Tyler O'Neal, Staff Editor INDUSTRY

Cornell developers create a new tool that predicts where coronavirus binds to human proteins

A computational tool allows researchers to precisely predict locations on the surfaces of human and COVID-19 viral proteins that bind with each other, a breakthrough that will greatly benefit our understanding of the virus and the development of drugs that block binding sites.

The tool’s developers have provided a user-friendly interactive web server that displays all of the protein structures, such that virologists and clinicians without computational skills can make use of the protein models to see if existing drugs, or those in development, fit into the proper binding sites.

The study describes the tool and uses it to predict how the SARS-COV-2 diverged structurally from SARS-COV-1 (which caused a SARS outbreak in 2002-04); how genetic variation of proteins in human populations may contribute to virus-human binding and higher risk of infection; and which existing drugs show promise for binding to targets on surfaces of human proteins. new tool predicts where c9da3

“Our computational tool allows you to see with an unprecedented resolution where the viral proteins are binding on the human protein, and therefore, we can really understand what part of these proteins are key for these interactions,” said Haiyuan Yu, the study’s senior author, and a professor in the Department of Biological Statistics and Computational Biology and the Weill Institute for Cell and Molecular Biology. Shayne Wierbowski, a graduate student in Yu’s lab, is the paper’s first author.

A previous study by other scientists described interactions between COVID-19 and human proteins, to repurpose human drugs to block the virus from binding. But binding interfaces are small compared to the overall protein’s surface, and previous research has lacked the detailed resolution to understand exactly where drugs might block a binding site.

“The tool we developed to predict protein-to-protein interfaces is the most accurate,” Yu said, “and we can use it to make the most informed predictions for any interactions.” 

The pandemic spurred a surge of research worldwide to understand the structure of SARS-COV-2, with scientists using advanced imaging technologies to reveal proteins that make the virus infectious. As a result, Yu and colleagues were able to validate their computationally predicted structures against those described by others using imaging technologies.

The tool also allows researchers to predict how genetic variations in human proteins affect viral-protein interactions, as two people of similar health and age can have diverging responses to catching COVID-19, with some being asymptomatic and others showing dramatic negative reactions.

“Because of our structural models, we can predict how mutations to proteins in individuals potentially affect viral interactions,” Yu said. The results could one day shed light on whether some individuals may be at higher risk due to their genetics, which could prioritize them for monitoring, vaccines, and treatments.

Additionally, the tool will not only help clinicians develop drugs that precisely target human protein binding sites, but it can also help reduce toxic or negative effects that could result when drugs bind to the wrong sites.

Co-authors include Gary Whittaker, professor of virology, and Dr. Steven Lipkin, a clinical geneticist at Weill Cornell Medicine.

A novel quantum supercomputer design

Tyler O'Neal, Staff Editor INDUSTRY
An animation of the photonic quantum supercomputer was proposed by the researchers.On the left is the storage ring, which holds several counter-propagating photons.On the right is the scattering unit, which is used to manipulate the photonic qubits.The spheres at the top, called “Bloch spheres,” depict the mathematical state of the atom and one of the photons.Because the atom and the photon ar...
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Stanford researchers propose a simpler design for quantum supercomputers

Tyler O'Neal, Staff Editor INDUSTRY

A relatively simple quantum supercomputer design that uses a single atom to manipulate photons could be constructed with currently available components.

Today’s quantum supercomputers are complicated to build, difficult to scale up, and require temperatures colder than interstellar space to operate. These challenges have led researchers to explore the possibility of building quantum computers that work using photons — particles of light. Photons can easily carry information from one place to another, and photonic quantum supercomputers can operate at room temperature, so this approach is promising. However, although people have successfully created individual quantum “logic gates” for photons, it’s challenging to construct large numbers of gates and reliably connect them to perform complex calculations.  Stanford graduate student Ben Bartlett and Shanhui Fan, professor of electrical engineering, have proposed a simpler design for photonic quantum computers using readily available components. (Image credit: Courtesy Ben Bartlett / Rod Searcey)

Now, Stanford University researchers have proposed a simpler design for photonic quantum supercomputers using readily available components. Their proposed design uses a laser to manipulate a single atom that, in turn, can modify the state of the photons via a phenomenon called “quantum teleportation.” The atom can be reset and reused for many quantum gates, eliminating the need to build multiple distinct physical gates, vastly reducing the complexity of building a quantum supercomputer.

“Normally, if you wanted to build this type of quantum computer, you’d have to take potentially thousands of quantum emitters, make them all perfectly indistinguishable, and then integrate them into a giant photonic circuit,” said Ben Bartlett, a Ph.D. candidate in applied physics and lead scientist of the study. “Whereas with this design, we only need a handful of relatively simple components, and the size of the machine doesn’t increase with the size of the quantum program you want to run.”

This remarkably simple design requires only a few pieces of equipment: a fiber optic cable, a beam splitter, a pair of optical switches, and an optical cavity.

Fortunately, these components already exist and are even commercially available. They’re also continually being refined since they’re currently used in applications other than quantum computing. For example, telecommunications companies have been working to improve fiber optic cables and optical switches for years.

“What we are proposing here is building upon the effort and the investment that people have put in for improving these components,” said Shanhui Fan, the Joseph and Hon Mai Goodman Professor of the School of Engineering and senior scientist on the study. “They are not new components specifically for quantum computation.” 

A novel design 

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The scientists’ design consists of two main sections: a storage ring and a scattering unit. The storage ring, which functions similarly to memory in a regular computer, is a fiber-optic loop holding multiple photons that travel around the ring. Analogous to bits that store information in a classical computer, in this system, each photon represents a quantum bit, or “qubit.” The photon’s direction of travel around the storage ring determines the value of the qubit, which as a bit, can be 0 or 1. Additionally, because photons can simultaneously exist in two states at once, an individual photon can flow in both directions at once, which represents a value that is a combination of 0 and 1 at the same time.

The researchers can manipulate a photon by directing it from the storage ring into the scattering unit, where it travels to a cavity containing a single atom. The photon then interacts with the atom, causing the two to become “entangled,” a quantum phenomenon whereby two particles can influence one another even across great distances. Then, the photon returns to the storage ring, and a laser alters the state of the atom. Because the atom and the photon are entangled, manipulating the atom also influences the state of its paired photon.

“By measuring the state of the atom, you can teleport operations onto the photons,” Bartlett said. “So we only need the one controllable atomic qubit and we can use it as a proxy to indirectly manipulate all of the other photonic qubits.”

Because any quantum logic gate can be compiled into a sequence of operations performed on the atom, you can, in principle, run any quantum program of any size using only one controllable atomic qubit. To run a program, the code is translated into a sequence of operations that direct the photons into the scattering unit and manipulate the atomic qubit. Because you can control the way the atom and photons interact, the same device can run many different quantum programs.

“For many photonic quantum computers, the gates are physical structures that photons pass through, so if you want to change the program that’s running, it often involves physically reconfiguring the hardware,” Bartlett said. “Whereas in this case, you don’t need to change the hardware – you just need to give the machine a different set of instructions.”