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DNA computer settles in thermodynamic equilibrium

A DNA computer that calculates as it settles into thermal equilibrium has been unveiled in Ireland. Drawing together several earlier lines of research, Damien Woods and colleagues at Maynooth University created a DNA-based system that ran calculations far more quickly than they expected, and which could be easily implemented and reused with a relatively simple setup.

Much like a living organism, a computer runs far from thermal equilibrium. It expends energy to maintain encoded bits of information, and to switch between them quickly and reliably as it executes algorithms.

However, in the 1970s physicist Charles Bennett showed that any computation can, in principle, be modified to have reversible dynamics. Such a computer could operate close to thermal equilibrium, slashing its demand for energy.

Taking Bennett’s ideas a step further, others suggested that the output of an algorithm could be delivered in a system’s equilibrium state itself. Starting from a given set of inputs, the computer would then naturally drift towards the solution as it settles into its most stable state.

Multiple challenges

“The idea presents multiple challenges that include finding a physical implementation that is computationally expressive and programmable, has easily prepared initial states and has a controllable energy landscape for rapid navigation to target outputs with high probability,” Woods explains.

One promising platform is the DNA computer, which was first introduced in the 1990s. It replaces silicon chips and electrical currents with DNA strands and biochemical reactions.

Until now, much of the work on DNA computers has involved out-of-equilibrium systems, which are either driven by molecular fuel, or require carefully prepared initial states and tightly controlled experimental conditions. But because DNA strands bind to each other according to simple, predictable rules, researchers could engineer the energy landscape directly. Incorrectly bound strands would then detach and be replaced by better-fitting ones, until the system settles into its most stable state.

To build such a system, Woods’ team was inspired by “DNA origami”. In a 2006, US-based Paul Rothemund showed how a long, single-stranded DNA scaffold could bind to a chosen set of shorter strands. Depending on the strands chosen, the scaffold could fold into a wide array of shapes as it settled into thermal equilibrium.

Tile calculations

Applying these ideas to DNA computing, Woods’ team designed a DNA scaffold carrying an engineered sequence of binding domains, which they mixed into a solution of shorter DNA strands. Dubbed tiles by the researchers, these strands represent the possible values at each step of a calculation. They were also inspired by the notion of tiles competing to bind to each other, a form of molecular computing first devised by US-based Erik Winfree in the 1990s.

After mixing, the tiles compete with each other to bind to the scaffold. At each binding domain, the “winning” tile is the one that binds most favourably to both the scaffold and its neighbouring tiles. In this way, the role of bits in a conventional computer is played by the specific strands that win each position.

“Eventually, the system settles down into its energetically preferred state which encodes the answer to the computation: a sequence of tiles each bound to the scaffold and to neighbouring tiles on its left and right,” Woods describes. “The competitive process of binding executes the computation.”

Altogether, the team demonstrated 10 different programs with their DNA computer, across more than 700 individual computations: including addition, multiplication, and division. Simple computations took as little as a minute to complete, though larger ones took considerably longer.

Just add water

“The same molecular computer can be reused to perform new calculations, running the same program up to 25 times on different inputs,” explains Maynooth’s Abeer Eshra. In one case, the team repeated an experiment after 15 months, simply adding water to a setup that had partially dried out, and still obtained correct answers.

“Our system uses just a handful of different kinds of molecules, never really following an organized process of steps, never making irreversible steps, and yet ending up with the right answer,” adds Maynooth’s Constantine Evans. “When thinking about computation at a molecular level, reliably making even those seemingly simple computations is very hard.”

The programs turned out to be surprisingly fast and easy to implement. To run a computation, the researchers simply mixed all the strands together, heated the solution, and let it cool as the system settled towards equilibrium, without any need for molecular fuel or specially prepared initial states. Remarkably, the team created what is arguably one of the most complex DNA computers built to date, paving the way for a whole host of new directions.

“Although we optimized some aspects of the design, there remain many ways it could be improved and generalized,” Woods says. “The work opens the door to new ways of thinking about computation in a wet environment, and about energy use in computation overall.”

The computer is described in Nature.

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Researchers shrink double-slit experiment to atomic scale

Shrinking Young’s double-slit experiment
Shrinking Young’s experiment (a) The classical double-slit experiment using light (slit spacing ~1 mm, propagation distance ~1 m). (b) Schematic of atomic-scale interference in which a pair of neighbouring silicon atomic columns act as a “double slit” for a focused electron probe (spacing 136 pm; crystal thickness ~10 nm; distance to detector ~10 cm). (Courtesy: Koudai Tabata/University of Tokyo)

For the first time, physicists in Japan have carried out an atomic-scale version of the double-slit experiment. Using an ultraprecise electron beam channelled along two adjacent columns of atoms in a crystal of silicon, Naoya Shibata and colleagues at the University of Tokyo observed clear interference fringes in electrons scattered by the atoms: fringes that persisted even at high temperature, thanks to correlations in the atoms’ thermal vibrations.

The double-slit experiment is perhaps the most iconic demonstration in quantum mechanics: showing how a single particle’s wavefunction interferes with itself as it passes through two slits at once, with a tangible impact on where the particle is ultimately observed.

In practical research, this effect is now routinely harnessed in electron, neutron and atom interferometers. By observing the interference fringes that it creates, researchers can extract valuable information about both the quantum matter wave and whatever object is doing the diffracting.

Recently, physicists have attempted to push double-slit interferometry all the way down to the atomic scale, replacing conventional slits with crystal lattices. When a moving electron encounters an atom in a crystal, it scatters across a range of angles – producing an outgoing spherical wave that’s mathematically identical to the diffraction pattern from a classical slit.

Since atoms in a crystal sit at such well-defined separations, any neighbouring pair of them could, in principle, act as a double-slit interferometer. In reality, however, the many repeated unit cells in a crystal mean the resulting interference fringes are washed out, making it difficult to isolate the signal from a single atomic pair.

To address this challenge, Shibata’s team used the ultraprecise probe of a 4D scanning transmission electron microscope: an instrument designed to capture electron diffraction patterns with a pixellated detector. Fired into a pure silicon crystal at just the right orientation, the microscope’s precision let the researchers target two adjacent columns of aligned silicon atoms, separated by just 136 pm. As a result, the electron wave overlapped both columns, and no others.

“Our key idea was to use these two atomic columns as the two slits,” describes team member Takehito Seki. “By channelling the probe along both columns at once, we turned them into two coherent scattering sources – effectively making the crystal itself into an atomic-scale double-slit interferometer.”

At this scale, Shibata and Seki’s team created electron interference fringes some seven orders of magnitude smaller than in Thomas Young’s original double-slit experiment with light, first carried out in 1801.

Just as in a larger-scale experiment, these patterns encoded information about the crystal and the electron beam. But at this scale, the researchers could also detect the signature of individual phonon modes in the columns. Rather than destroying coherence as uncorrelated atomic motion would in a classical picture, these correlated vibrations between the two atomic columns kept them moving in sync, preserving the interference.

“In a which-path picture, relative motion of the two atomic columns makes the two electron pathways more distinguishable and reduces the interference, whereas correlated in-phase motion preserves coherence,” Shibata explains. As a result, distinct interference fringes remained visible across temperatures ranging from 300 to 900 K.

The team’s results already point to how an atomic-scale double-slit experiment could offer new ways to measure phonon correlations directly between single pairs of atoms. But as Shibata explains, the possible applications could stretch much further.

“It also opens a route to probing local lattice dynamics at the scale of individual atomic bonds, including at interfaces and defects, where local lattice dynamics can strongly influence thermal transport,” he says. “In the long run, such atomic-scale insight could help inform better thermal management strategies for future chip technologies.”

The study is published in Nature.

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Quantum voting system aims to keep ballots secret

A voting system with a high level of security intrinsically guaranteed by quantum mechanics has been demonstrated by two independent teams – one led by Federico Centrone at the Barcelona Institute of Technology and the other led by Rob Thew at the University of Geneva.

Their systems employ a quantum protocol that was first proposed by Centrone and colleagues in 2022 and uses a system of entangled qubits to ensure every voter has complete anonymity.

A conventional voting system – paper or electronic – could be hacked or corrupted at the counting stage, resulting in a rigged outcome or lack of anonymity. In 2007, Anne Broadbent and Alain Tapp at the University of Montreal proposed a possible solution: an e-voting protocol in which an election is broken into as many rounds as there are voters.

Before anyone casts a vote, Broadbent and Tapp’s system secretly assigns each participant to be the “real” voter in exactly one designated round. In that round, the chosen voter picks a value (either 0 or 1) representing their actual choice.

Secret ballot

In every other round, the system automatically submits a pre-assigned value on the voter’s behalf, engineered so the round’s total has a fixed parity – either always odd or always even. The real voter’s free choice then either flips this total to the opposite parity or leaves it unchanged, and the final odd or even result is recorded. Once every round is complete, each voter will have had their real say – but from the outside, the identity of the real voter in any given round is completely hidden.

Although this scheme is watertight in principle, there is still no guarantee that the e-voting system itself can be fully trusted. In 2022, a team led by Centrone proposed how this loophole could be closed by harnessing entanglement between quantum bits, or qubits.

In the quantum protocol, each voter is assigned a single qubit, prepared as part of one joint entangled state spanning all voters together. When measured, each qubit is randomly either a 0 or 1, But, because of the type of entanglement between the qubits, the total number of 1s across all voters is guaranteed to have the expected parity. Since not even the e-voting system itself can know the outcome of any individual measurement in advance, the protocol removes the need to trust whoever is distributing the values.

Easily adapted

Thew’s team realised that it could create this protocol in the lab. “We had just finished another experiment concerning distributed polarization entanglement and realized we could ‘easily’ adapt our setup to produce the entangled states required for the voting protocol,” says Geneva’s Joey Marcellino.

Both teams used spontaneous parametric down-conversion (SPDC) to create the entangled qubits, which were photons. Here, a laser is fired into a nonlinear crystal, splitting single photons into pairs of lower-energy photons that are entangled in terms of their polarization states.

SPDC is then repeated using the newly-entangled photons, chaining pairs together until reaching the same number of entangled photons as there are voters – albeit a small number in these demonstrations. The result is one single, large entangled state. Each individual photon then passes through a 50/50 beam splitter, is coupled into an optical fibre, and sent to a detector, where its state is measured.

Fidelity and success

In their first experimental tests of the technique, Centrone and colleagues were able to create the entanglement required for the voting protocol at success rate of about 96%. Meanwhile, Thew’s team achieved an 87% success rate.

Commenting on his colleagues’ result, Marcellino says, “This suffices as a proof-of-principle for the protocol and our modified approach, although obviously we would want to improve these numbers significantly for real-world applications”.

For now, the result demonstrates that e-voting systems with quantum-guaranteed security are achievable, using existing technologies including single-photon sources, detectors, and entanglement generation schemes.

“Moreover, in the end the protocol is just a way to anonymously distribute a bit with perfect security,” Marcellino adds. “While this is obviously useful for voting, it could also work as an anonymous message board, or to enable anonymous distributed computation.”

The research is described in Physical Review Letters: Thew and colleagues; Centrone and colleagues.

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Topology affects the crumpling of growing elastic sheets

Photo of a structure with topologically-induced dimples
More dimples A series of hollow objects made from elastic sheets. The size of the objects increases in the directions indicated by the arrows. The number of buckles in the object is seen to increase as its shape changes. (Courtesy: Yafei Zhang)

A new mechanism governing the geometric shapes of growing elastic sheets has been identified by a trio of physicists in Israel. Through a combination of simulations and experiments, Eran Sharon and colleagues at the Hebrew University of Jerusalem showed that the dimpled patterns that form in a growing elastic object have topological origins.

This mechanism is unrelated to geometric incompatibilities, which are known to dimple natural materials. The discovery could lead to a deeper understanding of how complex shapes emerge in the natural world – and to the development of new artificial materials.

Thin sheets are ubiquitous in nature: examples include leaves, petals, and the cellular linings of organs and blood vessels. The complex makeup of natural sheets means that local regions within them have preferred mechanical rest states that are incompatible with those of other regions. As a result, there is no way to arrange the sheet so that every part is simultaneously stress free – leading to effects like wrinkling, bending, and buckling.

Called geometric incompatibility, this phenomenon is responsible for numerous geometric forms in the natural world, enabling growing tissues to shape themselves without any external influence. For some time, researchers have attempted to mimic these natural mechanisms in synthetic materials.

Richness of shapes

“Looking at natural growth processes, as in plants growth, or embryo development, we see amazing richness of shapes and shape development that currently cannot be achieved with conventional fabrication methods,” says Sharon.

Sharon’s group has already shown that many patterns in nature can be understood in terms of the Gauss and Mainardi-Codazzi-Peterson incompatibilities – which were developed in the 19th century. Together with team member Michael Moshe, whose group explores the interplay between mechanics and geometry in soft materials, their work led to discoveries including the mechanical origins of shape selection in rose petals.

Now, Moshe and Sharon have teamed-up with Yafei Zhang to identify a phenomenon that cannot be explained by those mechanical instabilities. In their experiment, they started with a uniform elastic sheet formed into a hollow sphere, with circular holes at each pole. When they added wedges of material into the sheet to mimic growth, it initially behaved like a smooth, growing sphere – but only up to a certain point.

Missing mechanism

“The growing sheet satisfies the established local compatibility conditions, and is thus expected to show smooth ‘boring’ shape,” Moshe explains. “Yet it unexpectedly, develops a crumpled appearance, suggesting that an important shaping mechanism was missing from the existing framework.”

Important clues came when the team cut into the crumpled sphere along a meridian, from pole to pole. Instantly, the crumpling disappeared, and the sphere relaxed back to its original smooth shape. This effect also occurs in simulations of a smoothly growing sphere.

With no changes to the Gauss or Mainardi-Codazzi-Peterson incompatibilities governing the mechanical forces in the sheet, the trio concluded that the sudden transformation emerged from an entirely different mechanism, rooted in the mathematical principles of topology. In this view, unlike smooth geometric transformations such as bending, stretching, or twisting, which preserve a shape’s mechanical properties, cutting introduces a sudden transformation that changes its mechanical behaviour.

In this way, the meridional cut brought the sphere into a new topological state. “Unlike conventional incompatibility, this frustration is topological in character, and can be quantified by a global measure,” Moshe explains. “It provides a new mechanism by which growing sheets can select complex, wrinkled or dimpled shapes.”

The trio’s discovery now raises new mathematical questions about the limits of growing elastic sheets, beyond which their smooth geometries can no longer be maintained. “What we have discovered that the geometrical principles we knew before should be supplemented with topological considerations, leading to an even wider class of shaping principles,” Sharon says. “This allows a better understanding of morphogenetic processes and expands our abilities to shape synthetic structures.”

In turn, the team’s insights could uncover new understanding of how shaping mechanisms could be harnessed, perhaps leading to the discovery of new metamaterials, with shapes and mechanical functions programmed into their growth.

The research is described in Physical Review Letters.

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Structured light could deliver a new method for diagnosing eye disease

By controlling a type of polarized light widely used in quantum optics, researchers have transformed subtle optical patterns in our peripheral vision into vibrant, easily perceptible shapes. Led by Dusan Sarenac at the University of Waterloo, Canada, the team showed for the first time that the “Boehm’s brushes” perceived by participants can be altered by adjusting the topology of spin-orbit coupled light. Their results, reported in Proceedings of the National Academy of Sciences, could lead to promising new techniques for checking our eye health.

For the most part, human eyes are incapable of detecting polarization in visible light. But in some rare cases, structures inside the eye itself can scatter light in different ways depending on its polarization, creating subtle yet perceivable “entoptic” patterns. Perhaps the best-known examples of these are “Haidinger’s brushes”: hourglass-shaped patterns that can form in our central vision, but only when viewing linearly polarized light at blue wavelengths.

In 1940, Swiss biophysicist Gundo Boehm discovered another example: a two-lobed, bowtie-shaped entoptic pattern that forms when viewing linearly polarized light in the peripheral vision as it scatters from subcellular structures in the inner retina. Unlike Haidinger’s brushes, this lesser-known effect is driven by angular variations in scattering strength relative to the polarization direction.

But as Sarenac explains, these ethereal shapes are more than just a curiosity. “Because retinal disease may alter a person’s ability to perceive the pattern, researchers have long considered whether Boehm’s brushes could serve as a biomarker of retinal health,” he says. “However, their weak visibility has limited practical use.”

Whereas previous studies simply asked participants to passively observe the effect, Sarenac’s team considered what would happen if the light’s polarization was constantly varied. To explore this possibility, the researchers created a beam of spin-orbit coupled light, in which polarization is linked to the light’s orbital angular momentum – a property describing how the wavefront twists as the beam travels – so that the polarization direction rotates steadily across the beam.

In quantum optics, these structured waveforms are already being widely explored for their possibilities in imaging, communication and information processing. But for the first time, Sarenac’s team considered how our eyes could actually perceive this light. “We engineered the spatial polarization of the light to match the symmetry of the retinal scattering response,” Sarenac describes. “This allowed many weak local contributions to reinforce one another.”

The researchers then projected this structured light through a ring-shaped aperture, targeting specific regions in the periphery of participants’ retinas, which could also be adjusted to target varying distances from the centre of vision. Using an automated test, they measured how much contrast participants needed to reliably distinguish a Boehm’s brush from the background at these varying distances.

Based on the subject’s responses, Sarenac’s team determined that the use of spin-orbit coupled light not only made Boehm’s brushes appear far more vivid to the participants, it also transformed the bowtie shape into a multi-lobed pattern, with the number of lobes varying depending on the topology of the light’s twisting polarization.

“Across 11 participants, detection thresholds improved exponentially away from the centre of vision, and the pattern became robustly visible at approximately one degree of retinal angular distance,” Sarenac describes. These results reveal a fascinating link between human vision and quantum mechanics, which the team hope could be harnessed in practical healthcare. With further studies involving patients with retinal disease, they now envisage eye tests where retinal conditions could be diagnosed in people who can’t clearly perceive vibrant, multi-lobed Boehm’s brushes in their peripheral vision.

“In the longer term, these patterns may provide a non-invasive functional probe of retinal integrity because their shape and visibility can be measured across different retinal locations,” Sarenac says.

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Satellite-based sensor system designed to detect nuclear weapons in space

For decades, the Outer Space Treaty (OST) has prevented any nation from placing nuclear weapons in space. To date, however, no mechanisms have been put in place to determine whether a signing member’s satellite may be violating this treaty, or even developing other nuclear capabilities that the original treaty never considered.

Through new analysis of the problem, Areg Danagoulian at MIT suggests a safe and feasible approach to monitoring suspicious satellites, using neutrons emitted as radioactive material is impacted by naturally occurring protons in the Van Allen radiation belt.

At the height of the Cold War in the 1960s, there seemed a growing possibility that space could be used as a platform for developing nuclear weapons. With the prospect of nuclear strikes being launched from orbit with practically no warning, both the US and Soviet governments recognised the possibility of miscalculations by either side leading to a catastrophic nuclear conflict.

In 1967, this led to the signing of the OST: which in part, demands that no signing member should ever deploy nuclear weapons in orbit, on celestial bodies or in outer space. Today, it has been signed by 117 countries, including the US, Russia and China. However, in the decades since the treaty’s origins, both political and technological landscapes have profoundly transformed, creating entirely new concerns that nobody could have conceived in the 1960s.

“In 2022, Russia launched the Kosmos 2553 satellite, which the US has determined is a platform for testing components for a future nuclear anti-satellite weapon,” Danagoulian says. With the ability to target orbiting satellites, such a programme could ultimately destroy vital communication and navigation systems – bringing society to a standstill without any direct strike on the ground.

Despite this threat, no robust mechanism has ever been developed for verifying whether a country is violating the OST, and to date, very little research has even considered the problem.

To Danagoulian’s knowledge, the only related study was an undergraduate thesis by Stanford University student Isobel Portenous – who proposed that suspicious satellites could be probed for nuclear material by measuring radioactivity in the vicinity. However, not only is space already highly radioactive, likely drowning out the signal from a single satellite; it would also require spacecraft to closely approach the satellite, which could be interpreted as a hostile act.

To address this challenge, Danagoulian considered how satellites could instead by probed by naturally occurring, highly energetic protons in the Van Allen radiation belt: which mostly originate from the solar wind, and become trapped by Earth’s magnetosphere.

When interacting with nuclear material in a suspect satellite, “these protons would trigger a process known as spallation in the uranium radiation case of the thermonuclear weapon,” Danagoulian explains. “This would produce a large flux of neutrons that can be detected and used as a fairly specific signature of a nuclear weapon.”

Crucially, the kind of device needed to detect these neutrons wouldn’t need to be too close to the satellite. From a distance of 4 km, Danagoulian calculated that a standard CubeSat detection platform could accurately determine the composition of the nuclear payload of a satellite like Kosmos 2553, within just a week of measurement time.

For now, much more work will be needed before this kind of mechanism can be realistically applied. “Uncertainty remains regarding whether this approach will be practical, so much work is still needed,” Danagoulian says. “Can one build a reliable detector array to perform this measurement? That’s to be determined.”

Yet if these hurdles can be overcome, they could provide a valuable new layer of security in a fast-changing world, and could potentially guide new international policy decisions. “The required physics and basic technology are available to solve this problem,” Danagoulian continues. “If an inspector satellite can be built, it will finally create a mechanism for verifying the OST.”

The study is reported in Nature.

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