The previous homepage can be found here.

Curriculum Vitae

Awards

Research

• 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?
• CellVis

  The visualization tool CellVis allows the data analysis of the in silico simulation results. CellVis relies heavily on GPU-based visualizations like glyph-based rendering and volume ray casting. Two major techniques are available for the visualization of the cellular processes. The schematic visualization renders the data set as it is used during the simulation, i.e. the internal structures like cytoskeletal filaments and the moving proteins are considered. The second visualization generates images similar to confocal laser scanning microscopy.

  
• Cellular Stochastic Simulation

  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.

  
• 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

• Atomistic Visualization of Mesoscopic Whole-Cell Simulations

  With modern GPU ray casting approaches it is only possible to render several millions of atoms at interactive frame rates unless advanced acceleration methods are employed. But even simplified cell models of whole-cell simulations consist of at least several billion atoms. However, many instances of only a few different proteins occur in the intracellular environment, which is beneficial in order to fit the data into the graphics memory. One model is stored for each protein species and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes at interactive frame rates.

  Published at the EG Workshop on Visual Computing for Biology and Medicine (VCBM, 2012).

  
• Visualization of Receptor Clustering on the Cellular Membrane (2011)

  Apoptosis, the programmed cell death, is initiated by two pathways, the extra-cellular and the mitochondrial pathway. In the extra-cellular pathway, the binding of ligands to death receptors on the cellular membrane leads to the activation of the pathway. We developed a mathematical model to simulate the stochastic process of receptor-ligand clustering. The in-silico results are visualized in CellVis by highlighting certain cluster properties supporting the model development by visual data analysis.

  Published at IEEE Symposium on Biological Data Visualization (BioVis 2011).

  
• Interactive Exploration of Protein Cavities (2011)

  Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular
  dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens
  up to the environment, making the binding site accessible to the surrounding substrate. Volume ray casting is used to compute the boundary of the protein in real-time. Then, a partial segmentation is applied to the volume to obtain the user-selected cavity.

  Published in Computer Graphics Forum (EuroVis 2011).

  
• 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).

  
• 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).
  Accompanying movie.

  
• 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.

  
  
  
• 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.

  
• 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.

  
• Real-Time Rendering of Planets with Atmospheres (2007)
  
  
• Flight over Marsian Surface (2005)
  
  

Teaching

Winter Term 2010/11

• Lecture Assignments: Interactive Systems

Summer Term 2010

• Hauptseminar: Volume Rendering

Winter Term 2009/10

• Hauptseminar: Advanced Real-time Rendering Techniques

Winter Term 2008/09

• Hauptseminar: Synthesis and Rendering of Natural Phenomena
• Lecture Assignments: Numerische und Stochastische Grundlagen der Informatik

Summer Term 2008

• Lecture Assignments: Bildsynthese
• Graphics Lab (Fachpraktikum Grafik-Programmierung)

Winter Term 2007/08

• Lecture Assignments: Modellierung und Animation
• Graphics Lab (Fachpraktikum Grafik-Programmierung)

Student Supervision

Master Theses

• Ana Cristina Pintilie (2012):
  Statistical Analysis and Comparative Visualization of Cellular Particle-based Simulations
  (Statistische Analyse und vergleichende Visualisierung zellulärer partikelbasierter Simulationen)

Diploma Theses (Diplomarbeiten)

• Michael Ott (2009):
  Simulation and Visualization of Biological Processes Utilizing CUDA
  (Simulation und Visualisierung biologischer Prozesse mit CUDA)
• Mikael Vaaraniemi (2008):
  Very Detailed Navigation Maps on 3D Terrain Models
  (Hochdetaillierte Navigationskarten auf 3D Geländemodellen)

Student Research Projects (Studienarbeiten)

• Hendrik Hochstetter (2010):
  Modeling of a Biological Cell Model
  (Modellierung eines biologischen Zellmodells)

Software Laboratory (Software Praktikum)

• Louis Bergmann, Sanda Leko, Ernst Stamp:
  Animated fishes reacting to user interaction via camera
  (SOPRA - Software for Oceanic Pattern Recognition and Animation)
• Kai Jauch, Helena Löwenstein, Sebastian Konle, Bettina Ohlhausen:
  Helicopter simulation controlled by a home trainer

Publications

Poster

2012

	Falk, Martin; Ertl, Thomas: CellVis – Modeling, Simulating, and Analyzing Cellular Processes. Workshop on Statistical and Dynamical Models in Biology and Medicine, Stuttgart, Germany, 2012. [PDF], [Website]
	Falk, Martin; Ertl, Thomas: Stochastic Single-Cell Simulation: The External Signal. Visualizing Biological Data (VIZBI 2012), Heidelberg, Germany, 2012. [PDF], [Website]

2011

	Falk, Martin; Ertl, Thomas: Stochastic Simulation of Cellular Signal Transduction: Spatial Impact of the External Signal. International Conference on Simulation Technology, Stuttgart, Germany, 2011. [PDF], [Website]
	Falk, Martin; Ertl, Thomas: CellVis - Interactive Exploration and Simulation of Cellular Transport Processes. Visualizing Biological Data (VIZBI 2011), Cambridge, MA, USA, 2011. [PDF], [Website]

2010

Falk, Martin; Klann, Michael; Reuss, Matthias; Ertl, Thomas: 3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations. IEEE International Symposium on Biomedical Imaging (ISBI 2010), Rotterdam, The Netherlands, 2010. [PDF], [Website]

2009

Falk, Martin; Üffinger, Markus: GPU-based Visualization of Simulation Results. ASIM GMMS Workshop, Stuttgart, Germany, 2009. [PDF], [Website]