions.

The complexity of nitrogen cycle

Four case studies are included. For each study, there's an R markdown file detailing model setup, optimization and plot generation. All associated datasets are included.

• Dual substrate competition between Denitrification and DNRA

• Electron competition among different denitrification steps

• Coupled nitrification-denitrification dynamics

• A full model of N transformations, including OM mineralization (releasing Ammonium), aerobic respiration, nitrification, denitrification, DNRA and Anammox