Science Advances virtual reality paper


Working with academic colleagues from high-performance computing (HPC) and human-computer interaction (HCI), we recently published an open access paper entitled “Sampling molecular conformations and dynamics in a multiuser virtual reality framework” in the AAAS journal Science Advances. The paper described a scientifically rigorous, VR-enabled, multi-person, real-time interactive Molecular Dynamics (iMD) framework, , which lets researchers use virtual reality to literally reach out & touch real-time molecular physics using cloud-mounted supercomputing.

The paper presents the results of HCI experiments showing that VR (specifically the HTC Vive setup) enables users to carry out 3d molecular simulation tasks extremely efficiently compared to other platforms. Specifically, we asked users to perform three separate molecular manipulations, and timed how long each took on various platforms: in VR, on a touchscreen, and using a computer/mouse . The tasks included threading a molecule of methane through a simulated carbon nanotube; unwinding a left-handed helical molecule and rewinding it into a right-handed helix; and tying a knot in a simulated protein. The results showed that in VR, users were able to accomplish all of the tasks more quickly. The knot task, in particular, was completed nearly ten times as rapidly! By using 2D screen-based simulations of molecules, it seems pretty clear that we’re a lot less efficient than we could be.


interactive MD art installation

DS FESTIVAL -133-compressedIn collaboration with Bristol-based tech startup Interactive Scientific, more than 37,000 people had the chance to experience the acclaimed real-time interactive molecular dynamics art installation ‘danceroom Spectroscopy’ (dS) at the ‘We the Curious’ science museum in central Bristol. dS – whose architecture is described in a 2014 Faraday Discussion paper – fuses rigorous methods from computational physics, GPU computing, and computer vision to interpret people as fields whose movement creates ripples and waves in an unseen field. The result is a gentle piece comprised of interactive graphics and soundscapes, both of which respond in real-time to people’s movements – enabling them to sculpt the invisible fields in which they are embedded. Offering a unique and subtle glimpse into the beauty of our everyday movements, dS allows us to imagine how we interact with the hidden energy matrix and atomic world which forms the fabric of nature, but is too small for our eyes to see. It’s as much a next-generation digital arts installation as it is an invitation to contemplate the interconnected dynamism of the natural world and processes of emergence, fluctuation, and dissipation – from the microscopic to the cosmic. The installation ran from October 2017 through January 2018, and was open to anybody;  you can read more about it here.

OpenWorld San Francisco

During the first week of October, I attended the Oracle Open World conference in San Francisco, where I was invited to give a talk entitled “Collaborative Cloud-Based Virtual Reality for Scientific Research & Education”. In the talk, I outlined the virtual reality framework that we’ve been working to develop over the years, focusing on the cloud aspects of the project – particularly those which enable multiple users to simultaneously inhabit the same real-time virtual simulation environment.  Using modern cloud architectures, it’s now possible to build real-time interactive simulations that harness the power of cloud supercomputing. And the cloud allows anybody to login to the simulation server remotely. Another highlight of the trip was an invitation to a small get-together at Larry Ellison’s private SF residence, where he offered his insight into a wide range of different areas, all informed by his perspective as the founder of one of the planet’s biggest tech companies.  Amongst his most memorable statements was his claim that, were he to start over again, he’d consider starting a molecular science or biotech company. He also said that computational molecular biosciences is one of his hobbies. It’s an area he’s always been interested in, but wasn’t really a viable discipline back in the day. Things have definitely changed.


modern art oxford: future knowledge

On 17th June, Lisa May Thomas and I led a workshop at Modern Art Oxford entitled “Sculpting the Invisible World”. The work was part of the gallery’s ‘Future Knowledge’ program of events, curated by Emma Ridgway, and photographed by Stu Allsop. Using a pioneering multi-person virtual reality software framework, visitors were invited to interact within a virtual landscape as embodied energy fields. Methods from rigorous computational molecular physics and real-time digital rendering allowed digitally embodied participants to sculpt the dynamics of a simulated molecular nano-world, for example deforming buckminsterfullerene molecules, passing them back and forth, threading methane molecules through a carbon nanotube, and tying knots in proteins.

Sculpting the Invisible World follows on from the ‘dances with Avatars’ experiments carried out by Lisa May Thomas, which were designed as a sort of embodied Turing Test. During the Modern Art Oxford workshops, we were specifically interested in two aspects of multi-person interaction in VR: (1) what are the conventions which guided human-to-human interaction in virtual spaces, when we are rendered as digital bodies? (2) how do we begin to understand what ‘feeling’ means in an immersive scientific visualisation environment – particularly in order to understand workshop participants’ claims that different molecular structures “feel” different?

Photosynthetic excitation energy transport


Another paper to report on (open-access link available here). This work examines excitation energy transport in LH2, a supramolecular photosynthetic complex which is found in the cell membranes of purple bacteria. Lots of people have gotten interested in LH2 ever since Graham Fleming’s group published a paper in 2007 reporting on fancy 2d spectroscopy which observed coherent quantum “beating” between initially prepared electronic states. Beating patterns of this sort are certainly of fundamental interest, and the experiments used to observe it were very nice; however, the consensus which seems to be emerging is that the “beating” is in fact not so important for explaining the efficiency at which photosynthetic systems transport electronic energy across their membranes.

So why did I decide to get involved in LH2? Well, a few reasons. First, my colleague Dr. Tom Oliver has had a longstanding interest in this system. And second, I’ve been extremely confused by the LH2 modelling literature. When we think about excited state and non-adiabatic dynamics in small and medium sized molecules, we think about topological features like conical intersections, avoided crossings, near degeneracies, non-adiabatic coupling vectors, etc. For small molecules, we know that fluctuations in vibrational degrees of freedom are often responsible for bringing electronic states into near-degeneracy, and transferring amplitude between states.

Despite the fact that all of these concepts are extremely mature owing to developments over the years within the small molecule excited state dynamics community, they are nowhere to be found when one reads the LH2 literature. Instead, we read about master equation treatments where every single vibration is anonymised, and folded into a linearly coupled “spectral density function”. Conical intersections? Avoided crossings? Near degeneracies? Non-adiabatic coupling vectors? Entirely absent. It’s almost like LH2 is linked to an entirely different discipline with an entirely different vocabulary.

So my aim with the LH2 work was full representation of vibrations! No more nameless vibrations folded into some anonymous spectral density function. Full representation of each and every vibration, capturing the fullness of its unique dynamical anharmonic identity. It’s the kind of sentiment that seems particularly well aligned with the current populist zeitgeist sweeping the globe.

But LH2 is big, and it has has lots of excited states, so a full representation of all of its vibrations in atomistic detail is a non-trivial challenge. To do it, we built a multi-tiered parallel computational framework (using TDDFT parallelized across GPUs within nodes, and MPI to scale across nodes) for calculating atomic cartesian gradients on each and every excited state. We also introduced some approximations for how to treat cartesian gradients of the excited state dipole moments and the transition dipole moments. This builds on some work we published a couple years ago. Once all that was stabilised, we were then able to run surface-hopping simulations to treat the explicit dynamics of both the atoms and also the electronic degrees of freedom. The picture that emerges is shown in the movie. The key thing which this movie highlights (compared to previous simulations) is the fact that the atomic motion is explicitly being accounted for, along with the electronic motion (which is shown as diffuse blue clouds). You need to look closely at the video to see the atomic motion, because your eyes are more attuned to the flashing blue electronic amplitude than to the subtleties of the vibrational motion. But it’s definitely all in there if you look closely!

The dynamical picture of electronic energy transport which emerges from this work is one of excited states which fluctuate rapidly as a result of the underlying vibrational dynamics of the atoms which make up the constituent LH2 chromophores. The excited states are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale, as depicted in Fig 4A of the paper. Every crossing offers an opportunity to transfer amplitude from one excited state to another. The result is a sort of highly connected excited state network: the frequent crossings combine to create scenario where the states are in a sort of constant “communication” with one another, allowing excitation localized in any one state to travel far and fast. The take-home message? It’s all about the vibrations!