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Blueprints of self-assembly

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Blueprints of self-assembly


Many biological structures of impressive beauty and sophistication arise through processes of self-assembly. Indeed, the natural world is teeming with intricate and useful forms that come together from many constituent parts, taking advantage of the built-in features of molecules.

Scientists hope to gain a better understanding of how this process unfolds and how such bottom-up construction can be used to advance technologies in computer science, materials science, medical diagnostics and other areas.

In new research, Arizona State University Assistant Professor Petr Sulc and his colleagues have taken a step closer to replicating nature’s processes of self-assembly. Their study describes the synthetic construction of a tiny, self-assembled crystal known as a “pyrochlore,” which bears unique optical properties.

The key to creating the crystal is the development of a new simulation method that can predict and guide the self-assembly process, avoiding unwanted structures and ensuring the molecules come together in just the right arrangement.

The advance provides a steppingstone to the eventual construction of sophisticated, self-assembling devices at the nanoscale — roughly the size of a single virus.

The new methods were used to engineer the pyrochlore nanocrystal, a special type of lattice that could eventually function as an optical metamaterial, “a special type of material that only transmits certain wavelengths of light,” Sulc says. “Such materials can then be used to produce so-called optical computers and more sensitive detectors, for a range of applications.”

Sulc is a researcher in the Biodesign Center for Molecular Design and Biomimetics, the School of Molecular Sciences and the Center for Biological Physics at Arizona State University.

The research appears in the current issue of the journal Science.

From chaos to complexity

Imagine placing a disassembled watch into a box, which you then shake vigorously for several minutes. When you open the box, you find an assembled, fully functional watch inside. Intuitively, we know that such an event is nearly impossible, as watches, like all other devices we manufacture, must be assembled progressively, with each component placed in its specific location by a person or a robotic assembly line.

Biological systems, such as bacteria, living cells or viruses, can construct highly ingenious nanostructures and nanomachines — complexes of biomolecules, like the protective shell of a virus or bacterial flagella that function similarly to a ship’s propeller, helping bacteria move forward.

These and countless other natural forms, comparable in size to a few dozen nanometers — one nanometer is equal to one-billionth of a meter, or roughly the length your fingernail grows in one second — arise through self-assembly. Such structures are formed from individual building blocks (biomolecules, such as proteins) that move chaotically and randomly within the cell, constantly colliding with water and other molecules, like the watch components in the box you vigorously shake.

Despite the apparent chaos, evolution has found a way to bring order to the unruly process.

Molecules interact in specific ways that lead them to fit together in just the right manner, creating functional nanostructures inside or on the cell’s surface. These include various intricate complexes inside cells, such as machinary that can replicate entire genetic material. Less intricate examples, but quite complex nevertheless, include self-assembly of the tough outer shells of viruses, whose assembly process Sulc also previously studied with his colleague, Banu Ozkan from ASU’s Department of Physics.

Crafting with DNA

For several decades, the field of bionanotechnology has worked to craft tiny structures in the lab, replicating the natural assembly process seen in living organisms. The technique generally involves mixing molecular components in water, gradually cooling them and hoping that when the solution reaches room temperature, all the pieces will fit together correctly.

One of the most successful strategies, known as DNA bionanotechnology, uses artificially synthesized DNA as the basic building block. This molecule of life is not only capable of storing vast troves of genetic information — strands of DNA can also be designed in the lab to connect with each other in such a way that a clever 3D structure is formed.

The resulting nanostructures, known as DNA origami, have a range of promising applications, from diagnostics to therapy, where, for example, they are being tested as a new method of vaccine delivery.

A significant challenge lies in engineering molecule interactions to form only the specific, pre-designed nanostructures. In practice, unexpected structures often result due to the unpredictable nature of particle collisions and interactions. This phenomenon, known as a kinetic trap, is akin to hoping for an assembled watch after shaking a box of its parts, only to find a jumbled heap instead.

Maintaining order

To attempt to overcome kinetic traps and ensure the proper structure self-assembles from the DNA fragments, the researchers developed new statistical methods that can simulate the self-assembly process of nanostructures.

The challenges for achieving useful simulations of such enormously complex processes are formidable. During the assembly phase, the chaotic dance of molecules can last several minutes to hours before the target nanostructure is formed, but the most powerful simulations in the world can only simulate a few milliseconds at most.

“Therefore, we developed a whole new range of models that can simulate DNA nanostructures with different levels of precision,” Sulc says. “Instead of simulating individual atoms, as is common in protein simulations, for example, we represent 12,000 DNA bases as one complex particle.”

This approach allows researchers to pinpoint problematic kinetic traps by combining computer simulations with different degrees of accuracy. Using their optimization method, researchers can fine-tune the blizzard of molecular interactions, compelling the components to assemble correctly into the intended structure.

The computational framework established in this research will guide the creation of more complex materials and the development of nanodevices with intricate functions, with potential uses in both diagnostics and treatment.

The research work was carried out in collaboration with researchers from Sapienza University of Rome, Ca’ Foscari University of Venice and Columbia University in New York.



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Early dark energy could resolve cosmology’s two biggest puzzles

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A new study by MIT physicists proposes that a mysterious force known as early dark energy could solve two of the biggest puzzles in cosmology and fill in some major gaps in our understanding of how the early universe evolved.

One puzzle in question is the “Hubble tension,” which refers to a mismatch in measurements of how fast the universe is expanding. The other involves observations of numerous early, bright galaxies that existed at a time when the early universe should have been much less populated.

Now, the MIT team has found that both puzzles could be resolved if the early universe had one extra, fleeting ingredient: early dark energy. Dark energy is an unknown form of energy that physicists suspect is driving the expansion of the universe today. Early dark energy is a similar, hypothetical phenomenon that may have made only a brief appearance, influencing the expansion of the universe in its first moments before disappearing entirely.

Some physicists have suspected that early dark energy could be the key to solving the Hubble tension, as the mysterious force could accelerate the early expansion of the universe by an amount that would resolve the measurement mismatch.

The MIT researchers have now found that early dark energy could also explain the baffling number of bright galaxies that astronomers have observed in the early universe. In their new study, reported in the Monthly Notices of the Royal Astronomical Society, the team modeled the formation of galaxies in the universe’s first few hundred million years. When they incorporated a dark energy component only in that earliest sliver of time, they found the number of galaxies that arose from the primordial environment bloomed to fit astronomers’ observations.

You have these two looming open-ended puzzles,” says study co-author Rohan Naidu, a postdoc in MIT’s Kavli Institute for Astrophysics and Space Research. “We find that in fact, early dark energy is a very elegant and sparse solution to two of the most pressing problems in cosmology.”

The study’s co-authors include lead author and Kavli postdoc Xuejian (Jacob) Shen, and MIT professor of physics Mark Vogelsberger, along with Michael Boylan-Kolchin at the University of Texas at Austin, and Sandro Tacchella at the University of Cambridge.

Big city lights

Based on standard cosmological and galaxy formation models, the universe should have taken its time spinning up the first galaxies. It would have taken billions of years for primordial gas to coalesce into galaxies as large and bright as the Milky Way.

But in 2023, NASA’s James Webb Space Telescope (JWST) made a startling observation. With an ability to peer farther back in time than any observatory to date, the telescope uncovered a surprising number of bright galaxies as large as the modern Milky Way within the first 500 million years, when the universe was just 3 percent of its current age.

“The bright galaxies that JWST saw would be like seeing a clustering of lights around big cities, whereas theory predicts something like the light around more rural settings like Yellowstone National Park,” Shen says. “And we don’t expect that clustering of light so early on.”

For physicists, the observations imply that there is either something fundamentally wrong with the physics underlying the models or a missing ingredient in the early universe that scientists have not accounted for. The MIT team explored the possibility of the latter, and whether the missing ingredient might be early dark energy.

Physicists have proposed that early dark energy is a sort of antigravitational force that is turned on only at very early times. This force would counteract gravity’s inward pull and accelerate the early expansion of the universe, in a way that would resolve the mismatch in measurements. Early dark energy, therefore, is considered the most likely solution to the Hubble tension.

Galaxy skeleton

The MIT team explored whether early dark energy could also be the key to explaining the unexpected population of large, bright galaxies detected by JWST. In their new study, the physicists considered how early dark energy might affect the early structure of the universe that gave rise to the first galaxies. They focused on the formation of dark matter halos — regions of space where gravity happens to be stronger, and where matter begins to accumulate.

“We believe that dark matter halos are the invisible skeleton of the universe,” Shen explains. “Dark matter structures form first, and then galaxies form within these structures. So, we expect the number of bright galaxies should be proportional to the number of big dark matter halos.”

The team developed an empirical framework for early galaxy formation, which predicts the number, luminosity, and size of galaxies that should form in the early universe, given some measures of “cosmological parameters.” Cosmological parameters are the basic ingredients, or mathematical terms, that describe the evolution of the universe.

Physicists have determined that there are at least six main cosmological parameters, one of which is the Hubble constant — a term that describes the universe’s rate of expansion. Other parameters describe density fluctuations in the primordial soup, immediately after the Big Bang, from which dark matter halos eventually form.

The MIT team reasoned that if early dark energy affects the universe’s early expansion rate, in a way that resolves the Hubble tension, then it could affect the balance of the other cosmological parameters, in a way that might increase the number of bright galaxies that appear at early times. To test their theory, they incorporated a model of early dark energy (the same one that happens to resolve the Hubble tension) into an empirical galaxy formation framework to see how the earliest dark matter structures evolve and give rise to the first galaxies.

“What we show is, the skeletal structure of the early universe is altered in a subtle way where the amplitude of fluctuations goes up, and you get bigger halos, and brighter galaxies that are in place at earlier times, more so than in our more vanilla models,” Naidu says. “It means things were more abundant, and more clustered in the early universe.”

“A priori, I would not have expected the abundance of JWST’s early bright galaxies to have anything to do with early dark energy, but their observation that EDE pushes cosmological parameters in a direction that boosts the early-galaxy abundance is interesting,” says Marc Kamionkowski, professor of theoretical physics at Johns Hopkins University, who was not involved with the study. “I think more work will need to be done to establish a link between early galaxies and EDE, but regardless of how things turn out, it’s a clever — and hopefully ultimately fruitful — thing to try.”

We demonstrated the potential of early dark energy as a unified solution to the two major issues faced by cosmology. This might be an evidence for its existence if the observational findings of JWST get further consolidated,” Vogelsberger concludes. “In the future, we can incorporate this into large cosmological simulations to see what detailed predictions we get.”

This research was supported, in part, by NASA and the National Science Foundation.



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Plant-derived secondary organic aerosols can act as mediators of plant-plant interactions

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A new study published in Science reveals that plant-derived secondary organic aerosols (SOAs) can act as mediators of plant-plant interactions. This research was conducted through the cooperation of chemical ecologists, plant ecophysiologists and atmospheric physicists at the University of Eastern Finland.

It is well known that plants release volatile organic compounds (VOCs) into the atmosphere when damaged by herbivores. These VOCs play a crucial role in plant-plant interactions, whereby undamaged plants may detect warning signals from their damaged neighbours and prepare their defences. “Reactive plant VOCs undergo oxidative chemical reactions, resulting in the formation of secondary organic aerosols (SOAs). We wondered whether the ecological functions mediated by VOCs persist after they are oxidated to form SOAs,” said Dr. Hao Yu, formerly a PhD student at UEF, but now at the University of Bern.

The study showed that Scots pine seedlings, when damaged by large pine weevils, release VOCs that activate defences in nearby plants of the same species. Interestingly, the biological activity persisted after VOCs were oxidized to form SOAs. The results indicated that the elemental composition and quantity of SOAs likely determines their biological functions.

“A key novelty of the study is the finding that plants adopt subtly different defence strategies when receiving signals as VOCs or as SOAs, yet they exhibit similar degrees of resistance to herbivore feeding,” said Professor James Blande, head of the Environmental Ecology Research Group. This observation opens up the possibility that plants have sophisticated sensing systems that enable them to tailor their defences to information derived from different types of chemical cue.

“Considering the formation rate of SOAs from their precursor VOCs, their longer lifetime compared to VOCs, and the atmospheric air mass transport, we expect that the ecologically effective distance for interactions mediated by SOAs is longer than that for plant interactions mediated by VOCs,” said Professor Annele Virtanen, head of the Aerosol Physics Research Group. This could be interpreted as plants being able to detect cues representing close versus distant threats from herbivores.

The study is expected to open up a whole new complex research area to environmental ecologists and their collaborators, which could lead to new insights on the chemical cues structuring interactions between plants.



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Folded or cut, this lithium-sulfur battery keeps going

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Most rechargeable batteries that power portable devices, such as toys, handheld vacuums and e-bikes, use lithium-ion technology. But these batteries can have short lifetimes and may catch fire when damaged. To address stability and safety issues, researchers reporting in ACS Energy Letters have designed a lithium-sulfur (Li-S) battery that features an improved iron sulfide cathode. One prototype remains highly stable over 300 charge-discharge cycles, and another provides power even after being folded or cut.

Sulfur has been suggested as a material for lithium-ion batteries because of its low cost and potential to hold more energy than lithium-metal oxides and other materials used in traditional ion-based versions. To make Li-S batteries stable at high temperatures, researchers have previously proposed using a carbonate-based electrolyte to separate the two electrodes (an iron sulfide cathode and a lithium metal-containing anode). However, as the sulfide in the cathode dissolves into the electrolyte, it forms an impenetrable precipitate, causing the cell to quickly lose capacity. Liping Wang and colleagues wondered if they could add a layer between the cathode and electrolyte to reduce this corrosion without reducing functionality and rechargeability.

The team coated iron sulfide cathodes in different polymers and found in initial electrochemical performance tests that polyacrylic acid (PAA) performed best, retaining the electrode’s discharge capacity after 300 charge-discharge cycles. Next, the researchers incorporated a PAA-coated iron sulfide cathode into a prototype battery design, which also included a carbonate-based electrolyte, a lithium metal foil as an ion source, and a graphite-based anode. They produced and then tested both pouch cell and coin cell battery prototypes.

After more than 100 charge-discharge cycles, Wang and colleagues observed no substantial capacity decay in the pouch cell. Additional experiments showed that the pouch cell still worked after being folded and cut in half. The coin cell retained 72% of its capacity after 300 charge-discharge cycles. They next applied the polymer coating to cathodes made from other metals, creating lithium-molybdenum and lithium-vanadium batteries. These cells also had stable capacity over 300 charge-discharge cycles. Overall, the results indicate that coated cathodes could produce not only safer Li-S batteries with long lifespans, but also efficient batteries with other metal sulfides, according to Wang’s team.

The authors acknowledge funding from the National Natural Science Foundation of China; the Natural Science Foundation of Sichuan, China; and the Beijing National Laboratory for Condensed Matter Physics.



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