High quality rendering of protein dynamics in space filling mode

Producing high quality depictions of molecular structures has been an area of academic interest for years, with visualisation tools such as UCSF Chimera, Yasara and PyMol providing a huge number of different rendering modes and lighting effects. However, no visualisation program supports per-pixel lighting effects with shadows whilst rendering a molecular trajectory in space filling mode. In this paper, a new approach to rendering high quality visualisations of molecular trajectories is presented. To enhance depth, ambient occlusion is included within the render. Shadows are also included to help the user perceive relative motions of parts of the protein as they move based on their trajectories. Our approach requires a regular grid to be constructed every time the molecular structure deforms allowing per-pixel lighting effects and ambient occlusion to be rendered every frame, at interactive refresh rates. Two different regular grids are investigated, a fixed grid and a memory efficient compact grid. The algorithms used allow trajectories of proteins comprising of up to 300,000 atoms in size to be rendered at ninety frames per second on a desktop computer using the GPU for general purpose computations. Regular grid construction was found to only take up a small proportion of the total time to render a frame. It was found that despite being slower to construct, the memory efficient compact grid outperformed the theoretically faster fixed grid when the protein being rendered is large, owing to its more efficient memory access patterns. The techniques described could be implemented in other molecular rendering software

TetSplat: Real-time Rendering and Volume Clipping of Large Unstructured Tetrahedral Meshes

We present a novel approach to interactive visualization and exploration of large unstructured tetrahedral meshes. These massive 3D meshes are used in mission-critical CFD and structural mechanics simulations, and typically sample multiple field values on several millions of unstructured grid points. Our method relies on the pre-processing of the tetrahedral mesh to partition it into non-convex boundaries and internal fragments that are subsequently encoded into compressed multi-resolution data representations. These compact hierarchical data structures are then adaptively rendered and probed in real-time on a commodity PC. Our point-based rendering algorithm, which is inspired by QSplat, employs a simple but highly efficient splatting technique that guarantees interactive frame-rates regardless of the size of the input mesh and the available rendering hardware. It furthermore allows for real-time probing of the volumetric data-set through constructive solid geometry operations as well as interactive editing of color transfer functions for an arbitrary number of field values. Thus, the presented visualization technique allows end-users for the first time to interactively render and explore very large unstructured tetrahedral meshes on relatively inexpensive hardware

The 2D Continuum Radiative Transfer Problem: Benchmark Results for Disk Configurations

We present benchmark problems and solutions for the continuum radiative transfer (RT) in a 2D disk configuration. The reliability of three Monte-Carlo and two grid-based codes is tested by comparing their results for a set of well-defined cases which differ for optical depth and viewing angle. For all the configurations, the overall shape of the resulting temperature and spectral energy distribution is well reproduced. The solutions we provide can be used for the verification of other RT codes.We also point out the advantages and disadvantages of the various numerical techniques applied to solve the RT problem.Comment: 13 pages, 10 figures, To appear in Astronomy and Astrophysic