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“GPU-accelerated atom and dynamic bond visualization using HyperBalls, a unified algorithm for balls, sticks and hyperboloids”
M. Chavent, A. Vanel, A. Tek, B. Lévy, S. Robert, B. Raffin and M. Baaden
Journal of Computational Chemistry, 2011

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 & stick, space-filling van der Waals spheres and approximated solvent accessible surfaces using GPUs. We introduce HyperBalls, an improved ball & 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 non covalent bonds. It is furthermore well suited to represent coarse grained models as well as 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.

BibTex reference

   TITLE      = "GPU-accelerated atom and dynamic bond visualization using HyperBalls,
                    a unified algorithm for balls, sticks and hyperboloids",
   AUTHOR     = "M. Chavent and A. Vanel and A. Tek and B. Lévy and S. Robert a
                   nd B. Raffin and M. Baaden",
   JOURNAL    = "Journal of Computational Chemistry",
   YEAR       = "2011",