Protein with glycans for BEN Credits to Lorenzo Casalino Zied Gaieb Rommie Amaro UC San Diego Kopie

Lorenzo Casalino, Zied Gaieb, Rommie Amaro, UC San Diego

Digital Superlatives: Supercomputers Against Corona

Digital research is becoming increasingly important. We talked to two scientists about what can be achieved with computers in research – and how they can already help us with the Corona pandemic today.

Protein with glycans for BEN Credits to Lorenzo Casalino Zied Gaieb Rommie Amaro UC San Diego Kopie

Lorenzo Casalino, Zied Gaieb, Rommie Amaro, UC San Diego

It is impossible to imagine science without computers anymore. And it is no longer just computer scientists who are sitting in front of the screens. This is particularly evident in the current research on the corona pandemic. Using computers, economists calculate optimal supply chains for protective masks and medicines, epidemiologists simulate future scenarios with and without corona measures in place and physicians and chemists determine what possible vaccines and medicines have to look like in order to be effective.

Conducting corona research without a face mask – in the world of supercomputers

One of these chemists is Rommie Amaro. She and her team in Texas use one of the largest and most powerful computers in the world – a so-called supercomputer. It is called Frontera and works just like the computers we know from our everyday life. What makes it a supercomputer is its size: Instead of fitting into a backpack like a laptop, Frontera occupies an entire building.

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Frontera - the Fastest Academic Supercomputer in the World. Video: Texas Advanced Computing Center (TACC) at The University of Texas at Austin.

Rommie Amaro and her colleagues are working on a project that is unique in the world with the aim of creating a digital model of the corona virus SARS-CoV-2 on the computer. Using this digital corona virus, researchers can carry out experiments in complete safety and without having to get geared up in full-body protective suits. And that’s not the only advantage: "We can watch and see how all the virus atoms move," explains Rommie Amaro. "I like to call our software a 'computer microscope'. With our computer you can see things that would remain invisible in normal experiments." In this way the scientists want to learn to understand how the virus behaves in our bodies.

We can watch and see how all the virus atoms move.

Rommie Amaro

Right now, the San Diego research team is recreating the virus on the computer. This is a huge task, because a total of 200 million atoms must be arranged to find their proper place. If everything goes according to plan, the project should be ready to go next month. Then the huge computer model of the virus will be ready for use. Rommie Amaro and her team will use supercomputers to calculate how the virus attacks human cells.

This process takes only a few milliseconds in real life, about as long as a photo flash. Since millions of atoms are in motion during this minuscule period of time, the supercomputer will need several weeks or even months to calculate the process. But it's worth the wait: As a result, the scientists will receive a kind of movie that shows exactly how the virus moves and where its weak points lie. This information is important for developing and advancing tailor-made drugs and vaccines.

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Rommie Amaro (UC San Diego); Dominik Hangleiter (Freie Universität Berlin)

Credit: Rommie Amaro; Dominik Hangleiter

With the progressive development of computationally powerful computers, simulations such as these will become much more important in the future than they already are today. But what about the computers themselves? Will they work quite differently in the future?

Mysterious quantum computers

For some years now, research is being conducted on a new form of computer, the quantum computers. They are made up of tiny particles that are so small that the physical rules of our everyday world no longer apply to them. Instead, they function according to the rules of quantum mechanics, which give them special properties. Developers are hoping that quantum computers will be able to work much faster than the most powerful supercomputers thanks to their special properties. But is that true?

Dominik Hangleiter is a physicist and conducts research on quantum computers at the Free University of Berlin. "For certain problems, quantum computers could be much better than classical computers," he explains. This was proven for the first time in an experiment last year. This represents a milestone in research – even if it involved a very specific theoretical computational problem for which there is no concrete application as yet.

One of the major challenges now, is to find meaningful practical applications for quantum computers explains Dominik Hangleiter. And there is still a lot of work to be done in building the computers. So far, only a few quantum computer prototypes exist worldwide. In the future, they are to become much larger and thus more powerful than they are today.

Even though many questions remain unanswered with regard to quantum computers, they offer exciting prospects for the future. This for example applies to computational tasks similar to that of Rommie Amaro, where the behaviour of small particles such as electrons or molecules is to be predicted. This is because these particles are so small that they themselves possess quantum properties. While Rommie Amaro's supercomputer first has to simulate these properties laboriously using many calculation steps, a quantum computer could understand them intuitively and come to a result very quickly.

For certain problems, quantum computers could be much better than classical computers.

Dominik Hangleiter

Which direction are we heading in?

In order to do the immense and complex calculations that Rommie Amaro conducts on a quantum computer, they first have to become much more powerful than they are today. Nevertheless, Dominik Hangleiter is optimistic that this could be with a little luck during the development phase – possible in a few years or decades.

And Rommie Amaro sees a bright future ahead whether with or without quantum computers: "When people think of scientists, they think of lab coats, lab goggles, glass flasks and Bunsen burners, but there's this whole world of computers and theory out there, and it's becoming more and more powerful. How this will turn out – whether we will find new vaccines in the future using intelligent supercomputers or whether we will learn programming again from scratch on quantum computers – is not yet certain. What is certain, on the other hand, is that more and more research will be carried out on our computers in the future.

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The Fraunhofer Society and IBM are bringing quantum computers to Germany for industry and research. In 2021, such an IBM Q System One quantum computer will be installed in a computer centre at IBM Germany near Stuttgart.

Credit: IBM

Network power

Computer simulations have become indispensable in research. Nevertheless, not all scientists have access to supercomputers with high computing power. But in order to be able to conduct research, some of them use decentralized networks. A network like this connects thousands of small computers to each other and together possess real computing power.

Cover photo: The proteins that decorate the corona virus like prongs could be a potential target for a COVID-19 drug. In order to understand how drugs can render the virus harmless, Rommie Amaro and her team are studying the movements of the virus on the supercomputer. Credit: Lorenzo Casalino, Zied Gaieb, Rommie Amaro, UC San Diego.


Dr. Kristin Werner