Using Computations to Analyze and Reshape Metabolism for Bioproduction
Speaker
Costas D. Moranas
Penn State University
Abstract
Using Computations to Analyze and Reshape Metabolism for Bioproduction
In this talk, we will review ongoing efforts towards creating computational tools to elucidate insight and support engineering decisions in metabolism and protein design. We will highlight earlier contributions leveraging mathematical optimization to help reconstruct, analyze and redesign metabolic networks as well as design proteins with desired binding characteristics. We will next pivot towards more recent work that fuses both protein and metabolism design tasks to realize the assembly of carbon and energy efficient biosynthetic pathways by seamlessly blending known biochemical reactions with de novo steps. The emerging role of AI and large-language models will next be detailed in the context of enzyme kinetics and design prediction. Moving from stoichiometric to kinetic models of metabolism with genome-wide coverage, parameterization challenges will be described for several microbial production hosts. Insight and lessons gained from the application of these tools on a variety of biochemical engineering challenges that we have faced as members of the DOE bioenergy centers CBI and CABBI as well as the NSF AI Molecular Maker Laboratory Institute will be provided.
Bio
Costas D. Maranas (b. 1967) is the Waltemeyer Endowed Chemical Engineering Chair in the Pennsylvania State University. He received a Diploma in Chemical Engineering at the Aristotle University, Greece in 1990 and a Ph.D. in Chemical Engineering from Princeton University in 1995. He has been in the faculty of the department of Chemical Engineering at Penn State since 1995. Recent awards include the 2025 D.I.C. Wang Award for Excellence in Biochemical Engineering, 2021 Food, Pharmaceutical, and Bioengineering AIChE Division Award, 2020 Biotechnology Progress Award for Excellence in Biological Engineering Publication and the 2020 International Metabolic Engineering Award. Earlier accolades include the Allan P. Colburn Award for Excellence in Publications by a Young Member of AIChE (2002) and the Outstanding Young Investigator Award of the Computing and Systems Technology AIChE Division (2006). He is a member of several journal Editorial Boards including PLOS Computational Biology, BMC Systems Biology, Biotechnology Journal and Metabolic Engineering. He is a Fellow of the American Institute of Chemical Engineers (AIChE) and the American Institute of Medical and Biological Engineering (AIMBE). He is the Lead for the “Use Inspired Research” in the Center for Bioenergy Innovation (CBI) DOE center, a participant in the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) DOE center, and a founding member of the NSF Molecular Maker Lab Institute (MMLI).
The C. Maranas group develops and deploys computational frameworks informed by systems engineering, mathematical optimization, and machine learning to understand, analyze and redesign metabolism and redesign proteins. Research interests include computational protein design; enzyme and antibody engineering; reconstruction, curation and analysis of metabolic networks; computational strain design and synthetic biology; metabolism of photosynthetic organisms; metabolism of obligatory anaerobes; modeling of microbial communities; machine learning and large-language models; optimization theory and algorithms. Costas has co-authored over 250 refereed journal publications and proceedings including a textbook on “Optimization Methods in Metabolic Networks” (2016). He has supervised over 40 graduate students with many group alumni occupying leading positions in industry and academia. Costas lives in State College, PA with his wife Michelle Hutnik and german shepherd Lucca.