Robust Multi-Objective Global Optimization of Stochastic Processes With a Case Study in Gradient Elution Chromatography.

A novel algorithm for robust multi-objective process optimization under stochastic variability of environmental variables is introduced and applied to a case study in gradient elution chromatography. Process variability is accounted for by simultaneously optimizing several scenarios with random but fixed values of the environmental variables. These iterative optimizations are synchronized by planning the same experiments for all scenarios. Experiments are designed by maximizing the cumulative expected hypervolume improvement as predicted by several Gaussian process regression models. A straightforward method is presented for estimating the expected Pareto front and its variability based on the resulting data that maintains traceability of the corresponding process parameters. This information is required for robust process optimization, that is, determination of Pareto optimal processes that fulfil specific minimal criteria with a certain confidence. The presented algorithm can generally be applied to both in silico and wet lab experiments but involves an increased experimental effort as compared to the deterministic case.

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology.

A core business in industrial biotechnology using microbial production cell factories is the iterative process of strain engineering and optimization of bioprocess conditions. One important aspect is the improvement of cultivation medium to provide an optimal environment for microbial formation of the product of interest. It is well accepted that the media composition can dramatically influence overall bioprocess performance. Nutrition medium optimization is known to improve recombinant protein production with microbial systems and thus, this is a rewarding step in bioprocess development. However, very often standard media recipes are taken from literature, since tailor-made design of the cultivation medium is a tedious task that demands microbioreactor technology for sufficient cultivation throughput, fast product analytics, as well as support by lab robotics to enable reliability in liquid handling steps. Furthermore, advanced mathematical methods are required for rationally analyzing measurement data and efficiently designing parallel experiments such as to achieve optimal information content. The generic nature of the presented protocol allows for easy adaption to different lab equipment, other expression hosts, and target proteins of interest, as well as further bioprocess parameters. Moreover, other optimization objectives like protein production rate, specific yield, or product quality can be chosen to fit the scope of other optimization studies. The applied Kriging Toolbox (KriKit) is a general tool for Design of Experiments (DOE) that contributes to improved holistic bioprocess optimization. It also supports multi-objective optimization which can be important in optimizing both upstream and downstream processes.

A framework for accelerated phototrophic bioprocess development: integration of parallelized microscale cultivation, laboratory automation and Kriging-assisted experimental design.

BACKGROUND: Even though microalgae-derived biodiesel has regained interest within the last decade, industrial production is still challenging for economic reasons. Besides reactor design, as well as value chain and strain engineering, laborious and slow early-stage parameter optimization represents a major drawback. RESULTS: The present study introduces a framework for the accelerated development of phototrophic bioprocesses. A state-of-the-art micro-photobioreactor supported by a liquid-handling robot for automated medium preparation and product quantification was used. To take full advantage of the technology's experimental capacity, Kriging-assisted experimental design was integrated to enable highly efficient execution of screening applications. The resulting platform was used for medium optimization of a lipid production process using Chlorella vulgaris toward maximum volumetric productivity. Within only four experimental rounds, lipid production was increased approximately threefold to 212 ± 11 mg L-1 d-1. Besides nitrogen availability as a key parameter, magnesium, calcium and various trace elements were shown to be of crucial importance. Here, synergistic multi-parameter interactions as revealed by the experimental design introduced significant further optimization potential. CONCLUSIONS: The integration of parallelized microscale cultivation, laboratory automation and Kriging-assisted experimental design proved to be a fruitful tool for the accelerated development of phototrophic bioprocesses. By means of the proposed technology, the targeted optimization task was conducted in a very timely and material-efficient manner.

Kriging with trend functions nonlinear in their parameters: Theory and application in enzyme kinetics.

Kriging is an interpolation method commonly applied in empirical modeling for approximating functional relationships between impact factors and system response. The interpolation is based on a statistical analysis of given data and can optionally include a priori defined trend functions. However, Kriging can so far only be used with trend functions that are linear with respect to the parameters. In this contribution, we present an extension of the Kriging approach for handling trend functions that are nonlinear in their parameters. Our approach is based on Taylor linearization combined with an iterative parameter estimation procedure whose solution is practically computed via a root finding problem. We demonstrate our novel approach with measurement data from the application field of biocatalysis.

Multi-objective global optimization (MOGO): Algorithm and case study in gradient elution chromatography.

Biotechnological separation processes are routinely designed and optimized using parallel high-throughput experiments and/or serial experiments. Well-characterized processes can further be optimized using mechanistic models. In all these cases - serial/parallel experiments and modeling - iterative strategies are customarily applied for planning novel experiments/simulations based on the previously acquired knowledge. Process optimization is typically complicated by conflicting design targets, such as productivity and yield. We address these issues by introducing a novel algorithm that combines recently developed approaches for utilizing statistical regression models in multi-objective optimization. The proposed algorithm is demonstrated by simultaneous optimization of elution gradient and pooling strategy for chromatographic separation of a three-component system with respect to purity, yield, and processing time. Gaussian Process Regression Models (GPM) are used for estimating functional relationships between design variables (gradient, pooling) and performance indicators (purity, yield, time). The Pareto front is iteratively approximated by planning new experiments such as to maximize the Expected Hypervolume Improvement (EHVI) as determined from the GPM by Markov Chain Monte Carlo (MCMC) sampling. A comprehensive Monte-Carlo study with in-silico data illustrates efficiency, effectiveness and robustness of the presented Multi-Objective Global Optimization (MOGO) algorithm in determining best compromises between conflicting objectives with comparably very low experimental effort.