A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

Abstract

A GPU-accelerated immersive audiovisual framework for interaction with molecular dynamics using consumer depth sensors. Faraday Discussions, 169. pp. 63-87. ISSN 1359-6640 Available from: http://eprints.uwe.ac.uk/23115We recommend you cite the published version. The publisher's URL is: http://dx.doi.org/10.1039/C4FD00008K Refereed: Yes First published online 19 Mar 2014Disclaimer UWE has obtained warranties from all depositors as to their title in the material deposited and as to their right to deposit such material. UWE makes no representation or warranties of commercial utility, title, or fitness for a particular purpose or any other warranty, express or implied in respect of any material deposited. UWE makes no representation that the use of the materials will not infringe any patent, copyright, trademark or other property or proprietary rights.UWE accepts no liability for any infringement of intellectual property rights in any material deposited but will remove such material from public view pending investigation in the event of an allegation of any such infringement. PLEASE SCROLL DOWN FOR TEXT.A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors † With advances in computational power, the rapidly growing role of computational/ simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360 spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360 atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

“…The VR-enabled interactive MD shown in Video 1 effectively amounts to a real-time classical dynamics simulation which responds to real-time biasing forces, building on our previous work using optical tracking technologies to interactively steer real-time molecular simulations. 4 In classical mechanics, the timedependent dynamics of molecular systems are solved by numerically integrating Newton's equations of motion. The vector of forces acting on a set of atoms F(t) can be written in terms of the system's potential energy V, i.e.…”

“…Over the past several years, our laboratory has been carrying out an interdisciplinary research program exploring interactive molecular dynamics (iMD) beyond standard 2d interfaces, designed to enable direct multisensory interaction with molecular simulations. [4][5][6][7][8][9] The recent emergence of robust and affordable virtual reality (VR) technologies has been a key enabler in these efforts, allowing us to develop a framework where scientists can manipulate rigorous real-time simulations of molecular systems, as shown in Figure 1 and Video 1 (vimeo.com/244670465). Figure 1 shows two optically tracked participants (each wearing a VR headmounted display (HMD) and holding in each hand wireless controllers which function as atomic 'tweezers') manipulating the real-time MD of a C60 molecule using interactive molecular dynamics in virtual reality (iMD-VR).…”

danceroom Spectroscopy: At the Frontiers of Physics, Performance, Interactive Art and Technology

“…The system is so robust that it is possible for users to interactively manipulate a real-time protein dynamics simulation [20]. These scientific applications of dS are described fully in Glowacki et al [19]. The emphasis in this article is on how dS functions within an artistic context, where it has been deployed in two different capacities: (1) as an interactive installation for the public and (2) as an artistic tool providing the visual, sonic and choreographic fabric that knits together a dance performance called Hidden Fields.…”

“…The resulting effect enables participants to sculpt the dynamics of the atomic ensemble in real time. For a comprehensive overview of the algorithms, mathematics and implementation that underlie this process, see Glowacki et al [19].…”

Tangible Networks: A Toolkit for Exploring Network Science

“…For example, NetLogo 3 is an interactive visualisation software package developed for exploring agent-based systems in real time. Danceroom Spectroscopy [12,19] is an interactive model of molecular dynamics where the visualisation of the moving molecules is projected on a screen and the bodies of users become "energy landscapes" that directly affect the forces on the molecules. Danceroom Spectroscopy has been used as an art installation, in dance performances, for education and also for research.…”