VIA-MD: Visual Interactive Analysis of Molecular Dynamics

Robin Skånberg, Carolin König, Mathieu Linares, Daniel Jönsson, Patrick Norman, Ingrid Hotz, Anders Ynnerman
Workshop on Molecular Graphics and Visual Analysis of Molecular Data - 2018
Download the publication : molva18a-sub1008-cam-i5.pdf [4.3Mo]  

We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data. The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations of complex molecular systems. A key feature of our approach is the support for linked interactive 3D exploration of geometry and statistical analysis using dynamic temporal windowing and animation. Based on semantic level descriptions and hierarchical aggregation of molecular properties we enable interactive filtering, which enables the user to effectively find spatial, temporal and statistical patterns. The VIA-MD environment provides an unprecedented tool for analysis of complex microscopic interactions hidden in large data volumes. We demonstrate the utility of the VIA-MD environment with four use cases. The first two deal with simulation of amyloid plaque associated with development of Alzheimer's, and we study an aqueous solution of 100 probes and an amyloid fibril. The identification of interaction hotspots is achieved with the use of combined filter parameters connected with probe molecular planarity and probe-fibril interaction energetics. The third and fourth examples show the wide applicability of the environment by applying it to analysis of molecular properties in material design.

Presented at MOLVA 2018 in June 2018.

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BibTex references

  author       = {Skånberg, Robin and K{\"o}nig, Carolin and Linares, Mathieu and J{\"o}nsson, Daniel and Norman, Patrick and Hotz, Ingrid and Ynnerman, Anders},
  title        = {{VIA-MD: Visual Interactive Analysis of Molecular Dynamics}},
  booktitle    = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data},
  year         = {2018},
  editor       = {Jan Byska and Michael Krone and Bj{\"o}rn Sommer},
  publisher    = {The Eurographics Association}

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