Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

Doctor of Philosophy

dissertationRay tracing presents an efficient rendering algorithm for scientific visualization using common visualization tools and scales with increasingly large geometry counts while allowing for accurate physically-based visualization and analysis, which enables enhanced rendering and new visualization techniques. Interactivity is of great importance for data exploration and analysis in order to gain insight into large-scale data. Increasingly large data sizes are pushing the limits of brute-force rasterization algorithms present in the most widely-used visualization software. Interactive ray tracing presents an alternative rendering solution which scales well on multicore shared memory machines and multinode distributed systems while scaling with increasing geometry counts through logarithmic acceleration structure traversals. Ray tracing within existing tools also provides enhanced rendering options over current implementations, giving users additional insight from better depth cues while also enabling publication-quality rendering and new models of visualization such as replicating photographic visualization techniques

Spatial CPU-GPU data structures for interactive rendering of large particle data

In this work, I investigate the interactive visualization of arbitrarily large particle data sets which ft into system memory, but not into GPU memory. With conventional rendering techniques, interactivity of visualizations is drastically reduced when rendering tens- or hundreds of millions of objects. At the same time, graphics hardware memory capabilities limit the size of data sets which can be placed in GPU memory for rendering. To circumvent these obstacles, a progressive rendering approach is employed, which gradually streams and renders all particle data to the GPU without reducing or altering the particle data itself. The particle data is rendered according to a visibility sorting derived from occlusion relations between different parts of the data set, leading to a rendering order of scene contents guided by importance for the rendered image. I analyze and compare possible implementation choices for rendering particles as opaque spheres in OpenGL, which forms the basis of the particle rendering application developed within this work. The application utilizes a multi-threaded architecture, where data preprocessing on a CPU-thread and a rendering algorithm on a GPU-thread ensure that the user can interact with the application at any time. In particular it is guaranteed that the user can explore the particle data interactively, by ensuring minimal latency from user input to seeing the effects of that input. This is achieved by favoring user inputs over completeness of the rendered image at all stages during rendering. At the same time the user is provided with an immediate feedback about interactions by re-projecting all currently visible particles to the next rendered image. The re-projection is realized with an on-GPU particle-cache of visible particles that is built during particle data streaming and rendering, and drawn upon user interaction using the most recent camera confguration according to user inputs. The combination of the developed techniques allows interactive exploration of particle data sets with up to 1.5 billion particles on a commodity computer.In dieser Arbeit wird die interaktive Visualisierung beliebig großer Partikeldaten untersucht, wobei die Partikeldaten im Arbeitsspeicher hinterlegt sind, aber nicht zwangsläufig in den Grafikspeicher passen. Mit üblichen Rendering Methoden büßen Visualisierungen drastisch an Interaktivität ein, wenn mehrere zehn- bis hunderte Millionen Objekte dargestellt werden. Gleichzeitig ist die Größe möglicher zu visualisierender Datensätze begrenzt durch den Videospeicher von Grafikkarten, auf dem zu visualisierende Daten vorliegen müssen. Um diese Einschränkungen zu umgehen, wird in dieser Arbeit ein progressiver Rendering Ansatz verfolgt, der sukzessive alle Partikeldaten zur Grafikkarte hochlädt und rendert, ohne die Partikeldaten zu reduzieren oder anderweitig zu verändern. Die Partikeldaten werden entsprechend einer vorgenommenen Sichtbarkeitssortierung gerendert, die aus gegenseitigen Verdeckungen verschiedener Teile des Partikeldatensatzes berechnet wird. Dies führt dazu, dass Teile der Szene nach ihrer Wichtigkeit für das aktuelle Bild sortiert und dargestellt werden. Es werden verschiedene Möglichkeiten analysiert und verglichen, Partikel als opake Kugeln in OpenGL zu rendern. Dies formt die Grundlage für die Partikel-Rendering Software, die in dieser Arbeit entwickelt wurde. Die Architektur der Rendering-Software benutzt mehrere Threads, sodass durch eine Daten-Vorverarbeitung auf einem CPUThread und durch Rendering-Algorithmen auf einem GPU-Thread sichergestellt ist, dass der Benutzer mit der Software jederzeit interagieren kann. Insbesondere ist sichergestellt, dass der Benutzer die Partikeldaten interaktiv untersuchen kann, indem die Latenz zwischen Benutzereingaben und dem Anzeigen der daraus resultierenden Veränderungen minimal gehalten wird. Dies wird erreicht indem der Verarbeitung von Benutzereingaben an allen Stellen des Rendering-Prozesses höhere Priorität eingeräumt wird als der Vollständigkeit des gerenderten Bildes. Gleichzeitig wird dem Benutzer eine sofortige Rückmeldung über getätigte Benutzereingaben gegeben, indem alle sichtbaren Partikel in das nächste gerenderte Bild neu projeziert werden. Diese Neu-Projektion wird durch einen GPU-seitigen Partikel-Cache aller aktuell sichtbaren Partikel realisiert, der während des sukzessiven Partikelstreamings und -renderns aufgebaut wird. Sobald der Benutzer eine Eingabe tätigt, wird der auf der GPU liegende Partikel-Cache unter der aktuellsten benutzerdefinierten Kameraposition neu gerendert. Die Kombination dieser entwickelten Methoden erlaubt ein interaktives Betrachten von Partikeldaten mit bis zu 1,5 Milliarden Partikeln auf einem handelsüblichen Computer

An efficient multi-resolution framework for high quality interactive rendering of massive point clouds using multi-way kd-trees

We present an efficient technique for out-of-core multi-resolution construction and high quality interactive visualization of massive point clouds. Our approach introduces a novel hierarchical level of detail (LOD) organization based on multi-way kd-trees, which simplifies memory management and allows control over the LOD-tree height. The LOD tree, constructed bottom up using a fast high-quality point simplification method, is fully balanced and contains all uniformly sized nodes. To this end, we introduce and analyze three efficient point simplification approaches that yield a desired number of high-quality output points. For constant rendering performance, we propose an efficient rendering-on-a-budget method with asynchronous data loading, which delivers fully continuous high quality rendering through LOD geo-morphing and deferred blending. Our algorithm is incorporated in a full end-to-end rendering system, which supports both local rendering and cluster-parallel distributed rendering. The method is evaluated on complex models made of hundreds of millions of point sample

Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

Ray Tracing Gems

This book is a must-have for anyone serious about rendering in real time. With the announcement of new ray tracing APIs and hardware to support them, developers can easily create real-time applications with ray tracing as a core component. As ray tracing on the GPU becomes faster, it will play a more central role in real-time rendering. Ray Tracing Gems provides key building blocks for developers of games, architectural applications, visualizations, and more. Experts in rendering share their knowledge by explaining everything from nitty-gritty techniques that will improve any ray tracer to mastery of the new capabilities of current and future hardware. What you'll learn: The latest ray tracing techniques for developing real-time applications in multiple domains Guidance, advice, and best practices for rendering applications with Microsoft DirectX Raytracing (DXR) How to implement high-performance graphics for interactive visualizations, games, simulations, and more Who this book is for: Developers who are looking to leverage the latest APIs and GPU technology for real-time rendering and ray tracing Students looking to learn about best practices in these areas Enthusiasts who want to understand and experiment with their new GPU