Frederik Philippi

Ionic Liquids Research

Why does a chemist need to write code?

Picture of an outdated way of doing science

The times where we cut out peaks from a chromatogram to weigh them and then track the numbers on graph paper are over. Nowadays, almost every scientist needs to work with a lot of digital data. Even though most of the data I work can be handled with existing software, there are cases where I need to write a script or even a larger piece of code.
The difficult part is often not to create the data - but to extract interesting patterns!

Scheme showing the path data - software - result

There is one aspect of my work which is truly 'data science', and that is the analysis of molecular dynamics simulation results. Molecular dynamics simulations basically reveal how atoms move in space and time, based on a more or less educated guess of the physics involved (called a 'force field'). A typical simulation output would be the coordinates of ≈50000 atoms over ≈20000 time steps. Nothing special, yet this is already 3 billion numbers!

The prealpha software package

Lithium-anion-glyme oligomeric cluster identified with prealpha

'prealpha' is a software package for the analysis of molecular dynamics simulation data. A variety of structural and dynamic properties are implemented. My personal highlights are:

Automatic speciation and cluster analysis, great for complex coordination environments (see the picture above)
Bulk liquid structure, such as Coulomb interaction energy and distribution functions
Intramolecular structure, such as dihedral space, dipole moment / charge arm distribution
Time autocorrelation functions for various dynamics (species lifetime, rotational dynamics, conformer changes)
Trajectory processing, e.g. involving Drude particles or neighbouring molecules

Usually, I do not implement analyses that are already efficiently implemented in the famous TRAVIS software package. An exemption are for example the mean squared displacements, for which I usually use prealpha because it can run on several threads. If you are interested in the scope of what prealpha can do, you can download the manual here or have a look at my github repository.