BIG

Bristol Interaction Group

Designing Interactive Molecular Simulation Platforms

Molecular Simulation is amongst the fastest growing areas in the chemical sciences, an achievement highlighted by the award of the 2013 Nobel Prize in Chemistry to a group of scientists who the Nobel committee described as “taking the chemical experiment into cyberspace.” The dream is that one day we will perhaps be able to use computational design in order to engineer molecular materials in a similar way as we now use computational frameworks to design buildings and bridges. As attractive as this goal might seem, the path to get there is fraught with difficulties. One of the biggest hurdles arises from the fact that molecular systems are inherently hyper-dimensional. For example, even a relatively small biomolecule has 1000 atoms, which corresponds to 3000 degrees of freedom! A great deal of work has been devoted to designing algorithms in order to efficiently search and characterise the most promising regions of molecular design space. One particularly interesting strategy involves the development of interfaces that allow humans to use their molecular ‘design intuition’ to guide automated search algorithms. Two recent examples – FOLDIT [1] and Eterna [2] – have highlighted the ability of such approaches to significantly accelerate hyperdimensional molecular search tasks when compared to algorithms which do not allow for human interaction.

 

In this talk, I will describe recent work in my group aimed at designing interactive molecular simulation platforms which can be used for accelerating molecular research, scientific education, and artistic applications [3,4]. I will highlight a range of different approaches that we have been developing over the past few years: (1)  algorithms and hardware we designed to carry out interactive molecular dynamics utilizing an array of consumer depth sensors; (2) more recent work constructing cross-platform interactive molecular simulation frameworks which run on tablets; and (3) recent experiments with Oculus Rift and HTC Vive, aimed to furnish an interactive molecular simulation virtual reality environment. The interfaces that I will describe work by interpreting the human form (or bits of the human form) as an energy ‘avatar’, which can then be rigorously incorporated into the physical equations of motion. GPU acceleration has been key to achieving a relatively fluid interactive experience. Preliminary tests run in a chemistry/physics education context show that these tools allow non-expert users to accelerate simple molecular search tasks by 3–4 orders of magnitude compared to brute force ‘blind-search’ algorithms. Should time allow, I hope to demo some of the things we have been working on at the end of the talk.

 

[1] Cooper et al. “Predicting protein structures with a multiplayer online game.” Nature 466.7307 (2010): 756-760.

[2] Lee et al. “RNA design rules from a massive open laboratory.” Proceedings of the National Academy of Sciences 111.6 (2014): 2122-2127

[3] Glowacki et al., “A GPU-accelerated immersive audiovisual framework for interactive molecular dynamics using consumer depth sensors,” Faraday Discussion 169, 2014, 63 – 89, open access

[4] Mitchell et al., “danceroom Spectroscopy: at the frontiers of physics, performance, interactive art, and technology,” Leonardo, April 2016, 49(2), p 138-147, (2016), cover article

Dr David Glowacki (MA, PhD) is a Royal Society Research fellow at the University of Bristol (joint between the Department of Chemistry and Computer Science) and consulting professor at Stanford University. He is also chief scientific consultant to Interactive Scientific Ltd., a Bristol-based tech company that he co-founded in 2013. 

 

Glowacki’s research spans several areas, including: computational algorithms for simulating classical and quantum systems, energy flow in chemical systems, atmospheric chemistry, algorithm development, high-performance computing, and scientific visualization.

 

Glowacki also led development of danceroom spectroscopy (dS), a multi-award winning software/hardware platform that combines molecular physics simulations with state-of-the-art computing to facilitate an immersive interactive experience. High-profile dS installations have enabled hundreds of thousands of people across the UK, Europe, and the USA to experience the subtle beauty and complexity of the atomic world.