Developing hardware and software for real-time molecular simulation of binding free energies in virtual reality

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 project, the student will carry on these attempts to extend immersive technologies to the molecular sciences.

Specifically, the project will focus on developing a next-generation VR-data gloves, constructed using modern conductive fabrics, which detect when a participant closes one of two circuits, by making a pinching motion between (a) their thumb and index finger or (b) their thumb and forefinger. The absolute position of the hand is obtained from mounting an optical system on the back of the glove. Our preliminary results, obtained from a small set of user studies carried out in our own laboratory, suggest that participants find the molecular and atomic interaction afforded by this glove extremely intuitive, giving them a direct sense of "touching" virtual molecular simulations. To "touch" an atom and exert a force on it, the participant simply reaches out to the atom they wish to touch and brings together their thumb and forefinger as they would do if they were grasping a normal object. This project will develop the software and hardware required to apply the VR data glove to a number of different systems, including the binding of small molecules to the 5-HT2A serotonin receptors. In so doing, we will build open-source hardware and software frameworks tools which enable more efficient molecular simulation for calculating binding free energies in complex systems.

Modelling and simulation are playing an increasingly central role in all branches of science, both in Universities and in
industry, partly as a result of increasing computer power and partly through theoretical developments that provide more reliable models. Applications range from modelling chemical reactivity to simulation of hard, glassy, soft and biological materials; and modelling makes a decisive contribution to industry in areas such as drug design and delivery, modelling of reactivity and catalysis, and design of materials for opto-electronics and energy storage.

The UK (and all other leading economies) have recognised the need to invest heavily in High-Performance Computing to maintain economic competitiveness. We will deliver impact by training a generation of students equipped to develop new theoretical models; to provide software ready to leverage advantage from emerging computer architectures; and to pioneer the deployment of theory and modelling to new application domains in the chemical and allied sciences.

Our primary mechanisms for maximizing impact are:

(i) Through continual engagement, from the beginning, with industrial partners and academic colleagues to ensure clarity about their real training needs.
(ii) By ensuring that theory, as well as software and application, forms an integral part of training for all of our students: this is prioritised because the highest quality theoretical research in this area has led to game-changing impacts.
(iii) Through careful construction of a training model that emphasizes the importance of providing robust and sustainable software solutions for long-term application of modelling and simulation to real-world problems.
(iv) By an extensive programme of outreach activities, designed to ensure that the wider UK community derives direct and substantial benefit from our CDT, and that the mechanisms are in place to share best practice.