Microbial Fermentation and Bioprocess Simulation

Microbial fermentation and bioprocess simulation focuses on the quantitative modeling of microbial growth, product formation, and bioreactor dynamics. By integrating kinetic models, metabolic networks, and environmental factors, these simulations help optimize fermentation performance, scale-up processes, and enhance product yields. The approach bridges molecular-level understanding with industrial-scale applications, enabling rational design and predictive control of bioprocesses.

Fig. 1 Data-driven modeling steps. (Du YH, et al., 2022)

Modeling Principles

• Kinetic Modeling of Microbial Growth: Capturing growth rates, substrate uptake, and metabolite production using Monod-type or more complex kinetic equations.
• Dynamic Bioreactor Simulation: Modeling batch, fed-batch, continuous, and perfusion processes to predict culture behavior over time.
• Metabolic Flux Integration: Combining genome-scale metabolic models with fermentation dynamics for flux-based prediction of product formation.
• Environmental Parameter Effects: Assessing the influence of pH, temperature, dissolved oxygen, nutrient limitations, and stress factors on microbial productivity.
• Process Control and Optimization: Simulating feeding strategies, aeration, agitation, and other operational parameters to maximize yield and process stability.

This modeling method characterizes microbial growth and metabolic behavior through dynamic equations, coupling bioreactor dynamics with metabolic flux models, and integrating environmental factors and process control parameters to achieve systematic prediction and control of fermentation process performance, product formation, and process optimization.

Our Services

CD Biomodeling offers a comprehensive suite of modeling and simulation services designed to analyze, predict, and optimize microbial fermentation processes under a wide range of conditions.

• Development of kinetic and dynamic models for microbial fermentation

Construct detailed mathematical models capturing growth kinetics, substrate consumption, product formation, and inhibitory effects under batch, fed-batch, and continuous conditions.

• Integration of genome-scale metabolic models with bioreactor simulations

Combine GEM-based flux predictions with dynamic fermentation models to simulate intracellular metabolism and product synthesis in realistic process environments.

• Process optimization for enhanced product titer, yield, and productivity

Analyze metabolic and operational bottlenecks to design feeding strategies, aeration, agitation, and nutrient supply that maximize microbial productivity.

• Scale-up prediction from laboratory to industrial scales

Simulate changes in bioreactor volume, mixing, oxygen transfer, and heat management to predict performance during scale-up and reduce experimental trial-and-error.

• Simulation of multi-stage or co-culture fermentation systems

Model sequential or mixed microbial cultures, including interspecies interactions and cross-feeding, to optimize co-culture productivity and stability.

• Sensitivity and scenario analysis for process robustness

Evaluate the impact of environmental perturbations, parameter variability, and operational uncertainties on microbial growth and product formation.

• Custom modeling solutions for novel fermentation technologies

Develop tailored simulations for advanced systems such as perfusion reactors, continuous bioprocesses, or hybrid microbial/chemical production setups, supporting innovation and industrial application.

Tools & Resources

The state-of-the-art modeling and simulation software are leveraged to ensure accuracy, scalability, and industrial relevance.

Deliverables

Our final deliverables provide fully validated models, clear analytical outputs, and actionable insights to support your research, engineering, or bioprocess development goals.

Application Areas

At CD Biomodeling, we provide professional microbial fermentation and bioprocess simulation services that transform complex biological systems into predictive, data-driven models. By integrating microbial kinetics, metabolic behavior, and process engineering principles, we support the design, optimization, and scale-up of fermentation and biomanufacturing processes across industrial, pharmaceutical, environmental, and research applications. Our customized modeling and simulation solutions enable clients to reduce experimental costs, improve process robustness, and accelerate innovation from laboratory research to industrial production. If you would like to learn more about the service details or get technical support, please feel free to contact us.

For Research Use Only!

Related Services

• Microbial Physiological and Ecological Processes
• Genome-Scale Metabolic and Pathway Modeling
• Microbial Community and Interaction Modeling
• Data-Driven and AI-Assisted Microbial Modeling