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

Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, Bruno Raffin, Marc Baaden
Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique, CNRS UPR 9080/Universite Paris-7, 13, rue Pierre et Marie Curie, F-75005 Paris, France; CEA, DAM, DIF, 91297 Arpajon, France
J. Comput. Chem., Vol. 32, No. 13. (2011), pp. 2924-2935.

@article{chaventgpu,

   title={GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids},

   author={Chavent, M. and Vanel, A. and Tek, A. and Levy, B. and Robert, S. and Raffin, B. and Baaden, M.},

   journal={Journal of Computational Chemistry},

   year={2011},

   publisher={Wiley Online Library}

}

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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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