1: Molecular dynamics simulation of 2 million molecules forming a liquid layer of argon in vacuum, which gets ripped apart by its vapor pressure. The time steps shown are 5, 15, and 30 (from left to right). The lower row shows naïve ray casting of spheres for the individual molecules. The upper row shows the same rendering enhanced with our object-space ambient occlusion. Especially the break-up of the structure in time steps 5 and 15 is clearly visible. ABSTRACTIn many different application fields particle-based simulation, like molecular dynamics, are used to study material properties and behavior. Nowadays, simulation data sets consist of millions of particles and thousands of time steps challenging interactive visualization. Direct glyph-based representations of the particle data are important for the visual analysis process and these rendering methods can be optimized to be able to work sufficiently fast with huge data sets. However, the perception of the implicit spatial structures formed by such data is often hindered by aliasing and visual clutter. Especially the depth of these structures can be grasped better if visual cues are applied, even in interactive representations.We hence present a method to apply object-space ambient occlusion, based on local neighborhood information, to large timedependent particle-based data sets without the need for any precomputations. Based on density information collected in real-time, glyph-based representations of the data sets can be visually enhanced without significant impact on the rendering performance allowing to visualize multi-million particle data sets interactively on commodity workstations.

We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe. The Molecular Surface Map concisely shows arbitrary attributes of the original molecular surface, such as biochemical properties or geometrical features. This results in an intuitive overview, which allows researchers to assess all molecular surface attributes at a glance. Our representation can be used as a visual summarization of a molecule's interface with its environment. In particular, Molecular Surface Maps simplify the analysis and comparison of different data sets or points in time. Furthermore, the map representation can be used in a Space-time Cube to analyze time-dependent data from molecular simulations without the need for animation. We show the feasibility of Molecular Surface Maps for different typical analysis tasks of biomolecular data.

The comparison of molecular surface attributes is of interest for computer aided drug design and the analysis of biochemical simulations. Due to the non‐rigid nature of molecular surfaces, partial shape matching is feasible for mapping two surfaces onto each other. We present a novel technique to obtain a mapping relation between two surfaces using a deformable model approach. This relation is used for pair‐wise comparison of local surface attributes (e.g. electrostatic potential). We combine the difference value as well as the comparability as derived from the local matching quality in a 3D molecular visualization by mapping them to color. A 2D matrix shows the global dissimilarity in an overview of different data sets in an ensemble. We apply our visualizations to simulation results provided by collaborators from the field of biochemistry to evaluate the effectiveness of our results.

Conducting a current through a nanopore allows for the analysis of molecules inside the pore because a current modulation caused by the electrostatic properties of the passing molecules can be measured. This mechanism shows great potential for DNA sequencing, as the four different nucleotide bases induce different current modulations. We present a visualisation approach to investigate this phenomenon in our simulations of DNA within a nanopore by combining state-of-the-art molecular visualisation with vector field illustration. By spatial and temporal aggregation of the ions transported through the pore, we construct a velocity field which exhibits the induced current modulations caused by ion flux. In our interactive analysis using parametrisable three-dimensional visualisations, we encountered regions where the ion motion unexpectedly opposes the direction of the applied electric field.

T he 2012 IEEE Visualization Contest's topic was the detection of phase transitions in ferroelectric materials-in particular, barium titanate (BaTiO3). (For more on the contest, see the sidebar.) Ferroelectric materials' electric properties make them suitable for a variety of applications. One major application is high-permittivity capacitors. Several ferroelectric materials are promising alternatives for volatile-and nonvolatile-memory devices.A dielectric material is ferroelectric if it exhibits spontaneous polarization that can be reversed by applying an external electric field. Dielectric materials that show nonlinear polarization are called paraelectrics. In all ferroelectrics, a phase transition from a paraelectric to ferroelectric state occurs when the material's temperature decreases. 1 The visualization of phase transitions, or polarization domains in general, is a novel research field. Sebastian Grottel and his colleagues recently showed how a combination of glyph-based visualizations and isosurfaces derived from the anisotropy can reveal metal oxides' electrostatic properties. 2 We used the particle data from the contest to derive a vector field indicating the material's polarization. By combining several visualization methods, we qualitatively estimated the polarization domains' size and spatial distribution. We also investigated the development of the material's total volume over time and of the individual atoms' oscillation about their ideal lattice positions. The domains' development corresponded with that of the total volume and the atom mobility. On the basis of these observations, we estimated the phase transition's onset.Exploratory visualization is a useful tool to gain insights into new data. So, our contest submission focused on interactive visualizations that facili-tated exploratory analysis of the given dataset. We integrated our visualizations in MegaMol (www. vis.uni-stuttgart.de/megamol), a flexible framework for visualizing large, dynamic particle datasets.