The Motivus RNA Epic is a project that seeks to contribute to a better understanding of the assembly process of the capsid or protein shell of an RNA virus with the genetic material inside, such as the Coronavirus. A better understanding of this process could be crucial, as it could provide clues for scientists to not only find ways to interrupt its formation and -potentially- control its spread, but also to eventually create an explanatory model that could be extrapolated to other viruses.
How do we intend to do this? By running millions of parallel simulations of the possible geometries of the RNA attached to the capsid in search of an optimal configuration. Is the material compact, coiled, knotted, or concentrated over a specific region? What is the role of flexibility? The possibilities of how these fragments can be attached to the capsid are endless!
Simulations that produce a lower energy configuration will be the most likely to be found in nature. To carry them out, however, is a monumental challenge, as it requires powerful computational power. This is where the Motivus distributed processing network plays a crucial role!
To give you an idea, let's say a mid-range laptop takes an hour to run a simulation. The same simulation takes one minute on a supercomputer. Now, if we had 60 laptops running for an hour, we could do the same work a supercomputer can do in an hour.
But if we had 2,000 computers running at the same time, then we could be way more efficient than a supercomputer, which can only run 60 in an hour. This is what is known as horizontal scaling of distributed computing, and those thousands of simulations running in parallel are just what we need for our RNA Epic to be successful.
Fortunately, our distributed computing infrastructure is capable of bringing together the processing power of millions of computers around the world.
What will I be processing, anyway?
The virus to be studied will be the satellite tobacco mosaic virus (STMV), a small model virus known to infect tobacco plants and affect their plantations. It is composed of an icosahedron-shaped capsid (20-sided polyhedron), whose genome is folded and compact inside.
Each personal computer or device will perform simulations of possible conformations of the genetic material contained inside, which is in contact with the capsid. Information from other experiments will be used to account for the anchor points and the basic structure of the virus genome.
Based on this, and in order to obtain a more complete view and study which geometries would be the most appropriate, the three-dimensional structure of specific fragments will be built using a computational RNA model developed by Simón Poblete, physicist, academic, and researcher at the UACh, who developed the RNA model for this project and who leads its scientific component. S. Poblete, S. Bottaro and G. Bussi, Nucleic Acids Res. 46 (4), 1674 (2018)
The RNA Epic will play out in stages
According to Poblete, the genetic material within the virus "is a single strand of RNA, which is not randomly coiled and compacted. In fact, the genome adopts a specific conformation that although can be flexible, contains certain regions folded on themselves and others firmly attached to the capsid". He adds: "Today we only partially know the structure of some regions, so we need an important computational power to reconstruct the structure in detail. We will start with a small and structurally significant fragment, to continue with increasingly large, flexible and complex domains".
How can I participate?
As we understand the importance of this project and its potential contribution to science, we have everything ready to make your participation as easy as possible: just go to motivus.cl and look for the purple and white icon on the bottom right side of our website, either on your cell phone or on your laptop. It looks like this:
This icon opens the Motivus Floating Tool.
What is this? The Floating Tool allows you to register on our website with your email address and start sharing your device’s computing power. Registering will allow you to keep track of the amount of processing power you share to the project, monitor your progress, and resume sharing if, for example, you decide to stop processing one day and restart the next day.
The Floating Tool offers different indicators so that you can keep track of your own performance: number of simulations or tasks the processing power you have shared has managed to perform (Contributions); time you have been processing (Elapsed Time), and compare the work of your device with others that are also sharing their computational power (Ranking).
It may take a few minutes for the Floating Tool to show the first indicators, but trust us: it eventually will. You just need to cultivate your patience a little bit.
All these indicators are useful and essential for us as well, since in subsequent stages of the RNA Epic we will reward users who share more processing power to our network.
Other stuff you may want to know
The Options tab allows you to choose how many processing threads to share in Motivus. The more threads, the more processing power you are sharing at once.
It is important to clarify that sharing your processing power does not present any danger to your phone or computer, and that while sharing you may still use your device normally. However, we recommend you choose a number of threads in the mid-range, so that your device operates according to its normal performance.
You can minimize the Floating Tool and do other things on your device at any time. However, if you close the tab or your browser, processing will stop. Remember that, if you are logged in, you can resume processing at any time and you will not have lost what you have already done.