Scientists needed a lot of computational power to make the scale calculations they wanted.
"We used XSEDE to take these huge systems where there are many different parts interacting with each other, and we calculate everything about it at once, so when you start moving your system ahead with some likeness of time, you can get a clue "If you try to do the same kind of simulation we did on a laptop, it would take months, if not years, to figure out if I understand if a structure will be be stable. We can not use XSEDE for us, where you could use essentially 48 cores, 48 computing units at a time to make these calculations very parallel, and we would do so much more slowly. "
The TACC Stampede2 supercomputer contains 4,200 Intel Knights Landing and 1,736 Intel Skylake X computing nodes, each Skylake node having 48 cores, the main unit of the computer processor." The Stampede2 Supercomputer Skeleton Units were key to delivering the performance needed to calculate these electrostatic interactions that act between oppositely charged proteins in an effective way, "said Glaser." The presence of a Stampede2 supercomputer was just at the right time to be able to perform these simulations. "
Initially, the science gauge is testing its simulations on the Comet system in SDSC. "When we first discovered what model to use and whether this simplistic model would give us reasonable results, Comet was a great place to try these simulations," said Ramasubrama. a test of what we do. "
If we look at the larger scientific picture, scientists hope that this work will contribute to understanding why so many proteins in nature will oligomerize or merge to form more complex and interesting.
"We have shown that there is no need for a very specific, predetermined set of plans and interactions to form these structures," Simon said. "This is important because it means that maybe, and quite likely, we can pick up other groups of molecules that we want to do oligomerization and generate both positively charged and negatively charged variants, combine them and have specially ordered structures for them."
] Natural biomaterials like bones, feathers and shells can be healthy but light. "We think the assembly of supercharged proteins is an easier way to develop the kind of materials that have exciting synthetic properties without having to spend so much time or know exactly how they will get together in advance," Simon said. "We believe this will accelerate the ability to engineer synthetic materials and to detect and study these nanostructured protein materials."
The study "Super-Cutting Allows Organized Collection of Synthetic Biomolecules" was published in the journal in January 2019.
Scientists are forcing proteins to form synthetic structures with a method that mimics nature
Anna J. Simon et al., Supercharging allows organized assembling of synthetic biomolecules, Nature Chemistry (2019). DOI: 10.1038 / s41557-018-0196-3
Texas University in Austin
Supercomputers help to assemble the supercharged protein
drawn up on 30 March 2019
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