Systems Engineering for Biotechnology

Research Group

Welcome to the blog of the research group led by Sebastián Espinel Ríos in the School of Chemical and Bioprocess Engineering at University College Dublin (UCD).

The Systems Engineering for Biotechnology group is part of UCD’s School of Chemical and Bioprocess Engineering in Dublin, Ireland.

Overview

Our group develops tailored computational methods for advanced modeling, optimization, and control, enabling and supporting novel biotechnological applications and the digitalization of the biotechnology industry. This includes mechanistic, AI-based, and hybrid strategies applied across in-cell, external, and multiscale levels. To achieve this, we take a systems-of-systems approach that integrates concepts from Process Systems Engineering (PSE), Systems Biology (SB), and Scientific Machine Learning (SciML).

We focus on three core areas in the context of bioprocesses and biosystems, with the ultimate goal of integrating intracellular and extracellular degrees of freedom to enable efficient, automated, and self-driving bioproduction.

Knowledge abstraction: Digital twin technologies, model reduction, and knowledge transfer.
Knowledge exploitation: Methods for multilevel optimization and control, including soft sensors.
Knowledge facilitation: Software development for bioprocess digitalization and automation.

We have experience in hybrid physics-informed modeling and model-based and learning-based optimization and control. We have developed model predictive control approaches for dynamic metabolic control; hybrid metabolic cybergenetic models combining macroscopic bioprocess knowledge with machine-learning components informed by process data or mechanistic metabolic models; and automated frameworks for model selection and uncertainty quantification. Our work also spans virtual sensing and state estimation of partially observed bioprocesses, including the inference of intracellular proteins and metabolites, as well as reinforcement learning for robust multi-setpoint, multi-trajectory, and dynamic metabolic control.

Our areas of application span industrial biotechnology (e.g., chemical production) and biopharmaceutical manufacturing (e.g., recombinant protein production).

Overview of our research areas toward advancing the digitalization of the biotechnology industry.

Systems Engineering for Biotechnology: a unifying framework integrating Systems Biology (SB) and Process Systems Engineering (PSE). https://doi.org/10.3389/fsysb.2025.1583534.

Interested in joining the group?

We welcome applications from prospective students and researchers. See current opportunities here.