IEEE Transactions on Visualization and Computer Graphics · 2019 · 11 citations · 44 references
ComputingPhysicsVisualizationComputational ChemistryData VisualizationScientific VisualizationMolecular DynamicsMultiscale VisualizationProtein DynamicsAggregationExplorationLarge-scale Data ExplorationMultiscale ExplorationScale Space VisualizationSpace-time CubeSpatiotemporal Data AnalysisVisual Exploration
Understanding large amounts of spatiotemporal data from particle-based simulations, such as molecular dynamics, often relies on the computation and analysis of aggregate measures. These, however, by virtue of aggregation, hide structural information about the space/time localization of the studied phenomena. This leads to degenerate cases where the measures fail to capture distinct behaviour. In order to drill into these aggregate values, we propose a multi-scale visual exploration technique. Our novel representation, based on partial domain aggregation, enables the construction of a continuous scale-space for discrete datasets and the simultaneous exploration of scales in both space and time. We link these two scale-spaces in a scale-space space-time cube and model linked views as orthogonal slices through this cube, thus enabling the rapid identification of spatio-temporal patterns at multiple scales. To demonstrate the effectiveness of our approach, we showcase an advanced exploration of a protein-ligand simulation.
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VMD: Visual molecular dynamics
William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 66.6K citations
Scalable molecular dynamics with NAMD
J. C. Phillips, Rosemary Braun, Wei Wang et al. · Journal of Computational Chemistry · 2005 · 17.4K citations · Full text