Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents

Abstract

Figure 1: Demonstration of our system capabilities from three different zooming levels (left to right). We showcase a scene containing 10 6 diffusing and reacting molecules in real-time at 30 FPS. AbstractIn this paper we propose a new type of a particle systems, tailored for illustrative visualization purposes, in particular for visualizing molecular reactions in biological networks. Previous visualizations of biochemical processes were exploiting the results of agent-based modeling. Such modeling aims at reproducing accurately the stochastic nature of molecular interactions. However, it is impossible to expect events of interest happening at a certain time and location, which is impractical for storytelling. To obtain the means of controlling molecular interactions, we propose to govern passive agents with an omniscient intelligence, instead of giving to the agents the freedom of initiating reaction autonomously. This makes it possible to generate illustrative animated stories that communicate the functioning of the molecular machinery. The rendering performance delivers for interactive framerates of massive amounts of data, based on the dynamic tessellation capabilities of modern graphics cards. Finally, we report an informal expert feedback we obtained from the potential users.

Physics-Based Visual Characterization of Molecular Interaction Forces

“…Thus, a lot of effort has been undertaken in order to reduce the involved polygon count and thus enable interactive visualization of complex molecular models. The proposed algorithms span a wide range of underlying concepts, such as level-of-detail [29,32,38], impostors and glyphs [40,51,3,15,11] or geometric instancing [10,33]. Often, geometry or tessellation shaders, provided by modern GPUs, are also exploited to create spherical or ribbon-based representations of molecules [27,52,21].…”

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

“…Atomic structure visualization. Many authors focused on massive atomic model rendering [24,39], such as LOD approaches [11,30,37], instancing [12], or billboards and glyphs [13,17,45,40]. Grottel et al described an approach which exploits two-level coherent culling to render large-scale molecular dynamics results [18].…”

cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets

“…Le Muzic et al . [LMPSV14], introduced another technique for fast rendering of large particle-based datasets using the GPU rasterization pipeline instead. They were able to render up to 30 billions of atoms at 10 fps in full HD resolution on a NVidia GTX Titan.…”

“…Our rendering pipeline is based on the work of Le Muzic et al . [LMPSV14], which relies on the tessellation shader to dynamically inject sphere primitives in the pipeline for each molecule. However, without proper occlusion culling, the injection of sphere primitives would still be performed, even if a molecule is completely hidden behind occluders.…”

“…However, none of the currently available solutions are able to serve the ambitions of our domain experts, which is to model large macromolecular structures such as E. coli . Related works have already presented bleeding-edge techniques that can render large datasets with up to billions of atoms at interactive framerates on commodity graphics hardware [LBH12] [FKE13] [LMPSV14]. However, to our knowledge, the tools which implemented these techniques were either not publicly available, or remained in the prototyping stage.…”