Publications

Preprints

• Espinel-Ríos, S., Walser, R., Zhang, D., 2025. Reinforcement learning for robust dynamic metabolic control. arXiv preprint. https://doi.org/10.48550/ARXIV.2504.00735 

Peer-reviewed journal articles

• Espinel-Ríos, S., Avalos, J.L., Chanona, E.A. del R., Zhang, D., 2025. Reinforcement learning for efficient and robust multi-setpoint and multi-trajectory tracking in bioprocesses. Computers & Chemical Engineering. https://doi.org/10.1016/j.compchemeng.2025.109297

• Hoffman, S.M., Espinel‐Ríos, S., Kwartler, S.K., Lalwani, M.A., Avalos, J.L., 2025. Balancing doses of EL222 and light improves optogenetic induction of protein production in Komagataella phaffii. Biotechnology and Bioengineering. https://doi.org/10.1002/bit.29027 

• Espinel-Ríos, S., 2025. Biotechnology systems engineering: preparing the next generation of bioengineers. Frontiers in Systems Biology 5. https://doi.org/10.3389/fsysb.2025.1583534

• Alexis, E., Espinel-Ríos, S., Kevrekidis, I.G., Avalos, J.L., 2025. Biochemical implementation of acceleration sensing and PIDA control. npj Systems Biology and Applications 11. https://doi.org/10.1038/s41540-025-00514-0 

• Espinel-Ríos, S., Montaño López, J., Avalos, J.L., 2025. Omics-driven hybrid dynamic modeling of bioprocesses with uncertainty estimation. Biochemical Engineering Journal 216, 109637. https://doi.org/10.1016/j.bej.2025.109637 

• Pennington, O., Espinel Ríos, S., Sebastian, M.T., Dickson, A., Zhang, D., 2024. A multiscale hybrid modelling methodology for cell cultures enabled by enzyme-constrained dynamic metabolic flux analysis under uncertainty. Metabolic Engineering 86, 274–287. https://doi.org/10.1016/j.ymben.2024.10.013 

• Espinel-Ríos, S., Avalos, J.L., 2024. Hybrid physics-informed metabolic cybergenetics: process rates augmented with machine-learning surrogates informed by flux balance analysis. Industrial & Engineering Chemistry Research 63, 6685–6700. https://doi.org/10.1021/acs.iecr.4c00001

• Espinel-Ríos, S., Behrendt, G., Bauer, J., Morabito, B., Pohlodek, J., Schütze, A., Findeisen, R., Bettenbrock, K., Klamt, S., 2024. Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. Process Biochemistry 143, 174–185. https://doi.org/10.1016/j.procbio.2024.04.032 

• Espinel‐Ríos, S., Morabito, B., Pohlodek, J., Bettenbrock, K., Klamt, S., Findeisen, R., 2023. Toward a modeling, optimization, and predictive control framework for fed‐batch metabolic cybergenetics. Biotechnology and Bioengineering 121, 366–379. https://doi.org/10.1002/bit.28575 

• Boecker, S., Espinel-Ríos, S., Bettenbrock, K., Klamt, S., 2022. Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering 73, 50–57. https://doi.org/10.1016/j.ymben.2022.05.006 

• Espinel‐Ríos, S., Bettenbrock, K., Klamt, S., Findeisen, R., 2022. Maximizing batch fermentation efficiency by constrained model‐based optimization and predictive control of adenosine triphosphate turnover. AIChE Journal 68. https://doi.org/10.1002/aic.17555 

• Espinel-Ríos, S., Ruiz-Espinoza, J.E., 2018. Production of 1,3-propanediol from crude glycerol: bioprocess design and profitability analysis. Revista Mexicana de Ingeniería Química 18, 831–840. https://doi.org/10.24275/uam/izt/dcbi/revmexingquim/2019v18n3/espinel 

• Espinel-Ríos, S., Palmerín-Carreño, D.M., Hernández-Orihuela, A.L., Martínez-Antonio, A., 2018. A Plackett-Burman design for substituting MRS medium components with avocado seed hydrolysate for growth and lactic acid production by Lactobacillus sp. Revista Mexicana de Ingeniería Química 19, 131–141. https://doi.org/10.24275/uam/izt/dcbi/revmexingquim/2019v18n1/espinel 

• Gao, W., Tabil, L.G., Dumonceaux, T., Espinel Ríos, S., Zhao, R., 2017. Optimization of biological pretreatment to enhance the quality of wheat straw pellets. Biomass and Bioenergy 97, 77–89. https://doi.org/10.1016/j.biombioe.2016.12.012 

Peer-reviewed conference articles

• Espinel-Ríos, S., Mo, J.Q., Zhang, D., del Rio-Chanona, E.A., Avalos, J.L., 2024. Enhancing reinforcement learning for population setpoint tracking in co-cultures. IFAC-PapersOnLine 59, 61–66. https://doi.org/10.1016/j.ifacol.2025.07.122 

• Espinel-Ríos, S., Avalos, J.L., 2024. Linking intra- and extra-cellular metabolic domains via neural-network surrogates for dynamic metabolic control. IFAC-PapersOnLine 58, 115–120. https://doi.org/10.1016/j.ifacol.2024.10.020 

• Pennington, O., Ríos, S.E., Sebastian, M.T., Dickson, A., Zhang, D., 2024. Dynamic multiscale hybrid modelling of a CHO cell system for recombinant protein production. IFAC-PapersOnLine 58, 133–138. https://doi.org/10.1016/j.ifacol.2024.08.326 

• Espinel-Ríos, S., Kok, R., Klamt, S., Avalos, J.L., Findeisen, R., 2023. Batch-to-batch optimization with model adaptation leveraging Gaussian processes: the case of optogenetically assisted microbial consortia. IEEE Xplore, pp. 1292–1297. https://doi.org/10.23919/iccas59377.2023.10316811 

• Espinel-Ríos, S., Bettenbrock, K., Klamt, S., Avalos, J.L., Findeisen, R., 2023. Machine learning-supported cybergenetic modeling, optimization and control for synthetic microbial communities, in: 33rd European Symposium on Computer Aided Process Engineering. Elsevier, pp. 2601–2606. https://doi.org/10.1016/b978-0-443-15274-0.50413-3 

• Espinel-Ríos, S., Slaviero, G., Bettenbrock, K., Klamt, S., Findeisen, R., 2023. Monitoring intracellular metabolite concentrations by moving horizon estimation based on kinetic modeling. IFAC-PapersOnLine 56, 4608–4613. https://doi.org/10.1016/j.ifacol.2023.10.968 

• Espinel-Ríos, S., Huber, N., Alcalá-Orozco, E.A., Morabito, B., Rexer, T.F.T., Reichl, U., Klamt, S., Findeisen, R., 2022. Cell-free biosynthesis meets dynamic optimization and control: a fed-batch framework. IFAC-PapersOnLine 55, 92–97. https://doi.org/10.1016/j.ifacol.2023.01.021 

• Espinel-Ríos, S., Morabito, B., Pohlodek, J., Bettenbrock, K., Klamt, S., Findeisen, R., 2022. Optimal control and dynamic modulation of the ATPase gene expression for enforced ATP wasting in batch fermentations. IFAC-PapersOnLine 55, 174–180. https://doi.org/10.1016/j.ifacol.2022.07.440 

• Espinel-Ríos, S., Morabito, B., Bettenbrock, K., Klamt, S., Findeisen, R., 2022. Soft sensor for monitoring dynamic changes in cell composition. IFAC-PapersOnLine 55, 98–103. https://doi.org/10.1016/j.ifacol.2023.01.022 

• Morabito, B., Pohlodek, J., Kranert, L., Espinel-Ríos, S., Findeisen, R., 2022. Efficient and simple Gaussian process supported stochastic model predictive control for bioreactors using HILO-MPC. IFAC-PapersOnLine 55, 922–927. https://doi.org/10.1016/j.ifacol.2022.07.562 

Patents

• Hoffman, S. M., Espinel-Ríos, S., & Avalos, J. L. Optogenetic production of recombinant protein in Pichia pastoris. Patent filed.

• Martínez-Antonio, A., Minchaca-Acosta, A. Z., Hernández-Orihuela, A. L., Rosales-Colunga, L. M., Estévez-Palmas, J. M., Espinel-Ríos, S., 2016. Culture medium derived from avocado seed material. https://patents.google.com/patent/WO2016079568A1/en

Conference abstracts

• Enhancing the physical quality of barley straw pellets by optimizing biological pretreatment, 2016. ASABE International Meeting. American Society of Agricultural and Biological Engineers. https://doi.org/10.13031/aim.20162447920