A general illumination model for molecular visualization

Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-and-Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large-scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom-based molecular representations. The proposed model can be further evaluated in real-time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.Peer ReviewedPostprint (author's final draft

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