Current Projects

  • Visualization and Mesoscopic Simulation of Cellular Signal Transduction

    In systems biology, correlations play an important role and visualizations are a great way to make these visible. Hence, the focus of this work lies in the visualization and the interactive exploration of data from this environment. The data to be visualized will be generated by in silico simulations. Special emphasis is placed on the development of methods, which are carried out on graphic processing units (GPUs). The parallel architecture of GPUs is of interest, because it has the potential to allow high speed-ups of computations.

    The aim of this work is to develop a mesoscopic simulation of selected intra-cellular and extra-cellular processes and visualizations which are able to represent the simulation results in meaningful ways. In particular, cellular signal transduction processes will be studied.

    Subjects to research are:

    • How do different transport modes affect the signaling process?
    • What signaling molecule arrives first at the nucleus?
    • How does the signaling front look like?

    The underlying simulation of MAPK (mitogen-activated protein kinases) is a agent-based simulation with protein-protein interactions. It supports diffusion and transport by motor proteins as transport mechanisms of the signal toward the nucleus. CUDA and OpenMP are used for a parallel implementation on recent GPUs.

    Result of MAPK simulation
  • Modeling of a Biological Cell Model

    The cellular model of the previous project is refined concerning shape and interior of the cell to allow for comparisons with wet lab experiments. Key aspects are:

    • Modeling of the cell membrane with freeform surfaces allowing deformation
    • Structure and layout of the microtubuli of the cytoskeleton
    • Organelles like Golgi apparatus, endoplasmatic reticulum (ER), and mitochondria
    • Integration into existing simulation model

Completed Projects

  • Visualization of Lagrangian Coherent Structures in Unsteady Flow (2010)

    Lagrangian coherent structures (LCS) separate regions of qualitatively different flow behavior. The LCS can be identified, as shown by Haller in 2001, as ridges (local maximizing curves or surfaces) in the finite-time Lyapunov exponent (FTLE). We introduce a twofold approach to visualizing pathlines in the context of to LCS generation: the selection of significant trajectories and their individual visualization.

    Published at International Symposium on Flow Visualization (ISFV14) (Paper).

    Pathlines used for FTLE computation visualize a double-gyre Flow separation in a buoyant flow Flow behaviour leading to FTLE ridges
  • Visualizing Signal Concentrations (2010)

    An agent-based Monte Carlo simulation of a simplified Mitogen-Activated Protein Kinase (MAPK) is used to compute the trajectories of discrete signaling proteins. In this project, we create a continuous visualization from discrete particles for better insight. The concentration as well as the signaling front become visible.

    Published at IEEE International Symposium on Biomedical Imaging (ISBI '10) (Paper).
    Accompanying movie.

    Signal concentration of a virtual cell Signaling front evolving over time
  • CSB-Project A4 (Center Systems Biology) - Signal Transduction (2010)

    We developed two visualization techniques: a schematic cartoon-like representation and microscope-like images to allow comparison with wet lab experiments. Glyphs are used for interactive rendering of over 100,000 proteins and other cell structures. The data to be visualized is generated by a particle-based Monte Carlo simulation.

    Published at IEEE Pacific Visualization Symposium 2009 (Paper).

    Microscopic-like image for comparison with wet lab experiment Trajetory of a protein Schematic cell with closeup

    Diffusion of drug molecules into a tumor Transection of drug molecule diffusion
  • Panorama Maps with Non-linear Ray Tracing (2007)

    Non-linear Ray Tracing is used to generate panorama maps by minimizing occlusion. The viewing rays are deflected by the underlying terrain. Techniques of Berann, an Austrian cartograph, are employed in this work like progressive perspective, vertical exaggeration, and rotation and translation of features.

    Published at Graphite '07 (Paper).

    Skiing region of Kronplatz, Italy Panorama Map of Whistler, Canada Non-linear Effects in the Whistler Panorama
  • 3D Line Integral Convolution (2007)

    Our approach of view-dependent visualization tightly links the LIC generation with the volume rendering of the LIC result in order to avoid the computation of unnecessary LIC points. A range of illumination models is applied to the LIC streamlines: different codimension-2 lighting models as well as a novel gradient-based illumination model that relies on precomputed gradients and does not require any direct calculation of gradients after the LIC integral is evaluated. This 3D LIC method allows users to interactively explore 3D flow by means of high-quality, view-dependent, and adaptive LIC volume visualization.

    Published in IEEE Transactions on Visualization and Computer Graphics 2008.
    Accompanying material.

    Tornado Data Set: Oriented LIC Clipped Tornado Data Set Illumination based on Gradients Vortex Flow with highlighted Lambda2-values
  • Real-Time Rendering of Planets with Atmospheres (2007)

    Blue Marble The Alps in the Morning
  • Flight over Marsian Surface (2005)

    Mars Valles Marineris, Mars
Last Changed: 2010/08/09