GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.

Matthieu Chavent 1, 2, 3 Antoine Vanel 4 Alex Tek 3 Bruno Levy 2 Sophie Robert 5 Bruno Raffin 4 Marc Baaden 3, *
* Corresponding author
1 ORPAILLEUR - Knowledge representation, reasonning
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
2 ALICE - Geometry and Lighting
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
4 MOAIS - PrograMming and scheduling design fOr Applications in Interactive Simulation
Inria Grenoble - Rhône-Alpes, LIG - Laboratoire d'Informatique de Grenoble
Abstract : Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball-and-stick, space-filling van der Waals spheres, and approximated solvent-accessible surfaces using GPUs. We introduce HyperBalls, an improved ball-and-stick representation replacing tubes, linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of noncovalent bonds. It is furthermore well suited to represent coarse-grained models and spring networks. All these representations can be defined by a single general algebraic equation that is adapted for the ray-casting technique and is well suited for execution on the GPU. Using GPU capabilities, this implementation can routinely, accurately, and interactively render molecules ranging from a few atoms up to huge macromolecular assemblies with more than 500,000 particles. In simple cases, based only on spheres, we have been able to display up to two million atoms smoothly.
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https://hal.archives-ouvertes.fr/hal-00645162
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Submitted on : Saturday, November 26, 2011 - 11:54:49 PM
Last modification on : Tuesday, June 25, 2019 - 1:26:57 AM

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Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, et al.. GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.. Journal of Computational Chemistry, Wiley, 2011, 32 (13), pp.2924-35. ⟨10.1002/jcc.21861⟩. ⟨hal-00645162⟩

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