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Full-Text Articles in Engineering

K-Fit: Parameterizing Kinetic Models Of Metabolism Using Multiple Fluxomic Datasets, Costa Maranas Jul 2019

K-Fit: Parameterizing Kinetic Models Of Metabolism Using Multiple Fluxomic Datasets, Costa Maranas

Biochemical and Molecular Engineering XXI

Kinetic models predict the metabolic flows by directly linking metabolite concentrations and enzyme levels to reaction fluxes. Robust parameterization of organism-level kinetic models that faithfully reproduce the effect of different genetic or environmental perturbations remains an open challenge due to the intractability of existing algorithms. This paper introduces K-FIT, an accelerated kinetic parameterization workflow that leverages a novel decomposition approach to identify steady-state fluxes in response to genetic perturbations followed by a gradient-based update of kinetic parameters until predictions simultaneously agree with the fluxomic data in all perturbed metabolic networks. The applicability of K-FIT to large-scale models is demonstrated by ...


The Statistics Of Directed Evolution: From Library Generation To High Throughput Screens, Keith Tyo Jul 2019

The Statistics Of Directed Evolution: From Library Generation To High Throughput Screens, Keith Tyo

Biochemical and Molecular Engineering XXI

Directed evolution has been recognized as a powerful approach to creating enzymes and cells with desirable properties, such as growth on a new substrate, thermotolerance, or even novel reaction mechanisms. The directed evolution approach is to generate diversity through genetic mutations and screen the diversity for mutants that have improved properties compared to the parent. This diversification and screening can be repeated to generate mutants with superior properties.

While the concept is straightforward, the devil is in the details. How should I create diversity (error prone PCR, mutagenic primers, transposons…)? How much diversity do I need (103, 106 ...


Advanced Technologies And Computational Modeling In Continuous Bioprocessing Heather Brooke, Pall Corporation, Usa, Heather Brooke, Edita Botonjic-Sehic Jul 2019

Advanced Technologies And Computational Modeling In Continuous Bioprocessing Heather Brooke, Pall Corporation, Usa, Heather Brooke, Edita Botonjic-Sehic

Biochemical and Molecular Engineering XXI

Biotech companies have been emphasizing the implementation and utilization of process analytical technology (PAT) and chemometrics in biomanufacturing. Advanced technologies and computation modeling have contributed significantly in making this capability come to life. Although there are still gaps in the area of advanced analytics for the process, computation modeling has started to contribute towards process characterization, which will lead to real-time process control. PAT and modeling infrastructure can be utilized in integrated continuous bioprocessing to gain better process understating, reduce production cycle time, improve yield, advance efficiency by converting from a batch process into a continuous process, and reduce cost ...


Biologicalisation: A Nature-Based Digital Manufacturing Revolution, William Whitford Jul 2019

Biologicalisation: A Nature-Based Digital Manufacturing Revolution, William Whitford

Biochemical and Molecular Engineering XXI

Industry 4.0 is changing our manufacturing concepts [1]. Biologicalisation is the use of 4.0 principals in concert with biological and bio-inspired materials, chemistries and functions to support an efficient and sustainable manufacturing schema. From product design, to development and manufacturing, biomimetic product designs and bio-integrated manufacturing systems describe this biological transformation of manufacturing [2].

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Conference Program, Christina Chan, Mattheos Koffas, Steffen Schaffer, Rashmi Kshirsagar Jul 2019

Conference Program, Christina Chan, Mattheos Koffas, Steffen Schaffer, Rashmi Kshirsagar

Biochemical and Molecular Engineering XXI

No abstract provided.