Importance-Driven Exploration of Molecular Dynamics Simulations

Information

• Publication Type: Master Thesis
• Workgroup(s)/Project(s):
  • Visualization Group
  • Visual Information Foraging on the Desktop
• Date: October 2018
• Date (Start): January 2018
• Date (End): 3. November 2018
• Open Access: yes
• First Supervisor:
  • Manuela Waldner
  • Eduard Gröller
• Pages: 100
• Keywords: molecular dynamics simulation, realtime visualization

Abstract

The aim of this thesis is a novel real-time visualization approach for exploring molecular dynamics (MD-)simulations. Through the constantly improving hardware and everincreasing computing power, MD-simulations are more easily available. Additionally, they consist of hundreds, thousands or even millions of individual simulation frames and are getting more and more detailed. The calculation of such simulations is no longer limited by algorithms or hardware, nevertheless it is still not possible to efficiently explore this huge amount of simulation data, as animated 3D visualization, with ordinary and well established visualization tools. Using current software tools, the exploration of such long simulations takes too much time and due to the complexity of large molecular scenes, the visualizations highly suffer from visual clutter. It is therefore very likely that the user will miss important events. Therefore, we designed a focus & context approach for MD-simulations that guides the user to the most relevant temporal and spatial events, and it is no longer necessary to explore the simulation in a linear fashion. Our contribution can be divided into the following four topics: 1. Spatial importance through different levels of detail. Depending on the type of research task, different geometrical representations can be selected for both, focusand context elements. 2. Importance driven visibility management through ghosting, to prevent context elements from occluding focus elements. 3. Temporal importance through adaptive fast-forward. The playback speed of the simulation is thereby dependent on a single or a combination of multiple importance functions. 4. Visual declutter of accumulated frames through motion blur, which additionally illustrates the playback speed-up. Since the very beginning, this work was developed in close cooperation with biochemists from the Loschmidt Laboratories in Brno, Czech Republic. Together, we analyzed different use cases demonstrating the flexibility of our novel focus & context approach.

Additional Files and Images

Weblinks

• Entry in reposiTUm (TU Wien Publication Database)
• DOI: 10.34726/hss.2018.53541

BibTeX

@mastersthesis{trautner-2018-imd,
  title =      "Importance-Driven Exploration of Molecular Dynamics
               Simulations",
  author =     "Thomas Trautner",
  year =       "2018",
  abstract =   "The aim of this thesis is a novel real-time visualization
               approach for exploring molecular dynamics (MD-)simulations.
               Through the constantly improving hardware and everincreasing
               computing power, MD-simulations are more easily available.
               Additionally, they consist of hundreds, thousands or even
               millions of individual simulation frames and are getting
               more and more detailed. The calculation of such simulations
               is no longer limited by algorithms or hardware, nevertheless
               it is still not possible to efficiently explore this huge
               amount of simulation data, as animated 3D visualization,
               with ordinary and well established visualization tools.
               Using current software tools, the exploration of such long
               simulations takes too much time and due to the complexity of
               large molecular scenes, the visualizations highly suffer
               from visual clutter. It is therefore very likely that the
               user will miss important events. Therefore, we designed a
               focus & context approach for MD-simulations that guides the
               user to the most relevant temporal and spatial events, and
               it is no longer necessary to explore the simulation in a
               linear fashion. Our contribution can be divided into the
               following four topics: 1. Spatial importance through
               different levels of detail. Depending on the type of
               research task, different geometrical representations can be
               selected for both, focusand context elements. 2. Importance
               driven visibility management through ghosting, to prevent
               context elements from occluding focus elements. 3. Temporal
               importance through adaptive fast-forward. The playback speed
               of the simulation is thereby dependent on a single or a
               combination of multiple importance functions. 4. Visual
               declutter of accumulated frames through motion blur, which
               additionally illustrates the playback speed-up. Since the
               very beginning, this work was developed in close cooperation
               with biochemists from the Loschmidt Laboratories in Brno,
               Czech Republic. Together, we analyzed different use cases
               demonstrating the flexibility of our novel focus & context
               approach. ",
  month =      oct,
  pages =      "100",
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Institute of Computer Graphics and Algorithms, Vienna
               University of Technology ",
  keywords =   "molecular dynamics simulation, realtime visualization",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2018/trautner-2018-imd/",
}