LUMI drives advancements in biomolecular simulation research

Andrea Nedelnikova is a PhD student in Informatics and Computational Science at VSB – Technical University of Ostrava. She also works at the Czech Advanced Technology and Research Institute in Olomouc (CATRIN), within a research group focused on biomolecular simulations. In her research, she relies also on the LUMI supercomputer. For her, a supercomputer is a bridge between equations and the behaviour of biomolecules – a microscope that reveals their hidden dynamics through computation rather than light.

What is the focus of your research?

– In my research, I focus on the study of biostructures – specifically nucleic acids, lipids, and proteins; in short, the molecules that make up our bodies – and their interactions with drugs or nanomaterials. Before a new drug or material can be used in medicine, it is essential to thoroughly investigate both its therapeutic effects and its potential adverse impacts.

How does a supercomputer help you in this work?

– I use the computer as a ‘microscope’ at the atomic level. Using computational chemistry methods, I observe how molecules behave and interact with one another. And it is the supercomputer that performs these extensive calculations.

What difference does supercomputing make compared to standard computers?

– The difference is fundamental. When I was calculating on not so powerful machines, I had to wait weeks for results; now, with the help of supercomputers, I can analyse them after just a few days. This opens up possibilities for more complex research. A SUPERcomputer delivers calculation results SUPERfast. Which is simply SUPER.

When did you first encounter supercomputers?

– Before entering university, I knew almost nothing about supercomputers. I first encountered them in the context of computational chemistry during one of the introductory lectures. As an enthusiastic chemist back then, I imagined my future exclusively in a laboratory wearing a white coat – the idea of a chemist sitting at a computer seemed almost absurd to me. However, the school closures during the COVID-19 pandemic shifted my career path. Today, I can no longer imagine my work without a supercomputer.

While basic chemical calculations can be handled by a standard laptop or desktop, a supercomputer performs them much faster and allows us to work with larger and more complex systems. This not only yields results more quickly but also enables me to run a higher volume of simulations, significantly enhancing both the quality and depth of the research.

What impact can this research have?

– Insight into the behaviour of atoms – the fundamental building blocks of matter – helps us better understand processes occurring in living organisms. This can contribute to the development of more effective or entirely new drugs, as well as the preparation of novel materials. For example, we have studied the behaviour of doxorubicin (a drug used in cancer treatment) in interaction with DNA and polymyxin (an antibiotic) with bacterial membranes. Currently, I am also studying graphene for use in electrodes designed for deep brain stimulation in patients with Parkinson’s disease. In these research projects, I am using not only by the Ostrava-based Karolina supercomputer but also by LUMI, located in Kajaani, Finland.

Research articles:

Nucleic acids and doxorubicin (https://doi.org/10.1002/jcc.70035)

Nucleic acids and cabon dots (https://doi.org/10.1021/acs.jcim.5c02242).

Author: Barbora Poláková, IT4Innovations National Supercomputing Center

Image on top: CSC