Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers

Nucleation and growth of gold nanoparticles in the presence of different surfactants: a dissipative particle dynamics study

Colloids; Computational chemistry; NanoparticlesColoides; Química computacional; NanopartículasCol·loides; Química computacional; NanopartículesNanoparticles (NPs) show promising applications in biomedicine, catalysis, and energy harvesting. This applicability relies on controlling the material’s features at the nanometer scale. Surfactants, a unique class of surface-active molecules, have a remarkable ability to tune NPs activity; provide specific functions, avoid their aggregation, and create stable colloidal solutions. Surfactants also control nanoparticles’ nucleation and growth processes by modifying nuclei solubility and surface energy. While nucleation seems independent from the surfactant, NP’s growth depends on it. NP`s size is influenced by the type of functional group (C, O, S or N), length of its C chain and NP to surfactant ratio. In this paper, gold nanoparticles (Au NPs) are taken as model systems to study how nucleation and growth processes are affected by the choice of surfactants by Dissipative Particle Dynamics (DPD) simulations. DPD has been mainly used for studying biochemical structures, like lipid bilayer models. However, the study of solid NPs, and their conjugates, needs the introduction of a new metallic component. To represent the collective phenomena of these large systems, their degrees of freedom are reduced by Coarse-Grained (CG) models. DPD behaved as a powerful tool for studying complex systems and shedding some light on some experimental observations, otherwise difficult to explain.Authors are gratefully acknowledged for a fellowship to R.S-L provided by Universitat Autònoma de Barcelona, and for the financial support obtained through grant number RTI2018-099965-B-I00 from Ministerio de Ciencia, Innovación y Universidades, Spain. NGB and VP acknowledge financial support from R&D&I projects for international joint programming from MCIN/AEI (CONCORD, PCI2019-103436) cofunded by the European Union and from Generalitat de Catalunya (2017-SGR-1431). ICN2 is supported by the Severo Ochoa program from Spanish MINECO (SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya

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