Abstract
As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.
Highlights
In 1977, artificial and augmented reality (AR) pioneer Myron Krueger began his paper “Responsive Environments” with the observation that “human-machine interaction is usually limited to a seated poking at a machine with fingers or perhaps waving hands over a data tablet.”1 Krueger went on to speculate that real-time, multisensory interaction between humans and machines might enable exciting and efficient new approaches for exploring realities that are otherwise impossible to access
Our own research has explored interactive molecular dynamics in virtual reality—i.e., applications that emphasize simulation at interactive latencies, in which the affordances of two-handed interaction within the three-dimensional VR space enable a participant to “reach out and manipulate” rigorous MD simulations and carry out detailed three-dimensional structural manipulations in real-time, as shown in Fig. 1.8 Our experiments suggest that the utility of iMD-VR as a research tool arises from its ability to transform abstract molecular models into tangible dynamic realities
Narupa overcomes several limitations of the proofof-principle iMD-VR prototype framework we previously described in an article by O’Connor et al.:8 (a) it enables easy access to the multiperson functionality illustrated in Fig. 1 so that multiple participants can inhabit the same iMD-VR environment; (b) rather than the simulations being predefined in advance, it enables participants scitation.org/journal/jcp to set up and customize their own simulations using a flexible force application programming interface (API); and (c) it can be set up to run on local networks
Summary
In 1977, artificial and augmented reality (AR) pioneer Myron Krueger began his paper “Responsive Environments” with the observation that “human-machine interaction is usually limited to a seated (person) poking at a machine with (their) fingers or perhaps waving (their) hands over a data tablet.” Krueger went on to speculate that real-time, multisensory interaction between humans and machines might enable exciting and efficient new approaches for exploring realities that are otherwise impossible to access. Narupa is a rigorous scientific simulation environment, with three key emphases: (1) the integration of real-time simulation methodologies into our interaction framework, enabling participants to manipulate and “feel” the dynamical responses of molecular systems; (2) the ability to make the VR experience one in which facilitates communication, by enabling multiple participants to cohabit the same virtual world together, either together in the same room or distributed remotely; and (3) active engagement with designers, artists, and human-computer interaction (HCI) experts, in order to create a framework which has scientific utility but is aesthetically compelling.5,7,43 This latter point is important given the level of immersion which can be achieved in VR environments. In an attempt to deal with this difficulty, this article makes reference to a number of videos (listed in Table I), each with a hyperlinked URL, which we encourage the reader to watch alongside the corresponding text because we have found that they go a long way toward overcoming the difficulties capturing aspects of multiperson iMD-VR that are difficult to communicate with text alone
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