During our discussions with Hethel innovation we found it can be difficult to convey the concepts of molecular biology in an accurate and engaging way. I was hard to convey to non-experts exactly what we’re doing in a way that can be easily understood. As a result we decided to develop the molecular VR experience, this in an innovative new approach to science communication and human practices. In this we have created an immersive and educational VR experience which places the viewer inside the bacterial cell and shows them first hand the molecular system we have been working on in our project.
The VR video takes through a model of the periplasmic space of Shewanella oneidensis MR-1, the demo consists of two parts. Firstly we teach you about what you’re seeing, running through the protein network with textboxes the user can read at their own pace. These contain information about the proteins functions, teaching them about each protein in the pathway. In the second part you follow the path of the electron in first person, diving through proteins and examining their appearance from up close and and getting an in depth look at the complex structures. Some of these models, such as MtrC and and small tetraheme cytochrome (STC) are the crystal structures, taken from the protein data bank. For the rest we used the Phyre 2 server to model an approximate protein structure. The experience ends after you have been shown in first person the path electrons take through the molecular nanowires, MtrCAB, across the periplasm and ending after hydrogen has been generated from the hydrogenase enzymes.
This virtual reality experience was developed after our initial human practices exercises exposed to us the mismatch of communication between molecular biologists and both renewable energy industries and the general public. We demonstrated this VR experience at multiple public events, UEA’s open day, the Norwich Science Festival and we will also be displaying it at the iGEM jamboree in Boston. At the events we have taken part in thus far we received overwhelmingly positive feedback from members of the public who found it to be a very engaging way of learning about science.
Since our project faculty at our university have followed up this idea of using VR for science communication and education. The university have purchased some VR headsets and plan on working with the computer scientist on our team, Justinas Druskis, on how at the university can take this idea forward and use it for human practices and education.
See below for a video showing a preview of our molecular VR experience.
All software we used is free of charge and can be downloaded from their official websites. The models in the demo are proteins taken from the Protein Data Bank. However, we couldn’t use the .pdb files directly in Unity 3D, therefore some format conversion has to be done.
- Unity 3D - game development platform that allows you to build games for VR with a single click of a button.
- Chimera - great and easy tool to view the protein files and export them to .wrml format
- Maya - to import it to Unity the .wrml format has to be then converted to either .fbx or .obj formats. After that you’re good to go!
- Blender - some objects were too heavy for the smartphones we were developing for so we used blender to lower the quality and remove any extra unnecessary details.
- iTween great plugin to animate objects that has saved us a lot of time.