INDISIM-Denitrification, an individual-based model for study the denitrification process.

Area of Science:

• Biogeochemistry
• Microbial Ecology
• Computational Biology

Background:

• Denitrification is a critical bacterial process balancing the global nitrogen (N) cycle.
• Understanding bacterial growth kinetics in denitrification is essential for environmental and industrial applications.

Purpose of the Study:

• To develop an individual-based model, INDISIM-Denitrification, for simulating bacterial denitrification.
• To model cell growth kinetics, nutrient uptake, and metabolic pathways under aerobic and anaerobic conditions.

Main Methods:

• Utilized the INDISIM individual-based modeling platform.
• Integrated a thermodynamic model for bacterial yield prediction.
• Modeled microbial metabolic reactions for denitrification, maintenance, and mass degradation.

Main Results:

• The INDISIM-Denitrification model accurately simulates denitrifying bacteria growth kinetics.
• The model was validated against experimental data for two bacterial species under different conditions.
• The simulator is adaptable for various denitrifying bacteria by adjusting parameters.

Conclusions:

• INDISIM-Denitrification provides an interactive tool for studying bacterial denitrification.
• The model enhances understanding of microbial metabolism and bioreactor performance.
• This research contributes to the study of the global nitrogen cycle.