Visualization and Simulation of Laser-Induced Fullerene Fragmentation

The benefit from the research of carbon, an element with one of the highest variety of binding possibilities that is essential for life, has a strong impact in many fields in science as well as in industry. A molecule that is suited to explore more complex systems of carbon atoms due to its highly symmetrical hollow sphere-like structure is C60, one of the best known fullerenes. Still, its dynamics is far from being understood, especially its interaction with ultrashort and strong laser pulses. Simulations can help us to get insights into the dynamics of molecules. In combination with visualization, these dynamics can be analyzed and understood. Leaned to laser experiments with fullerene, performed at LCLS to get further insights into the dynamics of fullerene, this work examines some of their experiments by means of molecular dynamics simulations, which we analyze by our developed visualization techniques. The focus is on the fragmentation dynamics, induced by laser pulses that are used in the experiments. The contribution of this work can be summarized into simulation and visualization. Simulations are required to imitate the experiment, including the modeling of C60 by the choice of force field potentials, the modeling of laser pulses, and their intensities. The results of our simulations are adapted based on results from the experiments. Goals in the visualization are the development of novel analysis techniques. These techniques are for the fragmentation process of fullerene, the fragmentation dynamics by exibility methods, the reconstruction of diffraction images, which can be used as additional medium for the physical analysis, as well as the analysis of the achieved results of this work

Interactive ray tracing of solvent excluded surfaces

Domain experts in fields concerned with the behavior of molecules, for example biochemists, employ simulations to study a molecule’s individual properties and mutual interactions with other molecules. To obtain an intuitive spatial understanding of the returned data of the simulations, various visualization techniques such as molecular surfaces can be applied on the data. The solvent excluded surface depicts the boundary between the molecule’s and a solvent’s occupied space and therefore the molecules accessibility for the solvent. Insight about a molecule’s potential for interaction such as reactions can be gained by studying the surface’s shape visually. Current implementations for the visualization of the surface usually utilize GPU ray casting to achieve the performance required to allow interactivity such as viewpoint changing. However, this makes implementation of physically motivated effects like ambient occlusion or global illumination difficult. If compute resources do not contain GPUs, which is often the case in compute clusters, expensive software rasterization has to be employed instead. As CPUs offer less parallelism compared to GPUs, overhead introduced by the overdraw of thousands of primitives should be avoided. To mitigate these issues, CPU visualization approaches resurfaced again in recent times. In this work, the solvent excluded surface is visualized interactively using the classic ray tracing approach within the OSPRay CPU ray tracing framework. The described implementation is able to compute and visualize the solvent excluded surface for datasets composed of millions of atoms. Additionally, the surface supports transparency rendering, which allows implementation of a cavity visualization method that uses ambient occlusion