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Simplex-based optimization of numerical and categorical inputs in early bioprocess development: Case studies in HT chromatography

Konstantinidis, S; Titchener-Hooker, N; Velayudhan, A; (2017) Simplex-based optimization of numerical and categorical inputs in early bioprocess development: Case studies in HT chromatography. Biotechnology Journal , 12 (8) 10.1002/biot.201700174. Green open access

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Abstract

Bioprocess development studies often involve the investigation of numerical and categorical inputs via the adoption of Design of Experiments (DoE) techniques. An attractive alternative is the deployment of a grid compatible Simplex variant which has been shown to yield optima rapidly and consistently. In this work, the method is combined with dummy variables and it is deployed in three case studies wherein spaces are comprised of both categorical and numerical inputs, a situation intractable by traditional Simplex methods. The first study employs in silico data and lays out the dummy variable methodology. The latter two employ experimental data from chromatography based studies performed with the filter‐plate and miniature column High Throughput (HT) techniques. The solute of interest in the former case study was a monoclonal antibody whereas the latter dealt with the separation of a binary system of model proteins. The implemented approach prevented the stranding of the Simplex method at local optima, due to the arbitrary handling of the categorical inputs, and allowed for the concurrent optimization of numerical and categorical, multilevel and/or dichotomous, inputs. The deployment of the Simplex method, combined with dummy variables, was therefore entirely successful in identifying and characterizing global optima in all three case studies. The Simplex‐based method was further shown to be of equivalent efficiency to a DoE‐based approach, represented here by D‐Optimal designs. Such an approach failed, however, to both capture trends and identify optima, and led to poor operating conditions. It is suggested that the Simplex‐variant is suited to development activities involving numerical and categorical inputs in early bioprocess development.

Type: Article
Title: Simplex-based optimization of numerical and categorical inputs in early bioprocess development: Case studies in HT chromatography
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/biot.201700174
Publisher version: https://doi.org/10.1002/biot.201700174
Language: English
Additional information: This version is the version of record. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biochemical Research Methods, Biotechnology & Applied Microbiology, Biochemistry & Molecular Biology, Categorical variables, Chromatography, Filter plates, High throughput bioprocess development, RoboColumns, Simplex optimization, CATION-EXCHANGE CHROMATOGRAPHY, PROTEIN-A CHROMATOGRAPHY, MONOCLONAL-ANTIBODIES, RAPID IDENTIFICATION, PURIFICATION, PRECIPITATION, ALGORITHM, DESIGNS
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Biochemical Engineering
URI: https://discovery.ucl.ac.uk/id/eprint/10056950
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