VIA-MD: Visual Interactive Analysis of Molecular Dynamics
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Date
2018
Journal Title
Journal ISSN
Volume Title
Publisher
The Eurographics Association
Abstract
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.
Description
@inproceedings{10.2312:molva.20181102,
booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data},
editor = {Jan Byska and Michael Krone and Björn Sommer},
title = {{VIA-MD: Visual Interactive Analysis of Molecular Dynamics}},
author = {Skånberg, Robin and Linares, Mathieu and König, Carolin and Norman, Patrick and Jönsson, Daniel and Hotz, Ingrid and Ynnerman, Anders},
year = {2018},
publisher = {The Eurographics Association},
ISBN = {978-3-03868-061-1},
DOI = {10.2312/molva.20181102}
}