Automatic identification of structured process models based on biological phenomena detected in (fed-)batch experiments

Generic Workflow for the Setup of Mechanistic Process Models

Process models, consisting of transferable and applicable knowledge, can be used for various tasks such as process development and optimization, and for predicting and controlling critical process variables. In this regard, mechanistic process models, describing the mechanism of a system with a distinct model structure and characteristic parameters, are very promising.The development of a reliable and applicable model is usually the critical step, before model simulation and application show beneficial effects. In this chapter, a workflow for the generation of mechanistic process models is presented and applied on a typical cell culture process. The workflow includes the definition of critical reactions and the identification of their kinetics. By an iterative approach different reactions and kinetics are tested and model quality is assessed, leading to a final, target-oriented model.

Usage of Digital Twins Along a Typical Process Development Cycle

Digital methods for process design, monitoring, and control can convert classical trial-and-error bioprocess development to a quantitative engineering approach. By interconnecting hardware, software, data, and humans currently untapped process optimization potential can be accessed. The key component within such a framework is a digital twin interacting with its physical process counterpart. In this chapter, we show how digital twin guided process development can be applied on an exemplary microbial cultivation process. The usage of digital twins is described along a typical process development cycle, ranging from early strain characterization to real-time control applications. Along an illustrative case study on microbial upstream bioprocessing, we emphasize that digital twins can integrate entire process development cycles if the digital twin itself and the underlying models are continuously adapted to newly available data. Therefore, the digital twin can be regarded as a powerful knowledge management tool and a decision support system for efficient process development. Its full potential can be deployed in a real-time environment where targeted control actions can further improve process performance.

NMPC-Based Workflow for Simultaneous Process and Model Development Applied to a Fed-Batch Process for Recombinant C. glutamicum

For the fast and improved development of bioprocesses, new strategies are required where both strain and process development are performed in parallel. Here, a workflow based on a Nonlinear Model Predictive Control (NMPC) algorithm is described for the model-assisted development of biotechnological processes. By using the NMPC algorithm, the process is designed with respect to a target function (product yield, biomass concentration) with a drastically decreased number of experiments. A workflow for the usage of the NMPC algorithm as a process development tool is outlined. The NMPC algorithm is capable of improving various process states, such as product yield and biomass concentration. It uses on-line and at-line data and controls and optimizes the process by model-based process extrapolation. In this study, the algorithm is applied to a Corynebacterium glutamicum process. In conclusion, the potency of the NMPC algorithm as a powerful tool for process development is demonstrated. In particular, the benefits of the system regarding the characterization and optimization of a fed-batch process are outlined. With the NMPC algorithm, process development can be run simultaneously to strain development, resulting in a shortened time to market for novel products.

Digital Twins in Pharmaceutical and Biopharmaceutical Manufacturing: A Literature Review

The development and application of emerging technologies of Industry 4.0 enable the realization of digital twins (DT), which facilitates the transformation of the manufacturing sector to a more agile and intelligent one. DTs are virtual constructs of physical systems that mirror the behavior and dynamics of such physical systems. A fully developed DT consists of physical components, virtual components, and information communications between the two. Integrated DTs are being applied in various processes and product industries. Although the pharmaceutical industry has evolved recently to adopt Quality-by-Design (QbD) initiatives and is undergoing a paradigm shift of digitalization to embrace Industry 4.0, there has not been a full DT application in pharmaceutical manufacturing. Therefore, there is a critical need to examine the progress of the pharmaceutical industry towards implementing DT solutions. The aim of this narrative literature review is to give an overview of the current status of DT development and its application in pharmaceutical and biopharmaceutical manufacturing. State-of-the-art Process Analytical Technology (PAT) developments, process modeling approaches, and data integration studies are reviewed. Challenges and opportunities for future research in this field are also discussed.

Model-Based Process Optimization for the Production of Macrolactin D by Paenibacillus polymyxa

In this study, we show the successful application of different model-based approaches for the maximizing of macrolactin D production by Paenibacillus polymyxa. After four initial cultivations, a family of nonlinear dynamic biological models was determined automatically and ranked by their respective Akaike Information Criterion (AIC). The best models were then used in a multi-model setup for robust product maximization. The experimental validation shows the highest product yield attained compared with the identification runs so far. In subsequent fermentations, the online measurements of CO2 concentration, base consumption, and near-infrared spectroscopy (NIR) were used for model improvement. After model extension using expert knowledge, a single superior model could be identified. Model-based state estimation with a sigma-point Kalman filter (SPKF) was based on online measurement data, and this improved model enabled nonlinear real-time product maximization. The optimization increased the macrolactin D production even further by 28% compared with the initial robust multi-model offline optimization.

Application of dynamic metabolic flux analysis for process modeling: Robust flux estimation with regularization, confidence bounds, and selection of elementary modes

In macroscopic dynamic models of fermentation processes, elementary modes (EM) derived from metabolic networks are often used to describe the reaction stoichiometry in a simplified manner and to build predictive models by parameterizing kinetic rate equations for the EM. In this procedure, the selection of a set of EM is a key step which is followed by an estimation of their reaction rates and of the associated confidence bounds. In this paper, we present a method for the computation of reaction rates of cellular reactions and EM as well as an algorithm for the selection of EM for process modeling. The method is based on the dynamic metabolic flux analysis (DMFA) proposed by Leighty and Antoniewicz (2011, Metab Eng, 13(6), 745–755) with additional constraints, regularization and analysis of uncertainty. Instead of using estimated uptake or secretion rates, concentration measurements are used directly to avoid an amplification of measurement errors by numerical differentiation. It is shown that the regularized DMFA for EM method is significantly more robust against measurement noise than methods using estimated rates. The confidence intervals for the estimated reaction rates are obtained by bootstrapping. For the selection of a set of EM for a given st oichiometric model, the DMFA for EM method is combined with a multiobjective genetic algorithm. The method is applied to real data from a CHO fed‐batch process. From measurements of six fed‐batch experiments, 10 EM were identified as the smallest subset of EM based upon which the data can be described sufficiently accurately by a dynamic model. The estimated EM reaction rates and their confidence intervals at different process conditions provide useful information for the kinetic modeling and subsequent process optimization.

Model-Based Methods in the Biopharmaceutical Process Lifecycle

Model-based methods are increasingly used in all areas of biopharmaceutical process technology. They can be applied in the field of experimental design, process characterization, process design, monitoring and control. Benefits of these methods are lower experimental effort, process transparency, clear rationality behind decisions and increased process robustness. The possibility of applying methods adopted from different scientific domains accelerates this trend further. In addition, model-based methods can help to implement regulatory requirements as suggested by recent Quality by Design and validation initiatives. The aim of this review is to give an overview of the state of the art of model-based methods, their applications, further challenges and possible solutions in the biopharmaceutical process life cycle. Today, despite these advantages, the potential of model-based methods is still not fully exhausted in bioprocess technology. This is due to a lack of (i) acceptance of the users, (ii) user-friendly tools provided by existing methods, (iii) implementation in existing process control systems and (iv) clear workflows to set up specific process models. We propose that model-based methods be applied throughout the lifecycle of a biopharmaceutical process, starting with the set-up of a process model, which is used for monitoring and control of process parameters, and ending with continuous and iterative process improvement via data mining techniques.

Rapid process synthesis supported by a unified modular software framework

Although known to be very powerful, the widespread application of model-based techniques is still significantly hampered in the area of bio-processes. Reasons for this situation can be found along the whole chain to set up and implement such approaches. In a time-consuming step, models are typically hand-crafted. Whether alternatives of better models exist to actually fulfill the final goals is undocumented, most often even unknown. In a next step, model-based process control methods are hand-coded in an error-prone procedure. For many of these methods given in the literature, only simulation studies are shown, leaving the interested reader with the unanswered question whether the implementation of a specific method in a real process is viable. As the potentially time-consuming implementation of such a method presents a risk for a rapid process development, promising candidates may be overlooked. To remediate this unsatisfactory situation, a combination of theoretical methods and information technology is proposed here. By an exemplarily realized software tool, it is shown how such an environment helps to promote model-based optimization, supervision, and control of bio-processes and allows for an inexpensive test of new ideas as well in real-life experiments. The contribution concentrates on an overview of a possible software architecture with respect to necessary methods and a meaningful information strategy, highlighting some of the more crucial building blocks. Experimental results exploiting parts of the proposed methods are given for a yeast strain synthesizing a product of industrial interest.