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

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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

“…All these graphics techniques, available in real time, will be a great help for the users to interact in a wiser manner with their molecular structures. We have recently developed our implementation of molecular representations on the GPU [Chavent, Vanel, Tek, Lévy, Robert, Raffin & Baaden (2011)]. In this work, we introduced a visual molecular model, the HyperBalls representation, that offers a continuous representation smoothly connecting between classical representations such as licorice or ball-and-stick (figure 10).…”

Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

“…We have tested graphical methods available in Unity3D as well as our HyperBalls representation based on ray casting [13]. The purpose of implementing HyperBalls was to evaluate how difficult it is to port previously developed code to Unity3D and whether this approach facilitates and speeds up the creation of a molecular graphics application.…”

“…We have developed a molecular representation called HyperBalls [13]. This representation takes advantage of the programmability of graphics cards using high quality ray casting with good display performance.…”

“…We also implemented the HyperBalls representation [13] and molecular surfaces. The advantages and limitations of each approach are discussed.…”

Content and task based navigation for structural biology in 3D environments

“…Recently, these representations have undergone evolutions thanks to continuous improvement in the performance of computing systems. Game engines and their rendering algorithms have been used for example to set up new representations of atoms using GPU capabilities, aiming at dynamic representations of large scale molecular data [4]. Recent works still try to find the best compromise in terms of visual data and information load we can couple for molecular visualization [1].…”