Week 2 [30.03-05.04.20] Folding@home

With the current situation in the world, probably many of you have already heard about the Folding@home project. I hadn't heard of it before, so I decided to take a closer look at it.

The idea of creating a huge computing resource from a large number of loosely coupled machines is not new. This has long been done, for example, with volunteer computing, where people execute applications on their personal computers on behalf of others. Volunteer-computing systems usually require you to install certain software, which then runs when your computer has no higher-priority tasks to do. That application then uses your spare computing cycles to fetch and process data from some central server and upload the results back to the same server when it’s done.

This strategy works well for many scientific problems, for which a central controller can farm out pieces of the desired computation to workers that operate independently and in parallel. If one fails to return a result within some reasonable period, no problem: The same task is simply handed out to some other volunteer worker.

Folding@Home is one of several real ways to fight the COVID-19 pandemic. It doesn't require a lot of commitment and gives visible results. So far, Folding@Home has had about 30 thousand users, which translated into about 100 petaflops of computing power. After the promotion of NVIDIA and PC Master Race, the number of volunteers increased to 400 thousand. And the total computing power to a record 470 petaflops. This is more than twice the capacity of the Summit supercomputer, which is also used for coronavirus research. Its peak power is about 200 petaflops and 148.6 petaflops according to the LINPACK benchmark. The difference is that the power of Folding@Home consists of 400 thousand independent devices.

What is protein folding and how is it related to disease?

Proteins are necklaces of amino acids, long chain molecules. They are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions that make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome – the blueprint for all of the proteins in biology – but how can we understand what these proteins do and how they work?However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (e.g. as enzymes or antibodies), they must take on a particular shape, also known as a “fold.” Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called “folding.”

What happens if proteins don’t fold correctly?

Diseases such as Alzheimer’s disease, Huntington’s disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding. When proteins misfold, they can clump together (“aggregate”). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer’s disease. Nowadays most of the computing resources are redirected to coronavirus-related calculations to understand how its proteins work and how to fight them.

Questions:
1. Have you heard of the Folding@home project, and shared your computing power?
2. Do you know other projects of this type that are currently working or have been used in the past? What are they for?
3. What do you think, what problems of the modern world can we try to solve in a similar way?

Links:
https://foldingathome.org/ 
https://arxiv.org/ftp/arxiv/papers/0901/0901.0866.pdf
https://www.cnet.com/news/your-laptop-can-help-fight-covid-19-with-foldingathome-project/