Visual Verification and Analysis of Cluster Detection for Molecular Dynamics

In the years from 2007 to 2012 I worked at the Visualization Research Center of the University of Stuttgart, respectively at the Institute for Visualization and Interactive Systems. The core topic of my work was research and development of visualizations for data sets from molecular dynamics simulations. My work was financed by the Collaborative Research Center (SFB) 716 of the German Research Foundation (DFG). One goal was to be able to handle ever larger data sets in interactive visualization. A second goal was to support efficient visual analysis, utilizing meaningful representations derived from the original data.

Finally, in 2007 I presented my first work at the IEEE VIS Conference in Sacramento, a paper with the title “Visual Verification and Analysis of Cluster Detection for Molecular Dynamics” [1]. This work focuses on algorithms for detecting of clusters of molecules, predecessors of liquid droplets in vapor. Each of these detection algorithms has its strong and weak points. Therefore, the visual analysis and comparison of the results are very important. Especially the temporal stability of the detected clusters and their interaction with each other are crucial factors.

Thus we (my colleagues and I) defined “flow groups” to identify interesting areas within the data sets. A “flow group” is a group of molecules, moving from one point in time from one molecule cluster to a second molecule cluster at a second point in time, this this group comprises all molecules switch between two clusters together. This definition enables us to visually judge the stability of an algorithm and even to compare two different algorithms. This publication was the first corner stone for my dissertation thesis: “Point-based Visualization of Molecular Dynamics Data Sets”.

[1] S. Grottel, G. Reina, J. Vrabec, and T. Ertl, “Visual Verification and Analysis of Cluster Detection for Molecular Dynamics,” Visualization and Computer Graphics, IEEE Transactions on, vol. 13, iss. 6, pp. 1624-1631, 2007.
[Bibtex]

@article{Grottel2007nucleation,
  author = {Grottel, Sebastian and Reina, Guido and Vrabec, Jadran and Ertl, Thomas},
  journal={Visualization and Computer Graphics, IEEE Transactions on}, 
  number = 6,
  pages = {1624--1631},
  title = {{Visual Verification and Analysis of Cluster Detection for Molecular Dynamics}},
  volume = 13,
  year = 2007,
  doi={10.1109/TVCG.2007.70614},
}