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“In the human body, many processes such as energy production of the cells and the function of enzymes are dependent on the pH, so the acidity of the surrounding solution. To computationally model these processes we need to continuously develop modern simulation techniques“, Aho summarizes.

The aim of scientists is to gain understanding of the processes of nature. Traditionally, this understanding has arose from carrying out scientific experiments, where conclusions are drawn from relevant measurements. Nowadays, high-performance computer simulation techniques using the modern supercomputers have become a complementary tool to model the processes of nature.

The research of Aho has focused on applying and developing computer simulations to study biological systems, such as proteins and membranes, at the nanometer scale.

“To me, it’s fascinating that with the modern simulation techniques, we are able to gain knowledge of atomic scale events in biological systems using computers, at and beyond the limits of current experimental techniques”, Aho clarifies. 

Molecular dynamics models processes at the atomistic scale

The most widely used simulation method for studying biological systems is classical molecular dynamics. The basic idea of the method is to evolve the dynamics of the system by calculating the forces and numerically solving the Newton’s equations of motion for all the atoms part of the system of interest. In the first part of her doctoral research, Aho has applied molecular dynamics simulations to support experimental findings of proton diffusion on the surface of biological membranes.

As the main result of the doctoral thesis, Aho has further developed the general molecular dynamics simulation method by including the possibility to efficiently simulate biological systems at a constant pH:

“With computer simulations, we of course aim to mimic experimental conditions, such as constant temperature and pressure. Including the possibility to efficiently perform simulations also at a constant pH was a long-awaited feature by the user community of the most popular molecular dynamics software package for biological systems, GROMACS.”

The efficient constant pH molecular dynamics implementation enables the investigation of pH-dependent phenomena using computers. Being able to set the pH and change the protonation states and charges of acids and bases in biomolecular environments during the simulation along with atomic positions, broadens the applicability of molecular dynamics to processes that greatly depend on the pH of the surrounding solution.

Additionally, Aho has contributed to revising details and choices behind the method in order to improve the accuracy of constant pH molecular dynamics. The mentioned peer-reviewed publications related to the method have already gained abundant attention among the research community, showing the necessity of developing advanced computational techniques to supplement experimental research. In the future, the constant pH molecular dynamics could be applied to study the details of, for example, delivery of pH-dependent drug molecules, membrane transport and transport proteins, enzyme dynamics, os molecules part of the energy production of the cells.

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Noora Aho graduated from Heinola high school in 2012, completed her bachelor’s degree in physics at the Ģ��ֱ�� in 2015. After this she received her master’s degree in physics from the University of Helsinki in 2018, focusing already on physics-based computer simulations of biomolecular systems. Since then, she has worked as a doctoral researcher in the computational chemistry research group, supervised by Professor Gerrit Groenhof, at the Nanoscience Center of Ģ��ֱ��. In addition to research, Aho has also completed the subject teacher’s pedagogical studies in physics and mathematics.

M.Sc. Noora Aho defends her doctoral dissertation “Molecular dynamics simulations of acids and bases in biomolecular environments” on Friday 31st March 2023 at 12 noon. The opponent is Professor David van der Spoel from the University of Uppsala, Sweden, and custos is Professor Gerrit Groenhof from the Ģ��ֱ��. The language of the dissertation is English.