Anaerobic denitrification model for Paracoccus denitrificans

Nitrous oxide emissions make a significant contribution to global warming. The model given here[1] focuses on the anaerobic denitrification of the bacteria, Paracoccus denitrificans, which under certain conditions emits significant quantities of nitrous oxide.


When Paracoccus denitrificans respires anaerobically, nitrate (NO3-) is reduced to dinitrogen (N2) along the pathway, 2 NO3- → 2 NO2- → 2 NO → N2O → N2.

The copper-dependent enzyme Nitrous Oxide reductase (Nos) catalyses the reduction of N2O to N2. In certain low-copper conditions it has been shown[2] that Nos efficiency decreases resulting in significant N2O emissions. By applying Michaelis-Menten kinetics to the reactions a system of Ordinary Differential Equations (ODEs) is produced. The model solves these equations numerically given the initial conditions and published kinetic parameters for each step. The model predicts the steady-state level of each enzyme and time courses for each molecule. The model is described in detail in Woolfenden et al. (2013)[1].


The software is implemented in Matlab ™ (Mathworks, Inc.). Download the zip file, unzip and follow the instructions in the README file. Run the file named "anaerobic_pd_model_ui.m" to open a graphical user interface. 


This software is supplied as-is, with no warranty of any kind expressed or implied. We have made every effort to avoid errors in design and execution of this software, but we will not be liable for its use or misuse.

The user is solely responsible for the validity and consequences of any results generated. The Anaerobic denitrification model for Paracoccus denitrificans software is released under the GNU General Public License 3.0, the source code is freely available here to modify providing the copyright notice remains intact and due credit is given to the authors in publications.


  1. Woolfenden H.C., Gates, A.J., Bocking, C. Blyth, M.G., Richardson D.J., Moulton, V. (2013) Modelling the effect of copper availability on bacterial denitrification. MicrobiologyOpen (in press).
  2. Felgate, H., Giannopoulos, G., Sullivan, M.J., Gates, A.J., Clarke, T.A., Baggs, E., et al. (2012) The impact of copper, nitrate and carbon status on the emission of nitrous oxide by two species of bacteria with biochemically distinct denitrification pathways. Environ Microbiol 14: 1788­-1800

Research Team

Dr. Hugh Woolfenden, Prof. Vincent Moulton