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A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data
(The Eurographics Association, 2019) Schäfer, Marco; Krone, Michael; Byska, Jan and Krone, Michael and Sommer, Björn
The interactive visualization of molecular surfaces can help users to understand the dynamic behavior of proteins in molecular dynamics simulations. These simulations play an important role in biochemical and pharmaceutical research, e.g. in drug design. The efficient calculation of molecular surfaces in a fast and memory-saving way is a challenging task. For example, to gain a detailed understanding of complex diseases like Alzheimer, conformational changes and spatial interactions between molecules have to be investigated. Molecular surfaces, such as Solvent Excluded Surfaces (SES), are instrumental for identifying structures such as tunnels or cavities that critically influence transport processes and docking events, which might induce enzymatic reactions. Therefore, we developed a highly parallelized algorithm that exploits the massive computing power of modern graphics hardware. Our analytical algorithm is suitable for the real-time computation of dynamic SES based on many time steps, as it runs interactively on a single consumer GPU for more than 20 k atoms.
Evaluation of Visualizations for Interface Analysis of SPH
(The Eurographics Association, 2014) Krone, Michael; Huber, Markus; Scharnowski, Katrin; Hirschler, Manuel; Kauker, Daniel; Reina, Guido; Nieken, Ulrich; Weiskopf, Daniel; Ertl, Thomas; N. Elmqvist and M. Hlawitschka and J. Kennedy
We present a GPU-accelerated visualization application that employs methods from computer graphics and visualizationto analyze SPH simulations from the field of material science. To this end, we extract the isosurfacethat separates the stable phases in a fluid mixture via the kernel function that was used by the simulation. Ourapplication enables the analysis of the separation process using interactive 3D renderings of the data and an additionalline chart that shows the computed surface area over time. This also allows us to validate the correctnessof the simulation method, since the surface area can be compared to the power law that describes the change inarea over time. Furthermore, we compare the isosurface that is based on the simulation kernel with an establishedmethod to extract smooth high-quality SPH surfaces. The comparison focuses on demonstrating the applicabilityfor data analysis in the context of material science, which is based on the resulting surface area and how wellthe two phases are separated with respect to the original particles. The evaluation was carried out together withexperts in material science.
Interactive Exploration of Polymer-Solvent Interactions
(The Eurographics Association, 2011) Thomaß, Bertram; Walter, Jonathan; Krone, Michael; Hasse, Hans; Ertl, Thomas; Peter Eisert and Joachim Hornegger and Konrad Polthier
The interaction of three-dimensional linked hydrophilic polymers with surrounding solvents in time-dependent data sets is of great interest for domain experts and current research in molecular dynamics. These polymers are called hydrogels, and their most characteristic property is their swelling in aqueous solutions by absorbing the solvent. Their conformation transition can be studied by investigations of the interaction of the single polymer strand and the solvent directly around the polymer at an atomistic level. We present new visualization techniques to interactively study time-dependent data sets from molecular dynamics simulations-with special regard to polymer-solvent interactions like local concentrations and hydrogen bonds-as well as filtering methods to facilitate analysis. Such methods that visualize polymer-solvent interactions on a hydration shell around a polymer are not available in current tools and can greatly facilitate the visual analysis, which helps domain experts to extract additional information about hydrogel characteristics and gain new insights from the simulation results. While our visual analysis methods presented in this paper clearly facilitate the analysis of hydrogels and lead to new insight, the presented concepts are applicable to other domains like proteins or polymers in general that interact with solvents.
Interactive CPU-based Ray Tracing of Solvent Excluded Surfaces
(The Eurographics Association, 2019) Rau, Tobias; Zahn, Sebastian; Krone, Michael; Reina, Guido; Ertl, Thomas; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Depictions of molecular surfaces such as the Solvent Excluded Surface (SES) can provide crucial insight into functional molecular properties, such as the molecule's potential to react. The interactive visualization of single and multiple molecule surfaces is essential for the data analysis by domain experts. Nowadays, the SES can be rendered at high frame rates using shader-based ray casting on the GPU. However, rendering large molecules or larger molecule complexes requires large amounts of memory that has the potential to exceed the memory limitations of current hardware. Here we show that rendering using CPU ray tracing also reaches interactive frame rates without hard limitations to memory. In our results large molecule complexes can be rendered with only the precomputation of each individual SES, and no further involved representation or transformation. Additionally, we provide advanced visualization techniques like ambient occlusion opacity mapping (AOOM) to enhance the comprehensibility of the molecular structure. CPU ray tracing not only provides very high image quality and global illumination, which is beneficial for the perception of spatial structures, it also opens up the possibility to visualize larger data sets and to render on any HPC cluster. Our results demonstrate that simple instancing of geometry keeps the memory consumption for rendering large molecule complexes low, so the examination of much larger data is also possible.
Hybrid Visualization of Protein-Lipid and Protein-Protein Interaction
(The Eurographics Association, 2019) Alharbi, Naif; Krone, Michael; Chavent, Matthieu; Laramee, Robert S.; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
In the Molecular Dynamics (MD) visualization literature, different approaches are utilized to study protein-lipid interactions (PLI) and protein-protein interaction (PPI) in decoupled contexts. However, the two types of interaction occur in the same space-time domain. It is beneficial to study the PLI and PPI in a unified context. Nevertheless, the simulation's size, length, and complexity increase the challenge of understanding the dynamic behavior. We propose a novel framework consisting of four linked views, a time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. We introduce a selection of visual designs to convey the behavior of PLI and PPI through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, a projected tiled space is used to present both PLI and PPI at the particle level in a heat-map style visual design while glyphs are used to represent PPI at the molecular level. We couple visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately or together in a unified visual analysis framework. We also exemplify its use with case studies focusing on protein clustering and we report domain expert feedback.
Visualization of Biomolecular Structures: State of the Art
(The Eurographics Association, 2015) Kozlikova, Barbora; Krone, Michael; Lindow, Norbert; Falk, Martin; Baaden, Marc; Baum, Daniel; Viola, Ivan; Parulek, Julius; Hege, Hans-Christian; R. Borgo and F. Ganovelli and I. Viola
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
Web-based Volume Rendering using Progressive Importance-based Data Transfer
(The Eurographics Association, 2018) Mwalongo, Finian; Krone, Michael; Reina, Guido; Ertl, Thomas; Beck, Fabian and Dachsbacher, Carsten and Sadlo, Filip
WebGL 2.0 makes it possible to implement efficient volume rendering that runs in browsers using 3D textures and complex fragment shaders. However, a typical bottleneck for web-based volume rendering is the size of the volumetric data sets. Transferring these data to the client for rendering can take a substantial amount of time, depending on the network speed. This can introduce latency that can in turn affect interactive rendering at the client. We address this challenge by introducing a multi-resolution bricked volume rendering, where data is transferred progressively. Similar to MIP-Mapping, the volume data is divided into multiple levels of detail. Each level of detail is broken down into bricks. The client requests the data brick by brick starting with the lowest resolution and renders each brick immediately as it is received. The 3D volume texture is updated as bricks with higher resolution are received asynchronously from the server. The advantages of this algorithm are that it reduces latency, the user can see at least a reduced-detail version of the data almost immediately, and the application always stays responsive while the data is updated. We also implemented a prioritization scheme for the bricks, where each brick can be assigned an importance value. Using this information, the client can request more important bricks first. Furthermore, we investigated the influence of data compression on the transfer and processing times.
Atomistic Visualization of Mesoscopic Whole-Cell Simulations
(The Eurographics Association, 2012) Falk, Martin; Krone, Michael; Ertl, Thomas; Timo Ropinski and Anders Ynnerman and Charl Botha and Jos Roerdink
Molecular visualizations are a principal tool for analyzing the results of biochemical 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. We present two out-of-core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non-photorealistic rendering methods.
MolVA 2018: Frontmatter
(The Eurographics Association, 2018) Byška, Jan; Krone, Michael; Sommer, Björn; Jan Byska and Michael Krone and Björn Sommer
Atomistic Visualization of Mesoscopic Whole-Cell Simulations Using Ray-Casted Instancing
(The Eurographics Association and Blackwell Publishing Ltd., 2013) Falk, Martin; Krone, Michael; Ertl, Thomas; Holly Rushmeier and Oliver Deussen
Molecular visualization is an important tool for analysing the results of biochemical simulations. With modern GPU ray casting approaches, it is only possible to render several million of atoms interactively unless advanced acceleration methods are employed. Whole‐cell simulations consist of at least several billion atoms even for simplified cell models. However, many instances of only a few different proteins occur in the intracellular environment, which can be exploited to fit the data into the graphics memory. For each protein species, one model is stored 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. We present two out‐of‐core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non‐photorealistic rendering methods. We also show that the method can be used to render scenes that are composed of triangulated instances, not only implicit surfaces.Molecular visualization is an important tool for analyzing the results of biochemical simulations. With modern GPU ray casting approaches it is only possible to render several million of atoms interactively unless advanced acceleration methods are employed. Whole‐cell simulations consist of at least several billion atoms even for simplified cell models. However, many instances of only a few different proteins occur in the intracellular environment, which can be exploited to fit the data into the graphics memory. For each protein species, one model is stored 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 with implicit surfaces and triangular meshes.

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