Computers Math

An international team of scientists has recently developed a novel type of nano engine made of DNA. It is driven by a clever mechanism and can perform pulsing movements. The researchers are now planning to fit it with a coupling and install it as a drive in complex nano machines. Their results were just published today in the journal Nature Nanotechnology.
Petr Šulc, an assistant professor at Arizona State University’s School of Molecular Sciences and the Biodesign Center for Molecular Design and Biomimetics, has collaborated with professor Famulok (project lead) from the University of Bonn, Germany and professor Walter from the University of Michigan on this project.
Šulc has used his group’s computer modeling tools to gain insights into design and operation of this leaf-spring nano engine. The structure is comprised of almost 14,000 nucleotides, which form the basic structural units of DNA.
“Being able to simulate motion in such a large nanostructure would be impossible without oxDNA, the computer model that our group uses for design and design of DNA nanostructures,” explains Šulc. ” It is the first time that a chemically powered DNA nanotechnology motor has been successfully engineered. We are very excited that our research methods could help with studying it, and are looking forward to building even more complex nanodevices in the future.”
This novel type of engine is similar to a hand grip strength trainer that strengthens your grip when used regularly. However, the motor is around one million times smaller. Two handles are connected by a spring in a V-shaped structure.
In a hand grip strength trainer, you squeeze the handles together against the resistance of the spring. Once you release your grip, the spring pushes the handles back to their original position. “Our motor uses a very similar principle,” says professor Michael Famulok from the Life and Medical Sciences (LIMES) Institute at the University of Bonn. “But the handles are not pressed together but rather pulled together.”
The researchers have repurposed a mechanism without which there would be no plants or animals on Earth. Every cell is equipped with a sort of library. It contains the blueprints for all types of proteins that each cell needs to perform its function. If the cell wants to produce a certain type of protein, it orders a copy from the respective blueprint. This transcript is produced by the enzymes called RNA polymerases. More

Proteins are important molecules that perform a variety of functions essential to life. To function properly, many proteins must fold into specific structures. However, the way proteins fold into specific structures is still largely unknown. Researchers from the University of Tokyo developed a novel physical theory that can accurately predict how proteins fold. Their model can predict things previous models cannot. Improved knowledge of protein folding could offer huge benefits to medical research, as well as to various industrial processes.
You are literally made of proteins. These chainlike molecules, made from tens to thousands of smaller molecules called amino acids, form things like hair, bones, muscles, enzymes for digestion, antibodies to fight diseases, and more. Proteins make these things by folding into various structures that in turn build up these larger tissues and biological components. And by knowing more about this folding process, researchers can better understand more about the processes that constitute life itself. Such knowledge is also essential to medicine, not only for the development of new treatments and industrial processes to produce medicines, but also for knowledge of how certain diseases work, as some are examples of protein folding gone wrong. So, to say proteins are important is putting it mildly. Proteins are the stuff of life.
Encouraged by the importance of protein folding, Project Assistant Professor Koji Ooka from the College of Arts and Sciences and Professor Munehito Arai from the Department of Life Sciences and Department of Physics embarked on the hard task of improving upon the prediction methods of protein folding. This task is formidable for many reasons. In particular, the computational requirements to simulate the dynamics of molecules necessitate a powerful supercomputer. Recently, the artificial intelligence-based program AlphaFold 2 accurately predicts structures resulting from a given amino acid sequence; but it cannot give details of the way proteins fold, making it a black box. This is problematic, as the forms and behaviors of proteins vary such that two similar ones may fold in radically different ways. So, instead of AI, the duo needed a different approach: statistical mechanics, a branch of physical theory.
“For over 20 years, a theory called the Wako-Saitô-Muñoz-Eaton (WSME) model has successfully predicted the folding processes for proteins comprising around 100 amino acids or fewer, based on the native protein structures,” said Arai. “WSME can only evaluate small sections of proteins at a time, missing potential connections between sections farther apart. To overcome this issue, we produced a new model, WSME-L, where the L stands for ‘linker.’ Our linkers correspond to these nonlocal interactions and allow WSME-L to elucidate the folding process without the limitations of protein size and shape, which AlphaFold 2 cannot.”
But it doesn’t end there. There are other limitations of existing protein folding models that Ooka and Arai set their sights on. Proteins can exist inside or outside of living cells; those within are in some ways protected by the cell, but those outside cells, such as antibodies, require additional bonds during folding, called disulfide bonds, which help to stabilize them. Conventional models cannot factor in these bonds, but an extension to WSME-L called WSME-L(SS), where each S stands for sulfide, can. To further complicate things, some proteins have disulfide bonds before folding starts, so the researchers made a further enhancement called WSME-L(SSintact), which factors in that situation at the expense of extra computation time.
“Our theory allows us to draw a kind of map of protein folding pathways in a relatively short time; mere seconds on a desktop computer for short proteins, and about an hour on a supercomputer for large proteins, assuming the native protein structure is available by experiments or AlphaFold 2 prediction,” said Arai. “The resulting landscape allows a comprehensive understanding of multiple potential folding pathways a long protein might take. And crucially, we can scrutinize structures of transient states. This might be helpful for those researching diseases like Alzheimer’s and Parkinson’s — both are caused by proteins which fail to fold correctly. Also, our method may be useful for designing novel proteins and enzymes which can efficiently fold into stable functional structures, for medical and industrial use.”
While the models produced here accurately reflect experimental observations, Ooka and Arai hope they can be used to elucidate the folding processes of many proteins that have not yet been studied experimentally. Humans have about 20,000 different proteins, but only around 100 have had their folding processes thoroughly studied. More

A new electrical method to conveniently change the direction of electron flow in some quantum materials could have implications for the development of next-generation electronic devices and quantum computers. A team of researchers from Penn State developed and demonstrated the method in materials that exhibit the quantum anomalous Hall (QAH) effect — a phenomenon in which the flow of electrons along the edge of a material does not lose energy. The team described the work in a paper appearing today (Oct. 19) in the journal Nature Materials.
“As electronic devices get smaller and computational demands get larger, it is increasingly important to find ways to improve the efficiency of information transfer, which includes the control of electron flow,” said Cui-Zu Chang, Henry W. Knerr Early Career Professor and associate professor of physics at Penn State and co-corresponding author of the paper. “The QAH effect is promising because there is no energy loss as electrons flow along the edges of materials.”
In 2013, Chang was the first to experimentally demonstrate this quantum phenomenon. Materials exhibiting this effect are referred to as QAH insulators, which are a type of topological insulator — a thin layer of film only a couple dozen atoms thick — that have been made magnetic so that they only conduct current on their edges. Because the electrons travel cleanly in one direction, the effect is referred to as dissipationless, meaning no energy is lost in the form of heat.
“In a QAH insulator, electrons on one side of the material travel in one direction, while those on the other side travel in the opposite direction, like a two-lane highway,” Chang said. “Our earlier work demonstrated how to scale up the QAH effect, essentially creating a multilane highway for faster electron transport. In this study, we develop a new electrical method to control the transport direction of the electron highway and provide a way for those electrons to make an immediate U-turn.”
The researchers fabricated a QAH insulator with specific, optimized properties. They found that applying a 5-millisecond current pulse to the QAH insulator impacts the internal magnetism of the material and causes the electrons to change directions. The ability to change direction is critical for optimizing information transfer, storage, and retrieval in quantum technologies. Unlike current electronics, where data is stored in a binary state as on or off — as one or zero — quantum data can be stored simultaneously in a range of possible states. Changing the flow of electrons is an important step in writing and reading these quantum states.
“The previous method to switch the direction of electron flow relied on an external magnet to alter the material’s magnetism, but using magnets in electronic devices is not ideal,” said Chao-Xing Liu, professor of physics at Penn State and co-corresponding author of the paper. “Bulky magnets are not practical for small devices like smartphones, and an electronic switch is typically much faster than a magnetic switch. In this work, we found a convenient electronic method to change the direction of electron flow.”
The researchers previously optimized the QAH insulator so that they could take advantage of a physical mechanism in the system to control its internal magnetism. More

In a paper published today in Nature Photonics, researchers from the University of Oxford, along with collaborators from the Universities of Muenster, Heidelberg, and Exeter, report on their development of integrated photonic-electronic hardware capable of processing three-dimensional (3D) data, substantially boosting data processing parallelism for AI tasks.
Conventional computer chip processing efficiency doubles every 18 months, but the processing power required by modern AI tasks is currently doubling around every 3.5 months. This means that new computing paradigms are urgently needed to cope with the rising demand.
One approach is to use light instead of electronics — this allows multiple calculations to be carried out in parallel using different wavelengths to represent different sets of data. Indeed, in ground breaking work published in the journal Nature in 2021, many of the same authors demonstrated a form of integrated photonic processing chip that could carry out matrix vector multiplication (a crucial task for AI and machine learning applications) at speeds far outpacing the fastest electronic approaches. This work resulted in the birth of the photonic AI company, Salience Labs, a spin-out from the University of Oxford.
Now the team has gone further by adding an extra parallel dimension to the processing capability of their photonic matrix-vector multiplier chips. This “higher-dimensional” processing is enabled by exploiting multiple different radio frequencies to encode the data, propelling parallelism to a level far beyond that previously achieved.
As a test case the team applied their novel hardware to the task of assessing the risk of sudden death from electrocardiograms of heart disease patients. They were able to successfully analyse 100 electrocardiogram signals simultaneously, identifying the risk of sudden death with a 93.5% accuracy.
The researchers further estimated that even with a moderate scaling of 6 inputs × 6 outputs, this approach can outperform state-of-the-art electronic processors, potentially providing a 100-times enhancement in energy efficiency and compute density. The team anticipates further enhancement in computing parallelism in the future, by exploiting more degrees of freedom of light, such as polarization and mode multiplexing.
First author Dr Bowei Dong at the Department of Materials, University of Oxford said: ‘We previously assumed that using light instead of electronics could increase parallelism only by the use of different wavelengths — but then we realised that using radio frequencies to represent data opens up yet another dimension, enabling superfast parallel processing for emerging AI hardware.’
Professor Harish Bhaskaran, Department of Materials, University of Oxford and CO-founder of Salience Labs, who led the work said: ‘This is an exciting time to be doing research in AI hardware at the fundamental scale, and this work is one example of how what we assumed was a limit can be further surpassed.’ More

Researchers have invented an experimental wearable device that generates power from a user’s bending finger and can create and store memories, in a promising step towards health monitoring and other technologies.
The innovation features a single nanomaterial incorporated into a stretchable casing fitted to a person’s finger. The nanomaterial enabled the device to generate power with the user bending their finger.
The super-thin material also allows the device to perform memory tasks, as outlined below.
Multifunctional devices normally require several materials in layers, which involves the time-consuming challenge of stacking nanomaterials with high precision.
The team, led by RMIT University and the University of Melbourne in collaboration with other Australian and international institutions, made the proof-of-concept device with the rust of a low-temperature liquid metal called bismuth, which is safe and well suited for wearable applications.
Senior lead researcher Dr Ali Zavabeti said the invention could be developed to create medical wearables that monitor vital signs — incorporating the researchers’ recent work with a similar material that enabled gas sensing — and memorise personalised data.
“The innovation was used in our experiments to write, erase and re-write images in nanoscale, so it could feasibly be developed to one day encode bank notes, original art or authentication services,” said Zavabeti, an engineer from RMIT and the University of Melbourne. More

Robotic prosthetic ankles that are controlled by nerve impulses allow amputees to move more “naturally,” improving their stability, according to a new study from North Carolina State University and the University of North Carolina at Chapel Hill.
“This work focused on ‘postural control,’ which is surprisingly complicated,” says Helen Huang, corresponding author of the study and the Jackson Family Distinguished Professor in the Joint Department of Biomedical Engineering at NC State and UNC.
“Basically, when we are standing still, our bodies are constantly making adjustments in order to keep us stable. For example, if someone bumps into us when we are standing in line, our legs make a wide range of movements that we are not even necessarily aware of in order to keep us upright. We work with people who have lower limb amputations, and they tell us that achieving this sort of stability with prosthetic devices is a significant challenge. And this study demonstrates that robotic prosthetic ankles which are controlled using electromyographic (EMG) signals are exceptionally good at allowing users to achieve this natural stability.” EMG signals are the electrical signals recorded from an individual’s muscles.
The new study builds on previous work, which demonstrated that neural control of a powered prosthetic ankle can restore a range of abilities, including standing on challenging surfaces and squatting.
For this study, the researchers worked with five people who had amputations below the knee on one leg. Study participants were fitted with a prototype robotic prosthetic ankle that responds to EMG signals that are picked up by sensors on the leg.
“Basically, the sensors are placed over the muscles at the site of the amputation,” says Aaron Fleming, co-author of the study and recent Ph.D. graduate from NC State. “When a study participant thinks about moving the amputated limb, this sends electrical signals through the residual muscle in the lower limb. The sensors pick these signals up through the skin and translate those signals into commands for the prosthetic device.”
The researchers conducted general training for study participants using the prototype device, so that they were somewhat familiar with the technology. More

Taking inspiration from music streaming services, a team of engineers at the University of Michigan, Google and Georgia Tech has designed the simplest way for users to program their own exoskeleton assistance settings.
Of course, what’s simple for the users is more complex underneath, as a machine learning algorithm repeatedly offers pairs of assistance profiles that are most likely to be comfortable for the wearer. The user then selects one of these two, and the predictor offers another assistance profile that it believes might be better. This approach enables users to set the exoskeleton assistance based on their preferences using a very simple interface, conducive to implementing on a smartwatch or phone.
“It’s essentially like Pandora music,” said Elliott Rouse, U-M associate professor of robotics and mechanical engineering and corresponding author of the study in Science Robotics. “You give it feedback, a thumbs up or thumbs down, and it curates a radio station based on your feedback. This is a similar idea, but it’s with exoskeleton assistance settings. In both cases, we are creating a model of the user’s preferences and using this model to optimize the user’s experience.”
The team tested the approach with 14 participants, each wearing a pair of ankle exoskeletons as they walked at a steady pace of about 2.3 miles per hour. The volunteers could take as much time as they wanted between choices, although they were limited to 50 choices. Most participants were choosing the same assistance profile repeatedly by the 45th decision.
After 50 rounds, the experimental team began testing the users to see whether the final assistance profile was truly the best — pairing it against 10 randomly generated (but plausible) profiles. On average, participants chose the settings suggested by the algorithm about nine out of 10 times, which highlights the accuracy of the proposed approach.
“By using clever algorithms and a touch of AI, our system figures out what users want with easy yes-or-no questions,” said Ung Hee Lee, a recent U-M doctoral graduate from mechanical engineering and first author of the study, now at the robotics company Nuro. “I’m excited that this approach will make wearable robots comfortable and easy to use, bringing them closer to becoming a normal part of our day-to-day life.”
The control algorithm manages four exoskeleton settings: how much assistance to give (peak torque), how long to go between peaks (timing), and how the exoskeleton both ramps up and reduces the assistance on either side of each peak. This assistance approach is based on how our calf muscle adds force to propel us forward in each step. More

Ever since Antonie van Leeuwenhoek discovered the world of bacteria through a microscope in the late seventeenth century, humans have tried to look deeper into the world of the infinitesimally small.
There are, however, physical limits to how closely we can examine an object using traditional optical methods. This is known as the ‘diffraction limit’ and is determined by the fact that light manifests as a wave. It means a focused image can never be smaller than half the wavelength of light used to observe an object.
Attempts to break this limit with “super lenses” have all hit the hurdle of extreme visual losses, making the lenses opaque. Now physicists at the University of Sydney have shown a new pathway to achieve superlensing with minimal losses, breaking through the diffraction limit by a factor of nearly four times. The key to their success was to remove the super lens altogether.
The research is published today in Nature Communications.
The work should allow scientists to further improve super-resolution microscopy, the researchers say. It could advance imaging in fields as varied as cancer diagnostics, medical imaging, or archaeology and forensics.
Lead author of the research, Dr Alessandro Tuniz from the School of Physics and University of Sydney Nano Institute, said: “We have now developed a practical way to implement superlensing, without a super lens.
“To do this, we placed our light probe far away from the object and collected both high- and low-resolution information. By measuring further away, the probe doesn’t interfere with the high-resolution data, a feature of previous methods.”
Previous attempts have tried to make super lenses using novel materials. However, most materials absorb too much light to make the super lens useful. More