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.

In many disciplines, such as computer aided drug design, multiple simulation runs are performed with varying parameters, yielding ensembles of data sets. Comparative visualisation of these simulation results can help understanding the influence of different parameters. However, researchers might need to compare large numbers of variants. Single desktop monitors often do not have the resolution and screen size required for showing a whole ensemble at once with sufficient detail. Wall-sized high-resolution displays can be a solution for this problem. Although a number of studies has been conducted on how large high-resolution displays affect the speed and accuracy of certain tasks, only few of them are related to actual scientific visualisation tasks. We built a system for comparative visualisation of simulation results that can be used with conventional desktop monitors and with large high-resolution displays. We conducted a study using biochemical simulation data to evaluate the impact of screen size and 3D stereo display on a comparison task.

Abstract 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.

In 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.