Molecular Simulations

The use of the word molecular clearly implies that we are dealing with molecules of some kind. Knowledge of molecules is of great importance to many theories or applications. For instance, in the biological field, in understanding the workings of cell membranes and proteins.

On the other hand the word simulations tells us that we are in between theory and experiments, bridging between them and contributing to either one. Simulations can confirm experiments through theory or, from the same theory, predict behavior which can be observed in experiments.

There are quite a few advantages in the use of simulations compared to experiments. With simulations we can observe what is hard to measure with experiments, for instance the exact motion of individual molecules. Moreover, simulations offer a very precise control over circumstances.

Besides advantages there are however also several drawbacks in the use of simulations. An important one is that the time and length scales accessible with simulations are not always similar to the scales accessible with experiments. For instance in biology, the activation time of a protein is usually in the range of microseconds, but with atomistic molecular dynamics simulations one can only reach time intervals up to hundreds of nanoseconds.

Within our group we therefor use various molecular simulation techniques and often coarse grained models to study phenomena of interest at the appropriate time and length scale. Follow any of the links below to find out more about our research using these different techniques.

We also have our own in house molecular simulations program, called PumMa. This program is aimed for molecular dynamics simulations, Monte Carlo, as well as DPD simulations. PumMa has its own website.