Ambient occlusion and shadows for molecular graphics

Computer based visualisations of molecules have been produced as early as the 1950s to aid researchers in their understanding of biomolecular structures. An important consideration for Molecular Graphics software is the ability to visualise the 3D structure of the molecule in a clear manner. Recent advancements in computer graphics have led to improved rendering capabilities of the visualisation tools. The capabilities of current shading languages allow the inclusion of advanced graphic effects such as ambient occlusion and shadows that greatly improve the comprehension of the 3D shapes of the molecules. This thesis focuses on finding improved solutions to the real time rendering of Molecular Graphics on modern day computers. The methods of calculating ambient occlusion and both hard and soft shadows are examined and implemented to give the user a more complete experience when navigating large molecular structures

Doctor of Philosophy

dissertationReal-time global illumination is the next frontier in real-time rendering. In an attempt to generate realistic images, games have followed the film industry into physically based shading and will soon begin integrating global illumination techniques. Traditional methods require too much memory and too much time to compute for real-time use. With Modular and Delta Radiance Transfer we precompute a scene-independent, low-frequency basis that allows us to calculate complex indirect lighting calculations in a much lower dimensional subspace with a reduced memory footprint and real-time execution. The results are then applied as a light map on many different scenes. To improve the low frequency results, we also introduce a novel screen space ambient occlusion technique that allows us to generate a smoother result with fewer samples. These three techniques, low and high frequency used together, provide a viable indirect lighting solution that can be run in milliseconds on today's hardware, providing a useful new technique for indirect lighting in real-time graphics

Developing serious games for cultural heritage: a state-of-the-art review

Although the widespread use of gaming for leisure purposes has been well documented, the use of games to support cultural heritage purposes, such as historical teaching and learning, or for enhancing museum visits, has been less well considered. The state-of-the-art in serious game technology is identical to that of the state-of-the-art in entertainment games technology. As a result, the field of serious heritage games concerns itself with recent advances in computer games, real-time computer graphics, virtual and augmented reality and artificial intelligence. On the other hand, the main strengths of serious gaming applications may be generalised as being in the areas of communication, visual expression of information, collaboration mechanisms, interactivity and entertainment. In this report, we will focus on the state-of-the-art with respect to the theories, methods and technologies used in serious heritage games. We provide an overview of existing literature of relevance to the domain, discuss the strengths and weaknesses of the described methods and point out unsolved problems and challenges. In addition, several case studies illustrating the application of methods and technologies used in cultural heritage are presented

A general illumination model for molecular visualization

Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-and-Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large-scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom-based molecular representations. The proposed model can be further evaluated in real-time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.Peer ReviewedPostprint (author's final draft

Evaluating Tessellation and Screen-Space Ambient Occlusion in WebGL-Based Real-Time Application

abstract: Tessellation and Screen-Space Ambient Occlusion are algorithms which have been widely-used in real-time rendering in the past decade. They aim to enhance the details of the mesh, cast better shadow effects and improve the quality of the rendered images in real time. WebGL is a web-based graphics library derived from OpenGL ES used for rendering in web applications. It is relatively new and has been rapidly evolving, this has resulted in it supporting a subset of rendering features normally supported by desktop applications. In this thesis, the research is focusing on evaluating Curved PN-Triangles tessellation with Screen Space Ambient Occlusion (SSAO), Horizon-Based Ambient Occlusion (HBAO) and Horizon-Based Ambient Occlusion Plus (HBAO+) in WebGL-based real-time application and comparing its performance to desktop based application and to discuss the capabilities, limitations and bottlenecks of WebGL 1.0.Dissertation/ThesisWebGL ProgramOpenGL ProgramMasters Thesis Computer Science 201

Mobile graphics: SIGGRAPH Asia 2017 course

Peer ReviewedPostprint (published version

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

Interactive high fidelity visualization of complex materials on the GPU

Documento submetido para revisão pelos pares. A publicar em Computers & Graphics. ISSN 0097-8493. 37:7 (nov. 2013) p. 809–819High fidelity interactive rendering is of major importance for footwear designers, since it allows experimenting with virtual prototypes of new products, rather than producing expensive physical mock-ups. This requires capturing the appearance of complex materials by resorting to image based approaches, such as the Bidirectional Texture Function (BTF), to allow subsequent interactive visualization, while still maintaining the capability to edit the materials' appearance. However, interactive global illumination rendering of compressed editable BTFs with ordinary computing resources remains to be demonstrated. In this paper we demonstrate interactive global illumination by using a GPU ray tracing engine and the Sparse Parametric Mixture Model representation of BTFs, which is particularly well suited for BTF editing. We propose a rendering pipeline and data layout which allow for interactive frame rates and provide a scalability analysis with respect to the scene's complexity. We also include soft shadows from area light sources and approximate global illumination with ambient occlusion by resorting to progressive refinement, which quickly converges to an high quality image while maintaining interactive frame rates by limiting the number of rays shot per frame. Acceptable performance is also demonstrated under dynamic settings, including camera movements, changing lighting conditions and dynamic geometry.Work partially funded by QREN project nbr. 13114 TOPICShoe and by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within projectPEst-OE/EEI/UI0752/2011