The use of optogenetics in metabolic engineering for light-controlled microbial chemical production raises the prospect of utilizing control and optimization techniques routinely deployed in traditional chemical manufacturing. However, such mechanisms require well-characterized, customizable tools that respond fast enough to be used as real-time inputs during fermentations. Here, we present OptoINVRT7, a new rapid optogenetic inverter circuit to control gene expression in Saccharomyces cerevisiae. The circuit induces gene expression in only 0.6 h after switching cells from light to darkness, which is at least 6 times faster than previous OptoINVRT optogenetic circuits used for chemical production. In addition, we introduce an engineered inducible GAL1 promoter (P GAL1-S ), which is stronger than any constitutive or inducible promoter commonly used in yeast. Combining OptoINVRT7 with P GAL1-S achieves strong and lighttunable levels of gene expression with as much as 132.9 ± 22.6-fold induction in darkness. The high performance of this new optogenetic circuit in controlling metabolic enzymes boosts production of lactic acid and isobutanol by more than 50% and 15%, respectively. The strength and controllability of OptoINVRT7 and P GAL1-S open the door to applying process control tools to engineered metabolisms to improve robustness and yields in microbial fermentations for chemical production.

Thin film materials for photovoltaics such as cadmium telluride (CdTe), copper-indium diselenide-based chalcopyrites (CIGS), and lead iodide-based perovskites offer the potential of lower solar module capital costs and improved performance to microcrystalline silicon. However, for decades understanding and controlling hole and electron concentration in these polycrystalline films has been extremely challenging and limiting. Ionic bonding between constituent atoms often leads to tenacious intrinsic compensating defect chemistries that are difficult to control. Device modeling indicates that increasing CdTe hole density while retaining carrier lifetimes of several nanoseconds can increase solar cell efficiency to 25%. This paper describes in-situ Sb, As, and P doping and post-growth annealing that increases hole density from historic 1014 limits to 1016–1017 cm−3 levels without compromising lifetime in thin polycrystalline CdTe films, which opens paths to advance solar performance and achieve costs below conventional electricity sources.

Traditional process monitoring methods cannot evaluate and grade the degree of harm that faults can cause to an industrial process. Consequently, a process could be shut down inadvertently when harmless faults occur. To overcome such problems, we propose a hierarchical process monitoring method for fault detection, fault grade evaluation, and fault diagnosis. First, we propose fault grade classification principles for subdividing faults into three grades: harmless, mild, and severe, according to the harm the fault can cause to the process. Second, two‐level indices are constructed for fault detection and evaluation, with the first‐level indices used to detect the occurrence of faults while the second‐level indices are used to determine the fault grade. Finally, to identify the root cause of the fault, we propose a new online fault diagnosis method based on the square deviation magnitude. The effectiveness and advantages of the proposed methods are illustrated with an industrial case study. © 2017 American Institute of Chemical Engineers AIChE J, 63: 2781–2795, 2017

In manufacturing monoclonal antibodies (mAbs), it is crucial to be able to predict how process conditions and supplements affect productivity and quality attributes, especially glycosylation. Supplemental inputs, such as amino acids and trace metals in the media, are reported to affect cell metabolism and glycosylation; quantifying their effects is essential for effective process development. We aim to present and validate, through a commercially relevant cell culture process, a technique for modeling such effects efficiently. While existing models can predict mAb production or glycosylation dynamics under specific process configurations, adapting them to new processes remains challenging, because it involves modifying the model structure and often requires some mechanistic understanding. Here, a modular modeling technique for adapting an existing model for a fed‐batch Chinese hamster ovary (CHO) cell culture process without structural modifications or mechanistic insight is presented. Instead, data is used, obtained from designed experimental perturbations in media supplementation, to train and validate a supplemental input effect model, which is used to “patch” the existing model. The combined model can be used for model‐based process development to improve productivity and to meet product quality targets more efficiently. The methodology and analysis are generally applicable to other CHO cell lines and cell types.

Developing accurate dynamical system models from physical insight or data can be impeded when only partial observations of the system state are available. Here, we combine conservation laws used in physics and engineering with artificial neural networks to construct "grey-box" system models that make accurate predictions even with limited information. These models use a time delay embedding (c.f., Takens embedding theorem) to reconstruct effect of the intrinsic states, and can be used for multiscale systems where macroscopic balance equations depend on unmeasured micro/meso scale phenomena. By incorporating physics knowledge into the neural network architecture, we regularize variables and may train the model more accurately on smaller data sets than black-box neural network models. We present numerical examples from biotechnology, including a continuous bioreactor actuated using light through optogenetics (an emerging technology in synthetic biology) where the effect of unmeasured intracellular information is recovered from the histories of the measured macroscopic variables.

Dynamic control of engineered microbes using light via optogenetics has been demonstrated as an effective strategy for improving the yield of biofuels, chemicals, and other products. An advantage of using light to manipulate microbial metabolism is the relative simplicity of interfacing biological and computer systems, thereby enabling in silico control of the microbe. Using this strategy for control and optimization of product yield requires an understanding of how the microbe responds in real-time to the light inputs. Toward this end, we present mechanistic models of a set of yeast optogenetic circuits. We show how these models can predict short- and long-time response to varying light inputs and how they are amenable to use with model predictive control (the industry standard among advanced control algorithms). These models reveal dynamics characterized by time-scale separation of different circuit components that affect the steady and transient levels of the protein under control of the circuit. Ultimately, this work will help enable real-time control and optimization tools for improving yield and consistency in the production of biofuels and chemicals using microbial fermentations.

Model predictive control (MPC) is a de facto standard control algorithm across the process industries. There remain, however, applications where MPC is impractical because an optimization problem is solved at each time step. We present a link between explicit MPC formulations and manifold learning to enable facilitated prediction of the MPC policy. Our method uses a similarity measure informed by control policies and system state variables, to “learn” an intrinsic parametrization of the MPC controller using a diffusion maps algorithm, which will also discover a low‐dimensional control law when it exists as a smooth, nonlinear combination of the state variables. We use function approximation algorithms to project points from state space to the intrinsic space, and from the intrinsic space to policy space. The approach is illustrated first by “learning” the intrinsic variables for MPC control of constrained linear systems, and then by designing controllers for an unstable nonlinear reactor.

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