VIA-MD: Visual Interactive Analysis of Molecular Dynamics

Publikation: Beitrag in Buch/Bericht/Sammelwerk/KonferenzbandAufsatz in KonferenzbandForschung

Autoren

  • Robin Skånberg
  • Carolin König
  • Patrick Norman
  • Mathieu Linares
  • D. Jönnsen
  • Ingrid Hotz
  • Anders Ynnerman

Externe Organisationen

  • Linkoping University
  • Swedish e-Science Research Centre (SeRC)
  • Royal Institute of Technology (KTH)
Forschungs-netzwerk anzeigen

Details

OriginalspracheEnglisch
Titel des SammelwerksMolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data
Seiten19-27
Seitenumfang9
ISBN (elektronisch)9783038680611
PublikationsstatusVeröffentlicht - 2018
Extern publiziertJa
VeranstaltungMolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2018 - Brno, Tschechische Republik
Dauer: 4 Juni 20184 Juni 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 Sachgebiete

Zitieren

VIA-MD: Visual Interactive Analysis of Molecular Dynamics. / Skånberg, Robin; König, Carolin; Norman, Patrick et al.
MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data. 2018. S. 19-27.

Publikation: Beitrag in Buch/Bericht/Sammelwerk/KonferenzbandAufsatz in KonferenzbandForschung

Skånberg, R, König, C, Norman, P, Linares, M, Jönnsen, D, Hotz, I & Ynnerman, A 2018, VIA-MD: Visual Interactive Analysis of Molecular Dynamics. in MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data. S. 19-27, MolVa, Brno, Tschechische Republik, 4 Juni 2018. https://doi.org/10.2312/molva.20181102
Skånberg, R., König, C., Norman, P., Linares, M., Jönnsen, D., Hotz, I., & Ynnerman, A. (2018). VIA-MD: Visual Interactive Analysis of Molecular Dynamics. In MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data (S. 19-27) https://doi.org/10.2312/molva.20181102
Skånberg R, König C, Norman P, Linares M, Jönnsen D, Hotz I et al. VIA-MD: Visual Interactive Analysis of Molecular Dynamics. in MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data. 2018. S. 19-27 doi: 10.2312/molva.20181102
Skånberg, Robin ; König, Carolin ; Norman, Patrick et al. / VIA-MD: Visual Interactive Analysis of Molecular Dynamics. MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data. 2018. S. 19-27
Download
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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].

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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.

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