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   https://doi.org/10.1146/annurev-chembioeng-091720-125738  

   Ni, Cynthia; Dinh, Christina V.; Prather, Kristala L.J. (June 2021, Annual Review of Chemical and Biomolecular Engineering)

   null (Ed.)

   Metabolic engineering reprograms cells to synthesize value-added products. In doing so, endogenous genes are altered and heterologous genes can be introduced to achieve the necessary enzymatic reactions. Dynamic regulation of metabolic flux is a powerful control scheme to alleviate and overcome the competing cellular objectives that arise from the introduction of these production pathways. This review explores dynamic regulation strategies that have demonstrated significant production benefits by targeting the metabolic node corresponding to a specific challenge. We summarize the stimulus-responsive control circuits employed in these strategies that determine the criterion for actuating a dynamic response and then examine the points of control that couple the stimulus-responsive circuit to a shift in metabolic flux. 

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3. Theoretical Understanding of Dynamic Catalysis

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4. Dynamic Enumeration of Similarity Joins

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   Agarwal, Pankaj K.; Hu, Xiao; Sintos, Stavros; Yang, Jun (July 2021, Proceedings of the 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021))

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5. Dynamic control of DNA condensation

   https://doi.org/10.1038/s41467-024-46266-z  

   Agarwal, Siddharth; Osmanovic, Dino; Dizani, Mahdi; Klocke, Melissa A.; Franco, Elisa (March 2024, Nature Communications)

   Abstract Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics. 

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