A hybrid mechanistic-empirical model for in silico mammalian cell bioprocess simulation

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28 Scopus citations


In cell culture processes cell growth and metabolism drive changes in the chemical environment of the culture. These environmental changes elicit reactor control actions, cell growth response, and are sensed by cell signaling pathways that influence metabolism. The interplay of these forces shapes the culture dynamics through different stages of cell cultivation and the outcome greatly affects process productivity, product quality, and robustness. Developing a systems model that describes the interactions of those major players in the cell culture system can lead to better process understanding and enhance process robustness. Here we report the construction of a hybrid mechanistic-empirical bioprocess model which integrates a mechanistic metabolic model with subcomponent models for cell growth, signaling regulation, and the bioreactor environment for in silico exploration of process scenarios. Model parameters were optimized by fitting to a dataset of cell culture manufacturing process which exhibits variability in metabolism and productivity. The model fitting process was broken into multiple steps to mitigate the substantial numerical challenges related to the first-principles model components. The optimized model captured the dynamics of metabolism and the variability of the process runs with different kinetic profiles and productivity. The variability of the process was attributed in part to the metabolic state of cell inoculum. The model was then used to identify potential mitigation strategies to reduce process variability by altering the initial process conditions as well as to explore the effect of changing CO2 removal capacity in different bioreactor scales on process performance. By incorporating a mechanistic model of cell metabolism and appropriately fitting it to a large dataset, the hybrid model can describe the different metabolic phases in culture and the variability in manufacturing runs. This approach of employing a hybrid model has the potential to greatly facilitate process development and reactor scaling.

Original languageEnglish (US)
Pages (from-to)31-40
Number of pages10
JournalMetabolic Engineering
Early online dateApr 1 2021
StatePublished - Jul 2021

Bibliographical note

Funding Information:
The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing computational resources for the results reported in this paper.

Publisher Copyright:
© 2021


  • Cell culture
  • Metabolic model
  • Model
  • Optimization
  • Process variability
  • Scale-up


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