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Jun 19, 2020

Lab finds 125 naturally occurring compounds with potential against COVID-19

Posted by in categories: biotech/medical, supercomputing

The Baudry Lab at The University of Alabama in Huntsville (UAH) has identified 125 naturally occurring compounds that have a computational potential for efficacy against the COVID-19 virus from the first batch of 50,000 rapidly assessed by a supercomputer.

It’s the first time a supercomputer has been used to assess the treatment efficacy of naturally occurring compounds against the proteins made by COVID-19. Located in UAH’s Shelby Center for Science and Technology, the lab is searching for potential precursors to drugs that will help combat the global pandemic using the Hewlett Packard Enterprise (HPE) Cray Sentinel supercomputer.

The UAH team is led by molecular biophysicist Dr. Jerome Baudry (pronounced Bō-dre), the Mrs. Pei-Ling Chan Chair in the Department of Biological Sciences. Dr. Baudry is video blogging about his COVID-19 research journey using HPE’s Cray Sentinel system. His research is in collaboration with the National Center for Natural Products Research at the University of Mississippi School of Pharmacy and HPE.

Jun 13, 2020

Sugar coating locks and loads coronavirus for infection

Posted by in categories: biotech/medical, supercomputing

They say you can’t judge a book by its cover. But the human immune system does just that when it comes to finding and attacking harmful microbes such as the coronavirus. It relies on being able to recognize foreign intruders and generate antibodies to destroy them. Unfortunately, the coronavirus uses a sugary coating of molecules called glycans to camouflage itself as harmless from the defending antibodies.

Simulations on the National Science Foundation (NSF)-funded Frontera supercomputer at the Texas Advanced Computing Center (TACC) have revealed the atomic makeup of the coronavirus’s sugary shield. What’s more, simulation and modeling show that glycans also prime the coronavirus for infection by changing the shape of its spike . Scientists hope this basic research will add to the arsenal of knowledge needed to defeat the COVID-19 virus.

Sugar-like molecules called glycans coat each of the 65-odd spike proteins that adorn the coronavirus. Glycans account for about 40 percent of the spike protein by weight. The spike proteins are critical to cell infection because they lock onto the , giving the virus entry into the cell.

Jun 10, 2020

Machine learning predicts nanoparticle structure and dynamics

Posted by in categories: biotech/medical, chemistry, nanotechnology, robotics/AI, supercomputing

Researchers at the Nanoscience Center and at the Faculty of Information Technology at the University of Jyväskylä in Finland have demonstrated that new distance-based machine learning methods developed at the University of Jyväskylä are capable of predicting structures and atomic dynamics of nanoparticles reliably. The new methods are significantly faster than traditional simulation methods used for nanoparticle research and will facilitate more efficient explorations of particle-particle reactions and particles’ functionality in their environment. The study was published in a Special Issue devoted to machine learning in the Journal of Physical Chemistry on May 15, 2020.

The new methods were applied to ligand-stabilized metal , which have been long studied at the Nanoscience Center at the University of Jyväskylä. Last year, the researchers published a method that is able to successfully predict binding sites of the stabilizing ligand molecules on the nanoparticle surface. Now, a new tool was created that can reliably predict based on the atomic structure of the particle, without the need to use numerically heavy electronic structure computations. The tool facilitates Monte Carlo simulations of the atom dynamics of the particles at elevated temperatures.

Potential energy of a system is a fundamental quantity in computational nanoscience, since it allows for quantitative evaluations of system’s stability, rates of chemical reactions and strengths of interatomic bonds. Ligand-stabilized metal nanoparticles have many types of interatomic bonds of varying chemical strength, and traditionally the energy evaluations have been done by using the so-called density functional theory (DFT) that often results in numerically heavy computations requiring the use of supercomputers. This has precluded efficient simulations to understand nanoparticles’ functionalities, e.g., as catalysts, or interactions with biological objects such as proteins, viruses, or DNA. Machine learning methods, once trained to model the systems reliably, can speed up the simulations by several orders of magnitude.

Jun 8, 2020

Engineers put tens of thousands of artificial brain synapses on a single chip

Posted by in categories: robotics/AI, supercomputing

MIT engineers have designed a “brain-on-a-chip,” smaller than a piece of confetti, that is made from tens of thousands of artificial brain synapses known as memristors—silicon-based components that mimic the information-transmitting synapses in the human brain.

The researchers borrowed from principles of metallurgy to fabricate each memristor from alloys of silver and copper, along with silicon. When they ran the chip through several , the chip was able to “remember” stored images and reproduce them many times over, in versions that were crisper and cleaner compared with existing memristor designs made with unalloyed elements.

Their results, published today in the journal Nature Nanotechnology, demonstrate a promising new memristor design for neuromorphic devices—electronics that are based on a new type of circuit that processes information in a way that mimics the brain’s neural architecture. Such brain-inspired circuits could be built into small, , and would carry out complex computational tasks that only today’s supercomputers can handle.

Jun 8, 2020

MIT fit tens of thousands of artificial brain synapses on a single chip

Posted by in categories: internet, robotics/AI, supercomputing

Someday, we might be able to carry around tiny, AI brains that can function without supercomputers, the internet or the cloud. Researchers from MIT say their new “brain-on-a-chip” design gets us one step closer to that future. A group of engineers put tens of thousands of artificial brain synapses, known as memristors, on a single chip that’s smaller than a piece of confetti.

In a paper published in Nature Nanotechnology, the researchers explain how their brain-inspired chip was able to remember and recreate a gray-scale image of Captain America’s shield and reliably alter an image of MIT’s Killian Court by sharpening and blurring it. Those tests may seem minor, but the team believes the chip design could advance the development of small, portable AI devices and carry out complex computational tasks that today only supercomputers are capable of.

“So far, artificial synapse networks exist as software. We’re trying to build real neural network hardware for portable artificial intelligence systems,” says Jeehwan Kim, associate professor of mechanical engineering at MIT. “Imagine connecting a neuromorphic device to a camera on your car, and having it recognize lights and objects and make a decision immediately, without having to connect to the internet.”

Jun 6, 2020

Cracking open the proton

Posted by in categories: biotech/medical, supercomputing

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Physicists around the world are cracking open the proton, within the nucleus of the atom, to see what’s inside.

The proton is a fundamental building block of the atomic nucleus, and among other things it’s used as a medical probe in magnetic resonance imaging. It also has a rich inner structure made up of subatomic particles called quarks and gluons, which bind the quarks together.

Continue reading “Cracking open the proton” »

May 31, 2020

Microsoft Just Built a World-Class Supercomputer Exclusively for OpenAI

Posted by in categories: robotics/AI, supercomputing

Microsoft just built a huge supercomputer for AI research organization OpenAI. It’s a dream-machine for the company. What will they do with it?

May 23, 2020

Russian scientists expect achieving quantum supremacy in two years

Posted by in categories: particle physics, quantum physics, supercomputing

MOSCOW, Janaury 28. /TASS/. The quantum computer currently in development by Russian scientists will achieve the so-called “quantum supremacy,” or the ability to perform operations, practically impossible for the existing conventional supercomputers, in two years, says Sergei Kulik, the head of Quantum Technologies Center of the Moscow State University Faculty of Physics.

“There is a Perspective Research Fund project called ‘Priboy.’ According to the project’s goals, we must create a quantum simulator and achieve quantum supremacy in two years — i.e. show a calculation that is impossible for a classical computer,” Kulik said.

Currently, the laboratory has two physical platforms for building a quantum computer — the one based on neutral atoms and the other based on photon chips.

May 22, 2020

How Many Qubits Are Needed for Quantum Supremacy?

Posted by in categories: particle physics, quantum physics, supercomputing

Quantum computers theoretically can prove more powerful than any supercomputer, and now scientists calculate just what quantum computers need to attain such “quantum supremacy,” and whether or not Google achieved it with its claims last year.

Whereas classical computers switch transistors either on or off to symbolize data as ones or zeroes, quantum computers use quantum bits—qubits—that, because of the bizarre nature of quantum physics, can be in a state of superposition where they are both 1 and 0 simultaneously.

Superposition lets one qubit perform two calculations at once, and if two qubits are linked through a quantum effect known as entanglement, they can help perform 22 or four calculations simultaneously; three qubits, 23 or eight calculations; and so on. In principle, a quantum computer with 300 qubits could perform more calculations in an instant than there are atoms in the visible universe.

May 20, 2020

Microsoft OpenAI computer is world’s 5th most powerful

Posted by in categories: robotics/AI, supercomputing

Microsoft announced Tuesday that it has built the fifth most powerful computer on Earth.

Packed with 285,000 and 10,000 GPUs, the was built in collaboration with San Francisco-based artificial intelligence research organization OpenAI. Microsoft announced its partnership with OpenAI last year and contributed $1 billion to the project.

Continue reading “Microsoft OpenAI computer is world’s 5th most powerful” »

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