Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization

Jan Byska, Thomas Trautner, Sergio Marques, Jiri Damborsky, Barbora Kozlikova, Manuela Waldner
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization
Computer Graphics Forum, 38(3):441-453, June 2019. [paper] [video]

Information

Abstract

Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. Guided by requirements derived from multiple focus groups with protein engineering experts, we designed and developed a novel interactive visual analysis approach for long and crowded MD simulations. In this approach, we link a dynamic 3D focus+context visualization with a 2D chart of time series data to guide the detection and navigation towards important spatio-temporal events. The 3D visualization renders elements of interest in more detail and increases the temporal resolution dependent on the time series data or the spatial region of interest. In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. Finally, we derived design guidelines for interactive visual analysis of complex MD simulation data.

Additional Files and Images

Additional images and videos

Additional files

supplement: Domain expert report of findings supplement: Domain expert report of findings

Weblinks

BibTeX

@article{byska-2019-mdfc,
  title =      "Analysis of Long Molecular Dynamics Simulations Using
               Interactive Focus+Context Visualization",
  author =     "Jan Byska and Thomas Trautner and Sergio Marques and Jiri 
               Damborsky and Barbora Kozlikova and Manuela Waldner",
  year =       "2019",
  abstract =   "Analyzing molecular dynamics (MD) simulations is a key
               aspect to understand protein dynamics and function. With
               increasing computational power, it is now possible to
               generate very long and complex simulations, which are
               cumbersome to explore using traditional 3D animations of
               protein movements. Guided by requirements derived from
               multiple focus groups with protein engineering experts, we
               designed and developed a novel interactive visual analysis
               approach for long and crowded MD simulations. In this
               approach, we link a dynamic 3D focus+context visualization
               with a 2D chart of time series data to guide the detection
               and navigation towards important spatio-temporal events. The
               3D visualization renders elements of interest in more detail
               and increases the temporal resolution dependent on the time
               series data or the spatial region of interest. In case
               studies with different MD simulation data sets and research
               questions, we found that the proposed visual analysis
               approach facilitates exploratory analysis to generate,
               confirm, or reject hypotheses about causalities. Finally, we
               derived design guidelines for interactive visual analysis of
               complex MD simulation data.",
  month =      jun,
  doi =        "10.1111/cgf.13701",
  journal =    "Computer Graphics Forum",
  number =     "3",
  volume =     "38",
  pages =      "441--453",
  keywords =   "scientific visualization, user centered design",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/byska-2019-mdfc/",
}