Excited about the publication of a recent paper showing how our open source interactive molecular dynamics in virtual reality (iMD-VR) program Narupa can be used to investigate proteins which are relevant to the ongoing COVID pandemic. In the paper, we looked at the main protease (Mpro) of the SARS-CoV-2 virus, which is one focus of drug development efforts for COVID-19. The paper shows that iMD-VR offers a useful and effective tool for creating Mpro complexes in a physically rigorous and flexible way. Applying the iMD-VR approach to both an Mpro inhibitor and an oligopeptide substrate, we show that iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures were tested in MD simulations and found to be stable.
This Green Tara was painted as a lockdown meditation during spring/summer 2020.
Tārā is a buddha manifestation embodying the qualities of feminine energy within the universe. She offers warmth, compassion, and relief from suffering. Like a mother for her children, she engenders, nourishes, and smiles at the vitality of creation. In her Green form, Tārā offers protection from the variety of unfortunate circumstances encountered by beings trapped in cyclic existence. She is characterized by wind energy, enabling her to act quickly to ease the suffering of her children.Continue reading
We’ve just published a paper describing the use of interactive molecular dynamics in virtual reality (iMD-VR) for carrying out flexible protein-ligand docking, demonstrated through experiments carried out docking drug molecules into the binding pockets of trypsin, neuraminidase, and HIV-1 protease.
Our paper “Isness: Using Multi-Person VR to Design Peak Mystical-Type Experiences Comparable to Psychedelics” (doi:10.1145/3313831.3376649 & arxiv.2002.00940) has been recognized with a best paper award at the 2020 ACM CHI Conference on Human Factors in Computing! Less than 1% of all paper submissions receive this award, so it’s really exciting!
The paper describes our efforts adapting “Narupa” (our open source VR software platform) to elicit ‘mystical-type experiences’ comparable to those reported by participants in psychedelic psychotherapy sessions. It builds on a body of work by a number of researchers, including Prof. Roland Griffiths, a psychiatrist and neuroscientist at the Johns Hopkins Centre for Psychedelic & Consciousness Research, who has investigated both naturally occurring & drug-induced ‘mystical type experiences’, and also Dr. Robin Carhart-Harris at the Imperial College Centre for Psychedelic Research, who speculated in a March 2018 paper that psychedelics combined with VR might have therapeutic benefits in a neuro-psychopharmacology context.
We’re hard at work finalizing Narupa2, a massive rewrite of the Narupa VR framework which is pythonic on the back-end, and therefore should be much more customizable by our scientific colleagues. meanwhile enjoy this little a taster of some of the lovely new VR-enabled renderers that you can look forward to!
I’m super excited to announce that the European Research Commision (ERC) has agreed to fund a project which I pitched to them called NANOVR (NANOscale design using Virtual Reality) under their ‘Consolidator Grant’ scheme. The ERC’s generous financial support will commence in summer 2020, enabling us to continue our efforts developing the Narupa VR tools as open source community resources, and carry on exploring all sorts of interesting research applications across domains like biochemistry, materials engineering, and nanoscience!
The rise of machine learning (ML) has created an explosion in the potential strategies which may be used to learn from data in order to make scientific predictions. For physical scientists who wish to apply ML strategies to a particular domain, this has created a bewildering scenario, where it is difficult to make an a priori assessment of what strategy to adopt within a vast space of possibilities.
Really excited to see work by Dr. Simon Bennie featured on the cover of this month’s issue of the Journal of Chemical Education. The paper, which you can access here, outlines how Narupa, our open-source VR-enabled interactive simulation framework, was applied to develop a computational laboratory exercise enabling undergraduate students to better understand the dynamics and interactions that guide drug-protein binding.
In The Doors of Perception, Aldous Huxley recounted his experience taking mescaline under the guidance of the psychiatrist Humphrey Osmond. He wrote how it enabled him to glimpse the intrinsic energetic luminosity of matter: “the miracle, moment by moment, of naked existence… flowers shining with their own inner light and all but quivering under the pressure of the significance with which they were charged… [even] the folds of my grey flannel trousers were charged with Isness.”
“Isness” is our latest VR research project, designed to explore how the Narupa VR tools can be adapted to enable participants to experience the energetic essence of matter, and elicit perceptual responses comparable to psychedelic experiences. You can read more in an open-access paper we’ve just posted to the arXiv!