Details
| Original language | English |
|---|---|
| Title of host publication | MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data |
| Pages | 19-27 |
| Number of pages | 9 |
| ISBN (electronic) | 9783038680611 |
| Publication status | Published - 2018 |
| Externally published | Yes |
| Event | MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2018 - Brno, Czech Republic Duration: 4 Jun 2018 → 4 Jun 2018 |
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.
ASJC Scopus subject areas
- Materials Science(all)
- Materials Chemistry
- Chemistry(all)
- Spectroscopy
- Chemistry(all)
- Physical and Theoretical Chemistry
- Computer Science(all)
- Computer Graphics and Computer-Aided Design
Cite this
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MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data. 2018. p. 19-27.
Research output: Chapter in book/report/conference proceeding › Conference contribution › Research
}
TY - GEN
T1 - VIA-MD: Visual Interactive Analysis of Molecular Dynamics
AU - Skånberg, Robin
AU - König, Carolin
AU - Norman, Patrick
AU - Linares, Mathieu
AU - Jönnsen, D.
AU - Hotz, Ingrid
AU - Ynnerman, Anders
N1 - Acknowledgements The authors acknowledges funding by a Marie Skłodoswka–Curie International Fellowship “FreezeAlz” by the European Commission, the Swedish Research Council (Grant No. 621- 2014-4646) and SeRC (Swedish e-Science Research Center) for funding and providing a research environment enabling innovative research across e-science disciplines. The Swedish National Infrastructure for Computing (SNIC) at National Supercomputer Centre (NSC) are acknowledged for providing computer resources. The prototype of this project has been implemented using the visualization framework Inviwo [Inv] and immediate mode GUI Dear ImGui [Cor].
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85070065695&partnerID=8YFLogxK
U2 - 10.2312/molva.20181102
DO - 10.2312/molva.20181102
M3 - Conference contribution
SP - 19
EP - 27
BT - MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data
T2 - MolVa
Y2 - 4 June 2018 through 4 June 2018
ER -