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Algorithms supplementing the chemistry lab

Some chemical processes are so complex that it is almost impossible to say what is happening exactly. Computer-assisted methods, as developed by assistant professor Carolin König, can simulate these processes and thereby help us to understand them better.

Luminous molecules on black background
© Peter Nilsson

Special luminous molecules settle on abnormal protein structures and can thereby indicate certain brain diseases. Theoretical chemist Carolin König is researching the processes taking place here.

Proteins carry out different tasks in our bodies. If modified externally, they can be an indicator for various diseases. Special molecules target and dock on these “defective” protein structures and act as a type of warning signal. These so-called “biomarkers” are used as indicators for medical diagnoses.

“We could improve the function of biomarkers even further if we understood more exactly the mechanisms of the chemical processes taking place there,” said Carolin König, assistant professor at the Institute of Physical Chemistry. She is primarily researching biomarkers for amyloid fibrils – abnormal protein structures in the nerve cells of the brain, which occur in connection with diseases like Alzheimers or Parkinsons. With optimised biomarkers, even better distinctions could be made between individual diseases. Together with the Swedish Linköping University and KTH Royal Institute of Technology in Stockholm, König is examining biomarker molecules that settled on these defective amyloid fibril structures. Through experiments, however, it is almost impossible to examine which processes are taking place in detail.

There are so many parameters interacting in the reactions occurring around these biomarkers that we can never calculate all of them.

Carolin König

König uses methods from quantum mechanics to track the mechanisms behind the biomarkers. The idea of theoretical chemistry, that of mathematically calculating and therefore predicting the behaviour of molecules or individual atoms, as well as the required basic equations, has existed for quite a long time. But is it only in the last few decades that improved algorithms and more effective computers have enabled accurate results to be produced even for complex systems. Even with modern methods, calculations for these can take several weeks on large-scale computer equipment.

Portrait of Carolin König
© Julia Siekmann

Carolin König

Yet in examining biomarkers that indicate certain brain diseases, high-performance computers alone are almost no further help to König. “There are so many parameters interacting in the reactions occurring around these biomarkers that we can never calculate all of them,” said König, describing a basic problem of theoretical chemistry. Even with the expected improvement in computer performance, the calculations would take much too long. “The number of parameters involved will at some point equal the number of stars in the universe – that is the magnitude that we are dealing with here.”

In order to establish algorithms that can be realistically executed, König plans to concentrate primarily on parameters that have a decisive influence on the result. Reactions often only occur in a small part of a protein. König plans to examine these local processes with accurate but time-consuming calculations, while applying simpler approximations in regions where no central reaction steps take place. “This combination of methods gives us a calculation that is as accurate as possible but not too complex and can therefore still be executed,” explained the theoretical chemist.

The development of such “multi-scale methods”, which combine various approaches, is an emerging research field. “There is still a lot to discover here and a lot is still possible. I find that exciting,” said König. The awarding of the Nobel Prize for Chemistry in 2013 to three US researchers working in this field demonstrates the importance and potential of the subject.

Author: Julia Siekmann

Emmy Noether research group

The German Research Foundation (DFG) promotes the development of new methods in computer chemistry through its provision of an Emmy Noether research group and around half a million euros for five years. Group leader and assistant professor Carolin König plans to use this funding to examine, among other things, special biomarkers that indicate brain diseases like Alzheimers and Parkinsons. The Emmy Noether Programme enables outstanding young researchers to qualify early for a professorship by leading their own working group. (jus)