The spike caption of SARS-CoV2, the virus that causes COVID-19. RIKEN researchers have found that the D614G mutation restructures the Spike protein toward a state that is primed for infecting cells. © LAGUNA DESIGN/SCIENCE PHOTO LIBRARY
The spike caption of SARS-CoV2, the virus that causes COVID-19. RIKEN researchers have found that the D614G mutation restructures the Spike protein toward a state that is primed for infecting cells. © LAGUNA DESIGN/SCIENCE PHOTO LIBRARY

Japan's RIKEN Fugaku supercomputer reveals how an early mutation in the COVID-19 virus helped it spread so fast

Molecular supercomputer modeling suggests structural consequences of an early protein mutation that promoted the viral transmission

The rapid spread of COVID-19 may have been partly due to changes in the structure of the SARS-CoV-2 virus wrought by an early mutation in its genome, a detailed analysis by RIKEN researchers suggests. The finding could help inform the development of next-generation vaccines and antiviral drugs.

Alpha, Delta, Omicron, and other variants of concern have been making news throughout the COVID-19 pandemic. But the most significant mutation may have occurred in the early days of the pandemic, and it might have enabled the virus to spread so rapidly.

Yuji Sugita of the RIKEN Center for Computational Science (R-CCS) and Hisham Dokainish, who was at R-CCS at the time of the study, investigated the effect of mutations on the viral structure. They did this by simulating the atomic positions of molecules found in different forms of the virus’s important spike protein—a tool coronaviruses use to bind and enter human cells.

They found that the substitution of a single amino acid altered this protein’s shape, helping SARS-CoV-2 to adapt to human hosts. This finding demonstrates how even tiny mutations—swapping a single amino acid in this case—can greatly affect protein dynamics.

To understand why the mutation proved so advantageous to the virus, the pair ran detailed simulations of the protein’s structure and stability. Their analysis, done using the RIKEN Fugaku supercomputer, one of the fastest in the world, revealed how the mutation (known as D614G) breaks an ionic bond with a second subunit of the Spike protein. It also changes the shape of a nearby loop structure, which alters the orientation of the entire protein, locking it into a form that makes it easier for the virus to enter cells (Fig. 1).

“A single and local change in an interaction within the molecule caused by a single mutation could affect the global structure of the spike protein,” explains Sugita, who is additionally affiliated with the RIKEN Center for Biosystems Dynamics Research. The resulting mutant proved better at replicating and transmitting between human hosts, and the D614Glineage quickly outcompeted its ancestral lineages and spread across the globe. It remains a fixture of every dominant variant that has followed.

Sugita’s team is now performing similar investigations of adaptive viral mutations that arose later in the course of the pandemic, including those found in the Omicron variant.

“Information obtained from our molecular dynamics simulations should help increase the opportunities for us to find effective drugs and other medicines,” he says.

Researchers from Japan have utilized a vector optical vortex (left), a structured light with spatially variant polarization, for generating spatially structured spin states in a semiconductor quantum well (left). This is achieved by imprinting the vortex beam's structure on to the electron spins. Moreover, the combination of the excited spin texture and PSH fields leads to two helical spin waves with opposite phases.
Researchers from Japan have utilized a vector optical vortex (left), a structured light with spatially variant polarization, for generating spatially structured spin states in a semiconductor quantum well (left). This is achieved by imprinting the vortex beam's structure on to the electron spins. Moreover, the combination of the excited spin texture and PSH fields leads to two helical spin waves with opposite phases.

Japanese prof Ishihara creates structured spin states with spatially structured polarized light

Researchers generate a vector vortex light beam and imprint its spatial structure onto spins inside a semiconductor solid

Spin, a quantum property of particles, can be controlled using light waves to store information. This is conventionally achieved using a uniformly polarized light beam. Recently, researchers from Japan successfully generated a structured light beam with spatially variant polarization and transferred its structure to electron spins confined within a semiconductor solid. Additionally, they simultaneously generated two spin waves with inverted phases using this beam. Their results have important implications in optical communications and information storage.

Light is composed of electric and magnetic fields that oscillate perpendicular to each other. When these oscillations are restricted, say, along a plane, it results in polarized light. Polarized light is of great importance in optical communications and can similarly revolutionize how information is stored.

Current electronic devices store information in the form of electronic charges. However, spin-a uniquely quantum property of electrons offers an alternative. The spin can be controlled using polarized light to store information. A polarized light beam interacts with electron spins within a semiconductor to generate spin-polarized electrons, i.e., spins aligned along a specific direction. So far, only uniformly polarized light, i.e., light with a spatially uniform polarization, has been exploited to control electron spins. If, however, the polarization has an additional spatial structure (variation), it can produce spatially structured electron spins, opening up new ways to store information.

To this end, a group of researchers, led by Junior Associate Professor Jun Ishihara from and including Graduate Student Takachika Mori, Graduate Student (at the time of the research) Takuya Suzuki, and Professor Kensuke Miyajima from Tokyo University of Science (TUS), Japan, has now devised a method for generating such spatially structured electron spins using a structured light with spatially varying polarization profile. The study was done in collaboration with research groups from Chiba University, Tohoku University, and Tsukuba University in Japan.

"In this work, we generated a doughnut-shaped structured light-a vector optical vortex beam with an orbital angular momentum (OAM)-from a basic Gaussian beam using vortex half-wave plate and quarter-wave plate devices. We then used this beam to excite the electron spins confined within a gallium arsenide/aluminum gallium arsenide semiconductor quantum well. These spins, in turn, formed a helical spatial structure in a circle," explains Dr. Ishihara.

Interestingly, while the beam with an OAM number equal to one produced a helix with two spin periods-spin up and spin down around the circle, an OAM number of two resulted in a helix with four such alterations. These observations indicated that the spatial polarization structure of the optical vortex, determined by the OAM, was transferred to the electron spins inside the semiconductor. In addition, increasing the OAM number was suggested to enable higher information storage capacity, characterized by a higher spin repetition rate around the circle.

Moreover, the researchers utilized the effective magnetic field of the spin-orbit interaction acting on electron spins in the quantum well to simultaneously generate two spin waves with opposite phases in the vertical direction using a single beam. This suggested that various spin states with spatial structures could be produced by exploiting the effective magnetic fields (a characteristic of solids) alongside structured light beams.

With such exciting results, the researchers discuss the future prospects of their work. "The conversion of the spatial polarization structure of light into a spatial structure of spin along with the generation of new spin spatial structures in combination with effective magnetic fields in solids are expected to lead to elemental technologies for higher-order quantum media conversion and information capacity enhancement using spin textures," says Dr. Ishihara.

Intel and the Gordon and Betty Moore Foundation announced that company co-founder Gordon Moore died on March 24, 2023, at the age of 94. (Credit: Intel Corporation)
Intel and the Gordon and Betty Moore Foundation announced that company co-founder Gordon Moore died on March 24, 2023, at the age of 94. (Credit: Intel Corporation)

Gordon Moore, Intel co-founder, dies at 94

Moore, who set the course for the future of the semiconductor industry, devoted his later years to philanthropy. Intel and the Gordon and Betty Moore Foundation have announced that company co-founder Gordon Moore has passed away at the age of 94. The foundation reported he died peacefully on Friday, March 24, 2023, surrounded by family at his home in Hawaii.

Moore and his longtime colleague Robert Noyce founded Intel in July 1968. Moore initially served as executive vice president until 1975, when he became president. In 1979, Moore was named chairman of the board and chief executive officer, posts he held until 1987 when he gave up the CEO position and continued as chairman. In 1997, Moore became chairman emeritus, stepping down in 2006. Andy Grove (from left), Gordon Moore and Robert Noyce at Intel Corporation in a photo from the 1970s. Intel and the Gordon and Betty Moore Foundation announced that company co-founder Gordon Moore died on March 24, 2023, at the age of 94. (Credit: Intel Corporation)

During his lifetime, Moore also dedicated his focus and energy to philanthropy, particularly environmental conservation, science, and patient care improvements. Along with his wife of 72 years, he established the Gordon and Betty Moore Foundation, which has donated more than $5.1 billion to charitable causes since its founding in 2000.

“Those of us who have met and worked with Gordon will forever be inspired by his wisdom, humility, and generosity,” reflected foundation president Harvey Fineberg. “Though he never aspired to be a household name, Gordon’s vision and his life’s work enabled the phenomenal innovation and technological developments that shape our everyday lives. Yet those historic achievements are only part of his legacy. His and Betty’s generosity as philanthropists will shape the world for generations to come.”

Pat Gelsinger, Intel CEO, said, “Gordon Moore defined the technology industry through his insight and vision. He was instrumental in revealing the power of transistors and inspired technologists and entrepreneurs across the decades. We at Intel remain inspired by Moore’s Law and intend to pursue it until the periodic table is exhausted. Gordon’s vision lives on as our true north as we use the power of technology to improve the lives of every person on Earth. My career and much of my life took shape within the possibilities fueled by Gordon’s leadership at the helm of Intel, and I am humbled by the honor and responsibility to carry his legacy forward.”

Frank D. Yeary, chairman of Intel’s board of directors, said, “Gordon was a brilliant scientist and one of America’s leading entrepreneurs and business leaders. It is impossible to imagine the world we live in today, with computing so essential to our lives, without the contributions of Gordon Moore. He will always be an inspiration to our Intel family and his thinking is at the core of our innovation culture.”

Andy Bryant, former chairman of Intel’s board of directors, said, “I will remember Gordon as a brilliant scientist, a straight-talker, and an astute businessperson who sought to make the world better and always do the right thing. It was a privilege to know him, and I am grateful that his legacy lives on in the culture of the company he helped to create.”

Before establishing Intel, Moore and Noyce participated in the founding of Fairchild Semiconductor, where they played central roles in the first commercial production of diffused silicon transistors and later the world’s first commercially viable integrated circuits. The two had previously worked together under William Shockley, the co-inventor of the transistor and founder of Shockley Semiconductor, which was the first semiconductor company established in what would become Silicon Valley. Upon striking out on their own, Moore and Noyce hired future Intel CEO Andy Grove as the third employee, and the three of them built Intel into one of the world’s great companies. Together they became known as the “Intel Trinity,” and their legacy continues today.

In addition to Moore’s seminal role in founding two of the world’s pioneering technology companies, he famously forecast in 1965 that the number of transistors on an integrated circuit would double every year – a prediction that came to be known as Moore’s Law.

“All I was trying to do was get that message across, that by putting more and more stuff on a chip we were going to make all electronics cheaper,” Moore said in a 2008 interview.

With his 1965 prediction proven correct, in 1975 Moore revised his estimate to the doubling of transistors on an integrated circuit every two years for the next 10 years. Regardless, the idea of chip technology growing at an exponential rate, continually making electronics faster, smaller, and cheaper, became the driving force behind the semiconductor industry and paved the way for the ubiquitous use of chips in millions of everyday products.

In 2022, Gelsinger announced the renaming of the Ronler Acres campus in Oregon – where Intel teams develop future process technologies – to Gordon Moore Park at Ronler Acres. The RA4 building that’s home to much of Intel’s Technology Development Group was also renamed The Moore Center along with its café, The Gordon.

“I can think of no better way to honor Gordon and the profound impact he’s had on this company than by bestowing his name on this campus,” Gelsinger said at the event. “I hope we did you proud today, Gordon. And the world thanks you.”

Gordon Earle Moore was born in San Francisco on Jan. 3, 1929, to Walter Harold and Florence Almira “Mira” (Williamson) Moore. Moore was educated at San Jose State University, the University of California at Berkeley, and the California Institute of Technology, where he was awarded a Ph.D. in chemistry in 1954.

He started his research career at the Johns Hopkins Applied Physics Laboratory in Maryland. He returned to California in 1956 to join Shockley Semiconductor. In 1957, Moore co-founded Fairchild Semiconductor, a division of Fairchild Camera and Instrument, along with Robert Noyce and six other colleagues from Shockley Semiconductor. Eleven years later, Moore and Noyce co-founded Intel.

With Fairchild and Intel came financial success. Beginning with individual gifts, many of them anonymous, then forming the Moore Family Foundation, and eventually, in 2000, creating the Gordon and Betty Moore Foundation, Moore and his wife sought philanthropy to make the world a better place for future generations. His passion for impact and measurement were hallmarks of his philanthropic work and aspirations.

He received the National Medal of Technology from President George H.W. Bush in 1990, and the Presidential Medal of Freedom, the nation’s highest civilian honor, from President George W. Bush in 2002.

After retiring from Intel in 2006, Moore divided his time between California and Hawaii, serving as chairman of the board for the Gordon and Betty Moore Foundation until transitioning to chairman emeritus in 2018. Moore also served as a member of the board of directors of Conservation International and Gilead Sciences, Inc. He was a member of the National Academy of Engineering, a Fellow of the Royal Society of Engineers, and a Fellow of the Institute of Electrical and Electronics Engineers. He served as chairman of the board of trustees of the California Institute of Technology from 1995 until the beginning of 2001 and continued as a Life Trustee.

In 1950, Moore married Betty Irene Whitaker, who survives him. Moore is also survived by sons Kenneth and Steven and four grandchildren.