Behind The Scenes Of Folding@Home: How Do You Fight A Virus With Distributed Computing?

A great big Thank You to everyone who answered the call to participate in Folding@Home, helping to understand proteins interactions of SARS-CoV-2 virus that causes COVID-19. Some members of the FAH research team hosted an AMA (Ask Me Anything) session on Reddit to provide us with behind-the-scenes details. Unsurprisingly, the top two topics are “Why isn’t my computer doing anything?” and “What does this actually accomplish?”

The first is easier to answer. Thanks to people spreading the word — like the amazing growth of Team Hackaday — there has been a huge infusion of new participants. We could see this happening on the leader boards, but in this AMA we have numbers direct from the source. Before this month there were roughly thirty thousand regular contributors. Since then, several hundred thousands more started pitching in. This has overwhelmed their server infrastructure and resulted in what’s been termed a friendly-fire DDoS attack.

The most succinct information was posted by a folding support forum moderator.

Here’s a summary of current Folding@Home situation :
* We know about the work unit shortage
* It’s happening because of an approximately 20x increase in demand
* We are working on it and hope to have a solution very soon.
* Keep your machines running, they will eventually fold on their own.
* Every time we double our server resources, the number of Donors trying to help goes up by a factor of 4, outstripping whatever we do.

Why don’t they just buy more servers?

The answer can be found on Folding@Home donation FAQ. Most of their research grants have restrictions on how that funding is spent. These restrictions typically exclude capital equipment and infrastructure spending, meaning researchers can’t “just” buy more servers. Fortunately they are optimistic this recent fame has also attracted attention from enough donors with the right resources to help. As of this writing, their backend infrastructure has grown though not yet caught up to the flood. They’re still working on it, hang tight!

Computing hardware aside, there are human limitations on both input and output sides of this distributed supercomputer. Folding@Home need field experts to put together work units to be sent out to our computers, and such expertise is also required to review and interpret our submitted results. The good news is that our contribution has sped up their iteration cycle tremendously. Results that used to take weeks or months now return in days, informing where the next set of work units should investigate.

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Coronavirus And Folding@Home; More On How Your Computer Helps Medical Research

On Wednesday morning we asked the Hackaday community to donate their extra computer cycles for Coronavirus research. On Thursday morning the number of people contributing to Team Hackaday had doubled, and on Friday it had doubled again. Thank you for putting those computers to work in pursuit of drug therapies for COVID-19.

I’m writing today for two reasons, we want to keep up this trend, and also answer some of the most common questions out there. Folding@Home (FAH) is an initiative that simulates proteins associated with several diseases, searching for indicators that will help medical researchers identify treatments. These are complex problems and your efforts right now are incredibly important to finding treatments faster. FAH loads the research pipeline, generating a data set that researchers can then follow in every step of the process, from identifying which chemical compounds may be effective and how to deliver them, to testing they hypothesis and moving toward human trials.

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Join Team Hackaday To Crunch COVID-19 Through Folding@Home

Donate your extra computer cycles to combat COVID-19. The Folding@Home project uses computers from all over the world connected through the Internet to simulate protein folding. The point is to generate the data necessary to discover treatments that can have an impact on how this virus affects humanity. The software models protein folding in a search for pharmaceutical treatments that will weaken the virus’ ability to attack the human immune system. Think of this like mining for bitcoin but instead we’re mining for a treatment to Coronavirus.

Initially developed at Standford University and released in the year 2000, this isn’t the first time Hackaday has advocated for Folding@Home. The “Team Hackaday” folding group was started by readers back in 2005 and that team number is still active, so let’s pile on and work our way up the rankings. At the time of writing, we’re ranked 267 in the world, can we get back up to number 30 like we were in 2008? To use the comparison to bitcoin once again, this is like a mining pool except what we end up with is a show of goodwill, something I think we can all use right about now.

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Open-Source Collaboration Tackles COVID-19 Testing

When you think of open source, your mind likely jumps to projects such as Linux, Firefox, and other now-mainstream software. The ideals of the movement are applicable to other areas, too, however – and a group have come together to pool resources to tackle the COVID-19 pandemic.

The group has formed around Just One Giant Lab, a non-profit organisation operating out of Paris, France. They aim to create an open platform for scientific collaboration on a broad range of issues facing humanity. The current project aims to create an open-source method for safely testing for COVID-19 infection, in an attempt to help better manage cases popping up around the world.

Thus far, the group has collected a variety of resources and begun to host conference calls discussing best practices for testing for the virus. There’s discussion of various PCR assays and virus sequences that are all useful in detecting the virus, along with data from WHO reports in China. The current state of play has been boiled down in the lab notebook the group has prepared, available online.

It’s inspiring to see open-source ideals put to work in new arenas outside computer software. Time will tell if this is the new way forward, but it certainly can’t hurt to have more minds tackling the problems of today and tomorrow.

A Safer, Self-Healing Polymer Battery

Lithium-ion batteries are notorious for spontaneously combusting, with seemingly so many ways that it can be triggered. While they are a compact and relatively affordable rechargeable battery for hobbyists, damage to the batteries can be dangerous and lead to fires.

Several engineers from the University of Illinois have developed a solid polymer-based electrolyte that is able to self-heal after damage, preventing explosions.The material can also be recycled without the use of high temperatures or harsh chemical catalysts. The results of the study were published in the Journal of the American Chemical Society.

As the batteries go through cycles of charge and discharge, they develop branch-like structures known as dendrites. These dendrites, composed of solid lithium, can cause electrical shorts and hotspots, growing large enough to puncture internal parts of the battery and causing explosive chemical reactions between the electrodes and electrolyte liquids. While engineers have been looking to replace liquid electrolytes in lithium-ion batteries with solid materials, many have been brittle and not highly conductive.

The high temperatures inside a battery melt most solid ion-conducting polymers, making them a less attractive option for non-liquid electrolytes. Further studies producing solid electrolytes from networks of cross-linked polymer strands delays the growth of dendrites but produces structures that are too complex to be recovered after damage. In response, the researchers at University of Illinois developed a similar network polymer electrolyte where the cross-link point undergoes exchange reactions and swaps out polymer strands. The polymers stiffen upon heating, minimizing the dendrite problem and more easily breaking down and resolidifying the electrolyte after damage.

Unlike conventional polymer electrolytes, the new polymer also shows properties of conductivity and stiffness increasing with heating. The material dissolves in water at room temperature, making it both energy-efficient and environmentally friendly as well.

Tracking Vaccination History With Invisible Tattoos

Nowadays, we still rely on medical records to tell when our last vaccinations were. For social workers in developing countries, it’s an incredibly difficult task especially if there isn’t a good standard in place for tracking vaccinations already.

A team at the Massachusetts Institute of Technology may be providing a solution – they’ve developed a safe ink to be embedded into the skin alongside the vaccine, only visible under a special light provided by a smartphone camera app. It’s an inconspicuous way to document the patient’s vaccination history directly into their skin and low-risk enough to massively simplify the process of maintaining medical records for vaccines.

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A New High-Performance Camera That Detects Single Photons

There may soon be breakthroughs in the search for dark matter. A new publication in Optics Express reveals a camera consisting of superconducting nanowires capable of detecting single photons, a useful feature for detecting light at the furthest ends of the infrared band. The high-performance camera, developed by the National Institute of Standards and Technology (NIST), boasts some of the best performing photon counters in the world in terms of speed, efficiency, and color detection. The detectors also have some of the lowest dark count rates of any photon sensor, resisting false signals from noise.

The size of the detectors comes out to 1.6mm on each side, packed with 1024 sensors for high resolution imagery and fabricated from silicon wafers cut into chips. The nanowires are made from tungsten and silicon alloy with leads made from superconducting niobium.

In order to prevent the sensors from overheating, a readout architecture was used based on a previous demonstration on a smaller camera with 64 sensors adding data from rows and columns. The research has been in collaboration with the National Aeronautics and Space Administration (NASA), which seeks to include the camera in the Origins Space Telescope project.

The eventual goal is to use the arrays to analyze chemical compositions of planets outside of our solar system. By observing the absorption spectra of light passing through an exoplanet’s atmosphere, information can be gathered on the elements in the atmosphere. Currently, large-area single-photon counting detector arrays don’t exist for measuring the mid- to far-infrared signatures, the spectrum range for elements that may indicate signs of life. While fabrication success is high, the efficiency of the detectors remains quite low, although there are plans to extend the current project into an even bigger camera with millions of sensors.

In addition to searching for chemical life on other planets, futureĀ  applications may include recording measurements to confirm the existence of dark matter.

[Thanks Qes for the tip!]