CCK-13 & MGMS: Molecular VR

Please join us for our next “Comp Chem Kitchen”, CCK-13, being jointly held with the Molecular Graphics and Modelling Society:

We are  very pleased to announce Dr David Glowacki from the University of Bristol will be talking and giving live demonstrations of his molecular virtual reality system. He will also be presented with his MGMS Silver Jubilee Award. David’s work has been featured in The New York Times: “It’s Time for a Chemistry Lesson. Put on Your Virtual Reality Goggles.”

If you’re curious and would like to try out molecular VR, please come along!

David R. Glowacki: Carrying out nano-molecular surgery in virtual reality

  • School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
  • Department of Computer Science, University of Bristol, BS8 1UB, UK
  • Pervasive Media Studio, Watershed, 1 Canons Rd, Bristol BS1 5TX, UK
  • [email protected]

Over the past several years, we have been developing a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, which combines rigorous cloud-mounted atomistic physics simulations with commodity VR hardware. [1] It allows users to visualize and manipulate, with surgical precision, the structures of complex molecular structures whose dynamics are simulated in real-time onenterprise cloud architectures. [2] It also enables multiple users to inhabit the same virtual environment, facilitating new classes of digital interaction between those users – e.g.,enabling them to pass rigorously simulated virtual objects between one another. This represents a qualitatively new kind of virtual experience beyond what is presently possible even within the large-scale immersive stereoscopic CAVE environments. We have recently completed a series of controlled user studies to evaluate the benefit that this VR framework provides in accelerating research tasks which require sophisticated 3d spatial reasoning (threading methane through a nanotube, changing the screw-sense of a helical molecule, and tying a protein knot). Our studies quantitatively demonstrate that the interactive VR environment allows users to complete sophisticated 3d spatial modelling tasks more quickly than they can using more conventional screen-based interfaces like mice or tablets, especially for tasks like protein knotting which are intrinsically 3d. We have now begun to extend this framework to accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug-protein binding, [3] synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where 3-dimensional dynamics matter, spanning scientific research, communication, and education.

  1. O Connor et al., Sampling molecular conformations and dynamics in a multi-user virtual reality framework”, 2018, Science Advances.
  2. https://vimeo.com/244670465.
  3. https://vimeo.com/296300796.

 

Free tickets are available, and refreshments will be provided, including beer.

Future Lightning Talks

We love to hear from you! Get in touch if you would like to give a 5 minute Lightning Talk at a future CCK on your latest research or give a quick demo of your latest programming project, or even to nominate someone you’d like to hear from (students, postdocs, professionals, PIs, Emeritus Professors). The talks usually resemble one of the following styles:

  • an overview of computational chemistry in your research;
  • a (live!) demonstration of some software that you are developing or using; or
  • a summary of a computational chemistry paper, method, programming language, or tool that you’ve seen recently.

 

We would like to thank the University of Oxford’s MPLS Network and Interdisciplinary Fund for making CCK possible.

 

About CCK

Comp Chem Kitchen is a regular forum and seminar series to hear about and discuss computational methods for tackling problems in chemistry, biochemistry and drug discovery. It focuses principally on cheminformatics, computational chemistry, and molecular modelling, and overlaps with neighboring areas such as materials properties and bioinformatics.

We’re keen to encourage people involved in coding and methods development (i.e. hackers, in the original untarnished sense of the word) to join us. Our hope is that we will share best practices, even code snippets and software tools, and avoid re-inventing wheels.

In addition to local researchers, we invite speakers from industry and non-profits from time to time, and occasionally organize software demos and tutorials.

If you’re interested in giving a talk, here are some possible topics:

  • Software development (e.g.: Python, C, C++, CUDA, shell, Matlab);
  • Optimizing force field parameters & EVB models;
  • Cheminformatics (e.g.: RDKit);
  • X-ray and NMR crystallography, including small molecule and macromolecular;
  • Protein & RNA modeling, including Molecular Dynamics;
  • Virtual screening and Docking;
  • Machine Learning;
  • Quantum Methods, including DFT.

Bring your laptops, by the way, if you have something you’d like to show!

 

Want to speak? Ideas for speakers?

* If you have ideas for speakers, or would like to give a talk, let us know. We also invite lightning talks of 5 minutes (or fewer) from attendees, so if you have some cool code you’ve been working on and would like to demo, bring your laptop, smartphone, tablet, (wearable?) and tell us all about it. *

Please pass this message on to friends, colleagues, and students who may be interested too!

The main CCK web site is: http://compchemkitchen.org/
Follow us on Twitter: @CompChemKitchen
See you soon! We’re looking forward to seeing and hearing about the diverse range of computational molecular science that you’re cooking up…

—Garrett, Richard, Phil and Rob

garrett.morri[email protected]
[email protected]
philip.biggin@bioch.ox.ac.uk
[email protected]