About

Dr. Cournia is Director of Research and Vice President of the Scientific Board at the Biomedical Research Foundation, Academy of Athens. She leads research in high-performance computing (HPC) for biomolecular modeling and drug design, focusing on the molecular mechanisms of protein–membrane interactions and their role in disease. (http://www.drugdesign.gr). She graduated from the Chemistry Department, University of Athens, Greece and received her PhD degree from the University of Heidelberg, Germany. She then carried out postdoctoral research at Yale University, Department of Chemistry as an AACR Judah Folkman Postdoctoral Fellow. She has been awarded with the American Association for Cancer Research Angiogenesis Fellowship (2008), the “Woman of Innovation 2009” Award from the Connecticut Technology Council, USA, the Marie Curie Fellowship from the European Union (2010), the “Outstanding Junior Faculty Award” from the American Chemical Society (2014) and the first “Ada Lovelace Award” from the “Partnership for Advanced Computing in Europe” (2016). She is an Executive Editor with the Journal of Chemical information and Modeling, American Chemical Society and the representative of Greece in the Division of Computational and Theoretical Chemistry in the European Chemical Society.

Research interests

Our work focuses on exploring structure and dynamics of biological systems and linking those to function using computational methods. Our goal is to utilize this knowledge in order to understand the biophysics behind biomolecules and rationally design new chemical entities that could contribute in treating human disease. For this purpose we employ a wide range of physics-based and AI techniques, such as enhanced sampling and coarse-grained Molecular Dynamics, free energy perturbation calculations, Markov State models, Machine Learning, pharmacological property prediction, virtual screening. We also develop and apply machine learning models and molecular simulation methods. Particular research interests are structure-based drug design and free-energy calculations, protein–membrane interactions and allostery, high-performance computing in life sciences, development of machine learning methods and applications for biomolecular modeling.

Working with BioExcel

BioExcel’s ecosystem of software, training, and user support aligns closely with Zoe’s research in high-performance computing for biomolecular modeling and drug discovery. Her work relies heavily on large-scale molecular dynamics simulations and free-energy calculations, where robust, scalable, and well-supported tools are essential. Through BioExcel-supported software such as GROMACS, pmx and associated workflows, her research benefits from highly optimized simulation engines capable of efficiently exploiting modern HPC architectures. This is particularly relevant for her studies on complex biomolecular systems such as membrane-associated proteins and oncogenic mutations, which require extensive sampling and computational resources.

At the same time, Zoe is strongly committed to mentoring the next generation of scientists and fostering diversity and inclusion in computational science. This commitment closely resonates with BioExcel’s extensive training programme, which includes webinars, workshops, schools, and conferences across Europe, and has helped build a vibrant and collaborative community in advanced biomolecular simulation techniques.

Looking ahead, BioExcel’s continued development of interoperable tools, best practices, and user support is expected to further enhance the efficiency, reproducibility, and scalability of her research workflows. This will be particularly important as Zoe’s work increasingly leverages next-generation European supercomputing infrastructures and tackles more complex, data-intensive problems in precision medicine and targeted therapeutics.

Learn more about the BioExcel Ambassador Program