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New analog quantum computers to solve previously unsolvable problems
Physicists have invented a new type of analog quantum computer that can tackle hard physics problems that the most powerful digital supercomputers cannot solve.
New research published in Nature Physics by collaborating scientists from Stanford University in the U.S. and University College Dublin (UCD) in Ireland has shown that a novel type of highly-specialized analog computer, whose circuits feature quantum components, can solve problems from the cutting edge of quantum physics that were previously beyond reach. When scaled up, such devices may be able to shed light on some of the most important unsolved problems in physics.
For example, scientists and engineers have long wanted to gain a better understanding of superconductivity, because existing superconducting materials—such as those used in MRI machines, high speed train and long-distance energy-efficient power networks—currently operate only at extremely low temperatures, limiting their wider use. The holy grail of materials science is to find materials that are superconducting at room temperature, which would revolutionize their use in a host of technologies.
Dr. Andrew Mitchell is Director of the UCD Centre for Quantum Engineering, Science, and Technology (C-QuEST), a theoretical physicist at UCD School of Physics and a co-author of the paper.
He said, “Certain problems are simply too complex for even the fastest digital classical computers to solve. The accurate simulation of complex quantum materials such as the high-temperature superconductors is a really important example—that kind of computation is far beyond current capabilities because of the exponential computing time and memory requirements needed to simulate the properties of realistic models.”
“However, the technological and engineering advances driving the digital revolution have brought with them the unprecedented ability to control matter at the nanoscale. This has enabled us to design specialized analog computers, called ‘Quantum Simulators,’ that solve specific models in quantum physics by leveraging the inherent quantum mechanical properties of its nanoscale components. While we have not yet been able to build an all-purpose programmable quantum computer with sufficient power to solve all of the open problems in physics, what we can now do is build bespoke analog devices with quantum components that can solve specific quantum physics problems.”
The architecture for these new quantum devices involves hybrid metal-semiconductor components incorporated into a nanoelectronic circuit, devised by researchers at Stanford, UCD and the Department of Energy’s SLAC National Accelerator Laboratory (located at Stanford). Stanford’s Experimental Nanoscience Group, led by Professor David Goldhaber-Gordon, built and operated the device, while the theory and modeling was done by Dr. Mitchell at UCD.
Prof Goldhaber-Gordon, who is a researcher with the Stanford Institute for Materials and Energy Sciences, said, “We’re always making mathematical models that we hope will capture the essence of phenomena we’re interested in, but even if we believe they’re correct, they’re often not solvable in a reasonable amount of time.”
With a Quantum Simulator, “we have these knobs to turn that no one’s ever had before,” Prof Goldhaber-Gordon said.
Why analog?
The essential idea of these analog devices, Goldhaber-Gordon said, is to build a kind of hardware analogy to the problem you want to solve, rather than writing some computer code for a programmable digital computer. For example, say that you wanted to predict the motions of the planets in the night sky and the timing of eclipses. You could do that by constructing a mechanical model of the solar system, where someone turns a crank, and rotating interlocking gears represent the motion of the moon and planets.
In fact, such a mechanism was discovered in an ancient shipwreck off the coast of a Greek island dating back more than 2000 years. This device can be seen as a very early analog computer.
Not to be sniffed at, analog machines were used even into the late 20th century for mathematical calculations that were too hard for the most advanced digital computers at the time.
But to solve quantum physics problems, the devices need to involve quantum components. The new Quantum Simulator architecture involves electronic circuits with nanoscale components whose properties are governed by the laws of quantum mechanics. Importantly, many such components can be fabricated, each one behaving essentially identically to the others.
This is crucial for analog simulation of quantum materials, where each of the electronic components in the circuit is a proxy for an atom being simulated, and behaves like an ‘artificial atom.” Just as different atoms of the same type in a material behave identically, so too must the different electronic components of the analog computer.
The new design therefore offers a unique pathway for scaling up the technology from individual units to large networks capable of simulating bulk quantum matter. Furthermore, the researchers showed that new microscopic quantum interactions can be engineered in such devices. The work is a step towards developing a new generation of scalable solid-state analog quantum computers.
Quantum firsts
To demonstrate the power of analog quantum computation using their new Quantum Simulator platform, the researchers first studied a simple circuit comprising two quantum components coupled together.
The device simulates a model of two atoms coupled together by a peculiar quantum interaction. By tuning electrical voltages, the researchers were able to produce a new state of matter in which electrons appear to have only a 1/3 fraction of their usual electrical charge—so-called “Z3 parafermions.” These elusive states have been proposed as a basis for future topological quantum computation, but never before created in the lab in an electronic device.
“By scaling up the Quantum Simulator from two to many nano-sized components, we hope that we can model much more complicated systems that current computers cannot deal with,” Dr. Mitchell said. “This could be the first step in finally unraveling some of the most puzzling mysteries of our quantum universe.”
More information:
Andrew Mitchell, Quantum simulation of an exotic quantum critical point in a two-site charge Kondo circuit, Nature Physics (2023). DOI: 10.1038/s41567-022-01905-4. www.nature.com/articles/s41567-022-01905-4
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How will Google solve its AI conundrum?
In the AI arms race that has just broken out in the tech industry, Google, where much of the latest technology was invented, should be well positioned to be one of the big winners.
There is just one problem: With politicians and regulators breathing down its neck, and a hugely profitable business model to defend, the internet search giant may be hesitant to wield many of the weapons at its disposal.
Microsoft threw down a direct challenge to the search giant this week when it sealed a multibillion dollar investment in AI research company OpenAI. The move comes less than two months after the release of OpenAI’s ChatGPT, a chatbot that answers queries with paragraphs of text or code, suggesting how generative AI might one day replace internet search.
With preferential rights to commercialise OpenAI’s technology, Microsoft executives have made no secret of their goal of using it to challenge Google, reawakening an old rivalry that has simmered since Google won the search wars a decade ago.
DeepMind, the London research company that Google bought in 2014, and Google Brain, an advanced research division at its Silicon Valley headquarters, have long given the search company one of the strongest footholds in AI.
More recently, Google has broken ground with different variations on the so-called generative AI that underpins ChatGPT, including AI models capable of telling jokes and solving mathematics problems.
One of its most advanced language models, known as PaLM, is a general purpose model that is three times larger than GPT, the AI model that underlies ChatGPT, based on the number of parameters on which the models are trained.
Google’s chatbot LaMDA, or Language Model for Dialogue Applications can converse with users in natural language, in a similar way to ChatGPT. The company’s engineering teams have been working for months to integrate it into a consumer product.
Despite the technical advances, most of the latest technology is still only the subject of research. Google’s critics say it is hemmed in by its hugely profitable search business, which discourages it from introducing generative AI into consumer products.
Giving direct answers to queries, rather than simply pointing users to suggested links, would result in fewer searches, said Sridhar Ramaswamy, a former top Google executive.
That has left Google facing “a classic innovator’s dilemma” — a reference to the book by Harvard Business School professor Clayton Christensen that sought to explain why industry leaders often fall prey to fast-moving upstarts. “If I was the one running a $150bn business, I’d be terrified of this thing,” Ramaswamy said.
“We have long been focused on developing and deploying AI to improve people’s lives. We believe that AI is foundational and transformative technology that is incredibly useful for individuals, businesses and communities,” Google said. However, the search giant would “need to consider the broader societal impacts these innovations can have”. Google added that it would announce “more experiences externally soon”.
While leading to fewer searches and lower revenue, the spread of AI could also cause a jump in Google’s costs.
Ramaswamy calculated that, based on OpenAI’s pricing, it would cost $120mn to use natural language processing to “read” all the web pages in a search index and then use this to generate more direct answers to the questions that people enter into a search engine. Analysts at Morgan Stanley, meanwhile, estimated that answering a search query using language processing costs around seven times as much as a standard internet search.
The same considerations could discourage Microsoft from a radical overhaul of its Bing search engine, which generated more than $11bn of revenue last year. But the software company has said it plans to use OpenAI’s technology throughout its products and services, potentially leading to new ways for users to be presented with relevant information while they are inside other applications, thus reducing the need to go to a search engine.
A number of former and current employees close to Google’s AI research teams say the biggest constraints on the company’s release of AI have been concern about potential harms and how they would affect Google’s reputation, as well as an underestimation of the competition.
“I think they were asleep at the wheel,” said one former Google AI scientist, who now runs an AI company. “Honestly, everyone under-appreciated how language models will disrupt search.”
These challenges are exacerbated by the political and regulatory concerns caused by Google’s growing power, as well as the greater public scrutiny of the industry leader in the adoption of new technologies.
According to one former Google executive, the company’s leaders grew worried more than a year ago that sudden advances in the capabilities of AI could lead to a wave of public concern about the implications of such a powerful technology in the hands of a company. Last year it appointed former McKinsey executive James Manyika as a new senior vice-president to advise on the broader social impacts of its new technology.
Generative AI, which is used in services like ChatGPT, is inherently prone to giving incorrect answers and could be used to produce misinformation, Manyika said. Speaking to the Financial Times only days before ChatGPT was released, he added: “That’s why we’re not rushing to put these things out in the way that perhaps people might have expected us to.”
However, the huge interest stirred up by ChatGPT has intensified the pressure on Google to match OpenAI more quickly. That has left it with the challenge of showing off its AI prowess and integrating it into its services without damaging its brand or provoking a political backlash.
“For Google it’s a real problem if they write a sentence with hate speech in it and it’s near the Google name,” said Ramaswamy, a co-founder of search start-up Neeva. Google is held to a higher standard than a start-up that could argue that its service was just an objective summary of content available on the internet, he added.
The search company has come under fire before over its handling of AI ethics. In 2020, when two prominent AI researchers left in contentious circumstances after objections to a research paper assessing the risks of language-related AI, a furore erupted around Google’s attitude to the ethics and safety of its AI technologies.
Such events have left it under greater public scrutiny than organisations like OpenAI or open-source alternatives like Stable Diffusion. The latter, which generates images from text descriptions, has had several safety issues, including with the generation of pornographic imagery. Its safety filter can be easily hacked, according to AI researchers, who say that the relevant lines of code can be deleted manually. Its parent company, Stability AI, did not respond to request for comment.
OpenAI’s technology has also been abused by users. In 2021, an online game called AI Dungeon licensed GPT, a text-generating tool, to create choose-your-own storylines based on individual user prompts. Within a few months, users were generating gameplay involving child sexual abuse, among other disturbing content. OpenAI eventually lent on the company to introduce better moderation systems.
OpenAI did not respond to a request for comment.
Had anything like this happened at Google, the backlash would have been far worse, one former Google AI researcher said. With the company now facing a serious threat from OpenAI, they added, it was unclear whether anyone at the company was ready to take on the responsibility and risks of releasing new AI products more quickly.
Microsoft, however, faces a similar dilemma over how to use the technology. It has sought to paint itself as more responsible in its use of AI than Google. OpenAI, meanwhile, has warned that ChatGPT is prone to inaccuracy, making it hard to embed the technology in its current form in a commercial service.
But as the most dramatic demonstration yet of an AI force that is sweeping through the tech world, OpenAI has given notice that even entrenched powers like Google could be at risk.
Leprosy: the ancient disease scientists can’t solve
If an effective rapid diagnostic test were available – one that was non-invasive and effective, many of these missing cases of leprosy and close contacts of patients could be diagosed, without the need for blanket prescriptions of rifampicin to potentially healthy individuals. The good news is that these diagnostic tests are currently under development – though they may not be available for some time.
To study the disease and its progression and develop diagnostic tests, scientists often need to inject M. leprae into armadillos, a technique that was first attempted in 1971. “The fact that we cannot culture [grow] this bacteria so easily in laboratory settings is another factor hindering the progress of developing these tests,” says Sunkara.
New horizons
Since 2000, Novartis Foundation has partnered with the WHO, supplying drugs free of cost globally for multi-drug therapy. In February 2022, they partnered with Fiocruz for a study that uses artificial intelligence (AI) to accelerate leprosy diagnosis. “I call it applying state-of-the-art technology to an ancient disease,” says Sunkara.
There are at least 20-30 other skin diseases that present as white patches on the skin, says Sunkara. Using the AI algorithm to analyse the way light reflects differently off the surface of each skin disease, it’s possible to identify leprosy cases, distinguishing them from other similar conditions with far more accuracy. Their study, published in Lancet Regional Health, pegged the accuracy at 90% – but with 1,229 skin images, the data set remains small at the moment. If it succeeds on a larger scale, it might one day be a useful tool to help speed up diagnosis and treatment.
Continuing stigma
While modern advances in the treatment and diagnosis of leprosy have been life-changing for many patients, there’s one problem that has never quite gone away: relentless discrimination.
“Leprosy remains a deep-rooted human rights issue,” says Alice Cruz, the UN Special Rapporteur on the elimination of discrimination against persons affected by leprosy, a role she’s held since November 2017. There are more than a hundred laws that discriminate against people with leprosy worldwide, creating a strong stigma that can act as a barrier for getting treatment, she says.
In some countries, leprosy is grounds for divorce. In India, this was the case until laws were amended in 2019. Many people affected by the disease still struggle to get jobs, and the disease can hinder their access to healthcare and education.
“Countries should do everything in their power to have discriminatory laws abolished and to put in place policy that can guarantee economic and social rights to people affected by leprosy,” says Cruz. “Going forward, we should ask ourselves the question: are our healthcare systems working to afford full accessibility to persons affected by leprosy? This is because leprosy is much more than a disease, it became a label that dehumanises people who are affected by it.”
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Japanese scientists solve mystery of why babies kick in the womb
[Source]
A team of scientists from the University of Tokyo has finally solved the ongoing conundrum of why babies kick in the womb.
Using motion capture technology and a musculoskeletal computer model, the team analyzed muscle communications in newborns’ and infants’ bodies. They then identified patterns of muscle interactions based on the infants’ random body movements.
The team discovered that the neurons within each muscle produce muscular contractions that activate “sensors.”
These random movements assist in the development of the sensorimotor system, which includes the sensory organs, nervous system and motor controls. The team’s model shows these movements help infants learn to control their bodies while still in the womb.
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The discovery could lead to new methods for detecting and treating neurodegenerative disorders, such as multiple sclerosis and cerebral palsy.
Project Assistant Professor Hoshinori Kanazawa from the Graduate School of Information Science and Technology explained that past research on sensorimotor development was mainly centered on “kinematic properties, muscle activities which cause movement in a joint or a part of the body.”
Recordings of the joint movements of 12 newborns less than 10 days old and 10 infants of less than 3 months contributed to these findings.
The scientists were surprised to see that infants’ movements strayed during spontaneous movement as they discovered sensorimotor interactions. The team named this phenomenon “sensorimotor wandering”.
It has been commonly assumed that sensorimotor system development generally depends on the occurrence of repeated sensorimotor interactions, meaning the more you do the same action the more likely you are to learn and remember it. However, our results implied that infants develop their own sensorimotor system based on explorational behavior or curiosity, so they are not just repeating the same action but a variety of actions. In addition to this, our findings provide a conceptual linkage between early spontaneous movements and spontaneous neuronal activity.
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During the study, newborns displayed more random movements compared to the predictable, patterned movements of the infant group.
Next, Kanazawa plans to research how “sensorimotor wandering” affects walking and reaching, as well as more complex behavioral developments and cognitive functions.
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Surreal Video of Stressed Cells Helps Biologists Solve a Decades-Old Mystery
The University of Pittsburgh and Carnegie Mellon University scientists solved a decades-old mystery regarding how cells control their volume.
Crowded rooms: How Carnegie Mellon University and the University of Pittsburgh researchers solved a cell mystery.
A surreal video of stressed cells under a microscope inspired a group of kidney physiologists and biologists from the University of Pittsburgh and Carnegie Mellon University to investigate a mystery: how do cells control their volume?
Their research, which was recently published in the journal Cell, shows how the researchers connected the dots on a conundrum that was initially presented three decades ago with a little bit of luck.
“We were doing live fluorescence imaging experiments that were unrelated to this study, and when we added a salt solution to the cells, the internal cytoplasmic material rapidly turned into a fluorescent lava lamp,” said Daniel Shiwarski, Ph.D., a postdoctoral research fellow at Carnegie Mellon University, describing how he and his wife, co-lead author Cary Boyd-Shiwarski, M.D., Ph.D., turned a fortuitous bit of experimentation into an unexpected finding.
In this video, WNK kinases (a type of enzyme) are fluorescent and diffuse throughout the cell. When exposed to a salt solution, they coalesce into larger droplets, looking like the bright green goo in a lava lamp. This process, called “phase separation,” is how the cell knows it needs to bring both water and ions back in, returning to its original state within seconds. Credit: Boyd-Shiwarski, et al., Cell (2022)
“I looked at her, and she asked me what was going on, like I was supposed to know,” he said. “And I said, ‘I have no idea, but I think it’s probably something important!’”
When cells are abruptly exposed to an outside stressor, such as elevated salt or sugar levels, their volume can decrease. Early in the 1990s, scientists believed that cells regain their volume by somehow keeping track of their protein concentration, or how “crowded” the cell was. However, they were unaware of how the cell sensed crowding.
From left to right: Dr. Daniel Shiwarski, Dr. Arohan Subramanya, and Dr. Cary Boyd-Shiwarski. Credit: Jake Carlson/UPMC
Then, in the early 2000s, With-No-Lysine Kinases, or “WNKs,” were identified as a new type of enzyme. For years, scientists theorized that WNK kinases reversed cell shrinkage, but how they did so was unexplained.
The new study solves both puzzles by revealing how WNK kinases activate the “switch” that restores cell volume to equilibrium through a process known as phase separation.
“The inside of a cell contains cytosol, and generally people think that this cytosol is diffuse, with all kinds of molecules floating around in a perfectly mixed solution,” said senior author Arohan R. Subramanya, M.D., associate professor in the Renal-Electrolyte Division at Pitt’s School of Medicine and staff physician at the VA Pittsburgh Healthcare System. “But there has been this paradigm shift in our thinking of how cytosol works. It’s really like an emulsion with a bunch of little, tiny protein clusters and droplets, and then when a stress such as overcrowding happens, they come together into big droplets that you can often see with a microscope.”
Those liquid-like droplets were the “lava lamp” that Shiwarski and Boyd-Shiwarski were seeing that fateful day when they experimented with adding a salt solution to the cells. They had fluorescently tagged the WNKs, which were diffused throughout the cytosol, causing the whole cell to glow. When salt was added, the WNKs came together, forming large neon-green globules that oozed about the cell like the goo in a lava lamp.
The team characterized what they were seeing as phase separation, which is when WNKs condense into droplets along with the molecules that activate the cell’s salt transporters. This step allows the cell to import both ions and water, returning the cell’s volume to its original state within seconds.
Phase separation is an emerging area of interest, but whether or not this process was an important part of cell function has been controversial.
“There’s a lot of people out there who don’t believe phase separation is physiologically relevant,” explained Boyd-Shiwarski, assistant professor in the Renal-Electrolyte Division at Pitt’s School of Medicine. “They think it’s something that happens in a test tube when you overexpress proteins or occurs as a pathological process but doesn’t really happen in normal healthy cells.”
But over the past six years, the team conducted multiple studies using stressors similar to the fluctuations that occur within the human body to show that phase separation of the WNKs is a functional response to crowding.
Cell volume recovery has implications for human health as well, Subramanya explained: “One of the reasons why we’re so excited is that the next step for us is to take this back into the kidney.”
Other WNKs activate salt transport within kidney tubule cells when potassium levels are low by forming specialized condensates through phase separation, called WNK bodies. Modern Western diets are often low in potassium, so while attempting to regulate cell volume, WNK bodies may contribute to salt-sensitive hypertension.
While the new discovery won’t have immediate clinical applications, the team is excited to take what they’ve learned and explore the connections between WNKs, phase separation, and human health. Eventually, their work may lead to a better understanding of how to prevent strokes, high blood pressure, and potassium balance disorders.
Reference: “WNK kinases sense molecular crowding and rescue cell volume via phase separation” by Cary R. Boyd-Shiwarski, Daniel J. Shiwarski, Shawn E. Griffiths, Rebecca T. Beacham, Logan Norrell, Daryl E. Morrison, Jun Wang, Jacob Mann, William Tennant, Eric N. Anderson, Jonathan Franks, Michael Calderon, Kelly A. Connolly, Muhammad Umar Cheema, Claire J. Weaver, Lubika J. Nkashama, Claire C. Weckerly, Katherine E. Querry, Udai Bhan Pandey, Christopher J. Donnelly, Dandan Sun, Aylin R. Rodan and Arohan R. Subramanya, 31 October 2022, Cell.
DOI: 10.1016/j.cell.2022.09.042
The study was funded by the National Institutes of Health and the U.S. Department of Veterans Affairs.
Astrophysicists Solve 40-Year-Old Black Hole Jet Mystery With NASA’s IXPE
This illustration shows NASA’s IXPE spacecraft, at right, observing blazar Markarian 501, at left. A blazar is a black hole surrounded by a disk of gas and dust with a bright jet of high-energy particles pointed toward Earth. The inset illustration shows high-energy particles in the jet (blue). Credit: NASA/Pablo Garcia
Blazars are some of the brightest objects in the cosmos. They are composed of a supermassive
“This is a 40-year-old mystery that we’ve solved,” said Yannis Liodakis, lead author of the study and astronomer at FINCA, the Finnish Centre for Astronomy with 
Artist’s representation of IXPE in Earth orbit. Credit: NASA
Launched on December 9, 2021, the Earth-orbiting IXPE satellite, a collaboration between
“This is a 40-year-old mystery that we’ve solved. We finally had all of the pieces of the puzzle, and the picture they made was clear.” — Yannis Liodakis
“The first X-ray polarization measurements of this class of sources allowed, for the first time, a direct comparison with the models developed from observing other frequencies of light, from radio to very high-energy gamma rays,” said Immacolata Donnarumma, the project scientist for IXPE at the Italian Space Agency. “IXPE will continue to provide new evidence as the current data is analyzed and additional data is acquired in the future.”
The new study used IXPE to point at Markarian 501, a blazar located aproximately 450 million light years away from Earth in the constellation Hercules. This active black hole system sits at the center of a large elliptical galaxy.
IXPE watched Markarian 501 for three days in early March of 2022, and then again two weeks later. During these observations, astronomers used other telescopes in space and on the ground to gather information about the blazar in a wide range of wavelengths of light including radio, optical, and X-ray. While other studies have looked at the polarization of lower-energy light from blazars in the past, this was the first time scientists could get this perspective on a blazar’s X-rays, which are emitted closer to the source of particle acceleration.
This illustration shows NASA’s IXPE spacecraft, at right, observing blazar Markarian 501, at left. A blazar is a black hole surrounded by a disk of gas and dust with a bright jet of high-energy particles pointed toward Earth. The inset illustration shows high-energy particles in the jet (blue). When the particles hit the shock wave, depicted as a white bar, the particles become energized and emit X-rays as they accelerate. Moving away from the shock, they emit lower-energy light: first visible, then infrared, and radio waves. Farther from the shock, the magnetic field lines are more chaotic, causing more turbulence in the particle stream. Credit: NASA/Pablo Garcia
“Adding X-ray polarization to our arsenal of radio, infrared, and optical polarization is a game changer,” said Alan Marscher, an astronomer at Boston University who leads the group studying giant black holes with IXPE.
Scientists found that X-ray light is more polarized than optical, which is more polarized than radio. But the direction of the polarized light was the same for all the wavelengths of light observed and was also aligned with the jet’s direction.
After comparing their information with theoretical models, the team of astronomers realized that the data most closely matched a scenario in which a shock wave accelerates the jet particles. A shock wave is generated when something moves faster than the speed of sound of the surrounding material, such as when a supersonic jet flies by in our Earth’s atmosphere.
The study was not designed to investigate the origins of shock waves, which are still mysterious. But scientists hypothesize that a disturbance in the flow of the jet causes a section of it to become supersonic. This could result from high-energy particle collisions within the jet, or from abrupt pressure changes at the jet boundary.
“As the shock wave crosses the region, the magnetic field gets stronger, and energy of particles gets higher,” Marscher said. “The energy comes from the motion energy of the material making the shock wave.”
As particles travel outward, they emit X-rays first because they are extremely energetic. Moving farther outward, through the turbulent region farther from the location of the shock, they start to lose energy, which causes them to emit less-energetic light like optical and then radio waves. This is analogous to how the flow of water becomes more turbulent after it encounters a waterfall – but here, magnetic fields create this turbulence.
Scientists will continue observing the Markarian 501 blazar to see if the polarization changes over time. IXPE will also investigate a broader collection of blazars during its two-year prime mission, exploring more longstanding mysteries about the universe. “It’s part of humanity’s progress toward understanding nature and all of its exoticness,” Marscher said.
Reference: “Polarized blazar X-rays imply particle acceleration in shocks” by Ioannis Liodakis, Alan P. Marscher, Iván Agudo, Andrei V. Berdyugin, Maria I. Bernardos, Giacomo Bonnoli, George A. Borman, Carolina Casadio, Vi´ctor Casanova, Elisabetta Cavazzuti, Nicole Rodriguez Cavero, Laura Di Gesu, Niccoló Di Lalla, Immacolata Donnarumma, Steven R. Ehlert, Manel Errando, Juan Escudero, Maya Garci´a-Comas, Beatriz Agi´s-González, César Husillos, Jenni Jormanainen, Svetlana G. Jorstad, Masato Kagitani, Evgenia N. Kopatskaya, Vadim Kravtsov, Henric Krawczynski, Elina Lindfors, Elena G. Larionova, Grzegorz M. Madejski, Frédéric Marin, Alessandro Marchini, Herman L. Marshall, Daria A. Morozova, Francesco Massaro, Joseph R. Masiero, Dimitri Mawet, Riccardo Middei, Maxwell A. Millar-Blanchaer, Ioannis Myserlis, Michela Negro, Kari Nilsson, Stephen L. O’Dell, Nicola Omodei, Luigi Pacciani, Alessandro Paggi, Georgia V. Panopoulou, Abel L. Peirson, Matteo Perri, Pierre-Olivier Petrucci, Juri Poutanen, Simonetta Puccetti, Roger W. Romani, Takeshi Sakanoi, Sergey S. Savchenko, Alfredo Sota, Fabrizio Tavecchio, Samaporn Tinyanont, Andrey A. Vasilyev, Zachary R. Weaver, Alexey V. Zhovtan, Lucio A. Antonelli, Matteo Bachetti, Luca Baldini, Wayne H. Baumgartner, Ronaldo Bellazzini, Stefano Bianchi, Stephen D. Bongiorno, Raffaella Bonino, Alessandro Brez, Niccoló Bucciantini, Fiamma Capitanio, Simone Castellano, Stefano Ciprini, Enrico Costa, Alessandra De Rosa, Ettore Del Monte, Alessandro Di Marco, Victor Doroshenko, Michal Dovciak, Teruaki Enoto, Yuri Evangelista, Sergio Fabiani, Riccardo Ferrazzoli, Javier A. Garcia, Shuichi Gunji, Kiyoshi Hayashida, Jeremy Heyl, Wataru Iwakiri, Vladimir Karas, Takao Kitaguchi, Jeffery J. Kolodziejczak, Fabio La Monaca, Luca Latronico, Simone Maldera, Alberto Manfreda, Andrea Marinucci, Giorgio Matt, Ikuyuki Mitsuishi, Tsunefumi Mizuno, Fabio Muleri, Stephen C.-Y. Ng, Chiara Oppedisano, Alessandro Papitto, George G. Pavlov, Melissa Pesce-Rollins, Maura Pilia, Andrea Possenti, Brian D. Ramsey, John Rankin, Ajay Ratheesh, Carmelo Sgró, Patrick Slane, Paolo Soffitta, Gloria Spandre, Toru Tamagawa, Roberto Taverna, Yuzuru Tawara, Allyn F. Tennant, Nicolas E. Thomas, Francesco Tombesi, Alessio Trois, Sergey Tsygankov, Roberto Turolla, Jacco Vink, Martin C. Weisskopf, Kinwah Wu, Fei Xie and Silvia Zane, 23 November 2022, Nature.
DOI: 10.1038/s41586-022-05338-0
Princeton Scientists Solve a Bacterial Mystery
The researchers were able to observe bacterial colonies’ clumpy growth in three dimensions. Credit: Neil Adelantar/Princeton University
Researchers found that bacteria colonies form in three dimensions in rough shapes similar to crystals.
Bacterial colonies often grow in streaks on Petri dishes in laboratories, but no one has understood how the colonies arrange themselves in more realistic three-dimensional (3-D) environments, such as tissues and gels in human bodies or soils and sediments in the environment, until now. This knowledge could be important for advancing environmental and medical research.
A Princeton University team has now developed a method for observing bacteria in 3-D environments. They discovered that when the bacteria grow, their colonies consistently form fascinating rough shapes that resemble a branching head of broccoli, far more complex than what is seen in a Petri dish.
“Ever since bacteria were discovered over 300 years ago, most lab research has studied them in test tubes or on Petri dishes,” said Sujit Datta, an assistant professor of chemical and biological engineering at Princeton and the study’s senior author. This was a result of practical limits rather than a lack of curiosity. “If you try to watch bacteria grow in tissues or in soils, those are opaque, and you can’t actually see what the colony is doing. That has really been the challenge.”
Researchers Sujit Datta, assistant professor of chemical and biological engineering, Alejandro Martinez-Calvo, a postdoctoral researcher, and Anna Hancock, a graduate student in chemical and biological engineering. Credit: David Kelly Crow for Princeton University
Datta’s research group discovered this behavior using a ground-breaking experimental setup that enables them to make previously unheard-of observations of bacterial colonies in their natural, three-dimensional state. Unexpectedly, the scientists discovered that the growth of the wild colonies consistently resembles other natural phenomena like the growth of crystals or the spread of frost on a windowpane.
“These kinds of rough, branchy shapes are ubiquitous in nature, but typically in the context of growing or agglomerating non-living systems,” said Datta. “What we found is that growing in 3-D, bacterial colonies exhibit a very similar process despite the fact that these are collectives of living organisms.”
This new explanation of how bacteria colonies develop in three dimensions was recently published in the journal Proceedings of the National Academy of Sciences. Datta and his colleagues hope that their discoveries will help with a wide range of bacterial growth research, from the creation of more effective antimicrobials to pharmaceutical, medical, and environmental research, as well as procedures that harness bacteria for industrial use.
Princeton researchers in the lab. Credit: David Kelly Crow for Princeton University
“At a fundamental level, we’re excited that this work reveals surprising connections between the development of form and function in biological systems and studies of inanimate growth processes in materials science and statistical physics. But also, we think that this new view of when and where cells are growing in 3D will be of interest to anyone interested in bacterial growth, such as in environmental, industrial, and biomedical applications,” Datta said.
For several years, Datta’s research team has been developing a system that allows them to analyze phenomena that are usually cloaked in opaque settings, such as fluid flowing through soils. The team uses specially designed hydrogels, which are water-absorbent polymers similar to those in jello and contact lenses, as matrices to support bacterial growth in 3-D. Unlike those common versions of hydrogels, Datta’s materials are made up of extremely tiny balls of hydrogel that are easily deformed by the bacteria, allow for the free passage of oxygen and nutrients that support bacterial growth, and are transparent to light.
“It’s like a ball pit where each ball is an individual hydrogel. They’re microscopic, so you can’t really see them,” Datta said. The research team calibrated the hydrogel’s makeup to mimic the structure of soil or tissue. The hydrogel is strong enough to support the growing bacterial colony without presenting enough resistance to constrain the growth.
“As the bacterial colonies grow in the hydrogel matrix, they can easily rearrange the balls around them so they are not trapped,” he said. “It’s like plunging your arm into the ball pit. If you drag it through, the balls rearrange themselves around your arm.”
The researchers performed experiments with four different species of bacteria (including one that helps to generate kombucha’s tart taste) to see how they grew in three dimensions.
“We changed cell types, nutrient conditions, hydrogel properties,” Datta said. The researchers saw the same, rough-edged growth patterns in each case. “We systematically changed all those parameters, but this appears to be a generic phenomenon.”
Datta said two factors seemed to cause the broccoli-shaped growth on a colony’s surface. First, bacteria with access to high levels of nutrients or oxygen will grow and reproduce faster than ones in a less abundant environment. Even the most uniform environments have some uneven density of nutrients, and these variations cause spots in the colony’s surface to surge ahead or fall behind. Repeated in three dimensions, this causes the bacteria colony to form bumps and nodules as some subgroups of bacteria grow more quickly than their neighbors.
Second, the researchers observed that in three-dimensional growth, only the bacteria close to the colony’s surface grew and divided. The bacteria crammed into the center of the colony seemed to lapse into a dormant state. Because the bacteria on the inside were not growing and dividing, the outer surface was not subjected to pressure that would cause it to expand evenly. Instead, its expansion is primarily driven by growth along the very edge of the colony. And the growth along the edge is subject to nutrient variations that eventually results in bumpy, uneven growth.
“If the growth was uniform, and there was no difference between the bacteria inside the colony and those on the periphery, it would be like filling a balloon, said Alejandro Martinez-Calvo, a postdoctoral researcher at Princeton and the paper’s first author. “The pressure from the inside would fill in any perturbations on the periphery.”
To explain why this pressure was not present, the researchers added a fluorescent tag to proteins that become active in cells when the bacteria grow. The fluorescent protein lights up when bacteria are active and remains dark when they are not. Observing the colonies, the researchers saw that bacteria on the colony’s edge were bright green, while the core remained dark.
“The colony essentially self-organizes into a core and a shell that behave in very different ways,” Datta said.
Datta said the theory is that the bacteria on the colony’s edges scoop up most of the nutrients and oxygen, leaving little for the inside bacteria.
“We think they are going dormant because they are starved,” Datta said, although he cautioned that further research was needed to explore this.
Datta said the experiments and mathematical models used by the researchers found that there was an upper limit to the bumps that formed on the colony surfaces. The bumpy surface is a result of random variations in the oxygen and nutrients in the environment, but the randomness tends to even out within certain limits.
“The roughness has an upper limit of how large it can grow – the floret size if we are comparing it to broccoli,” he said. “We were able to predict that from the math, and it seems to be an inevitable feature of large colonies growing in 3D.”
Because the bacterial growth tended to follow a similar pattern as crystal growth and other well-studied phenomena of inanimate materials, Datta said the researchers were able to adapt standard mathematical models to reflect the bacterial growth. He said future research will likely focus on better understanding the mechanisms behind the growth, the implications of rough growth shapes for colony functioning, and applying these lessons to other areas of interest.
“Ultimately, this work gives us more tools to understand, and eventually control, how bacteria grow in nature,” he said.
Reference: “Morphological instability and roughening of growing 3D bacterial colonies” by Alejandro Martínez-Calvo, Tapomoy Bhattacharjee, R. Kōnane Bay, Hao Nghi Luu, Anna M. Hancock, Ned S. Wingreen and Sujit S. Datta, 18 October 2022, Proceedings of the National Academy of Sciences.
DOI: 10.1073/pnas.2208019119
The study was funded by the National Science Foundation, the New Jersey Health Foundation, the National Institutes of Health, The Eric and Wendy Schmidt Transformative Technology Fund, the Pew Biomedical Scholars Fund, and the Human Frontier Science Program.
Meteorite that landed in Cotswolds may solve mystery of Earth’s water | Space
Water covers three-quarters of the Earth’s surface and was crucial for the emergence of life, but its origins have remained a subject of active debate among scientists.
Now, a 4.6bn-year-old rock that crashed on to a driveway in Gloucestershire last year has provided some of the most compelling evidence to date that water arrived on Earth from asteroids in the outer solar system.
The Winchcombe meteorite, one of the “most pristine” available for analysis, offered scientists “a tantalising glimpse back through time to the original composition of the solar system 4.6bn years-ago”, said Dr Ashley King, a research fellow at the Natural History Museum in London and author of a new paper on the space rock.
A prevailing theory is that the Earth was barren when it formed, as the inner region of the solar system was too hot for water to condense. The boundary of the region where ice could form in the early solar system is known as the frost line, and is located in the modern asteroid belt. Scientists think that water could have arrived to Earth later, raining down in icy meteoroids and large impacts.
However, there are competing theories, including that water was brought on comets – made mostly of ice and dust – or other similar bodies.
The latest analysis adds weight to the theory that asteroids made a leading contribution to water on Earth. Most of the Winchcombe meteorite was recovered just hours after its spectacular fireball lit up the skies over the UK in February 2021 during lockdown. One of the largest pieces was discovered on the driveway of the Wilcock family home, and a few smaller pieces were found in nearby gardens.
It is the first-ever carbonaceous chondrite meteorite – the oldest class of meteorites, which contain materials present during the formation of the solar system – to have been found in the UK. Crucially, it was collected within hours of being detected, before any rainfall, and analysed almost immediately, making it a rare uncontaminated specimen.
The incoming meteorite was also recorded by 16 dedicated meteor cameras, and numerous doorbell and dashcam videos, meaning that scientists could produce an accurate trajectory of where it came from in the solar system. By contrast, most of the 70,000 known meteorites have been found without their impact being recorded – in some cases millions of years after they landed. “They’re just random rocks that have come to us from space,” said King.
The analysis, published in the journal Science Advances, concludes that the meteorite originated from an asteroid body somewhere near Jupiter. The research also found that the ratio of hydrogen isotopes in the water closely resembled the composition of water on Earth.
“Meteorites like Winchcombe are a pretty good match [to] the water in the Earth’s oceans and suggests asteroids were the main source of water,” said King.
Extracts from the Winchcombe meteorite also contain extraterrestrial amino acids – prebiotic molecules that are fundamental building blocks for the origin of life.
As the composition of the Winchcombe meteorite is so pristinely preserved, the analysis suggests that similar asteroids have played a significant role in delivering the ingredients needed to kickstart oceans and life on early Earth.