Monthly Archives: June 2023

Quantum Cryptography: The Cutting Edge of Secure Communication – CityLife

Posted: June 10, 2023 at 8:26 pm

Quantum Cryptography: The Cutting Edge of Secure Communication

Quantum cryptography, a cutting-edge technology that utilizes the principles of quantum mechanics, is revolutionizing the way we secure our communication channels. In an age where cyber threats are becoming increasingly sophisticated, the need for foolproof security measures has never been more critical. With the potential to provide unbreakable encryption, quantum cryptography is poised to redefine the landscape of secure communication.

At the heart of quantum cryptography is the concept of quantum key distribution (QKD), a technique that enables two parties to share a secret encryption key without the risk of interception by a third party. This is made possible by the unique properties of quantum particles, such as photons, which exhibit a phenomenon known as quantum superposition. In simple terms, quantum superposition allows particles to exist in multiple states simultaneously until they are measured. Once a measurement is made, the particle collapses into a single state, rendering any attempt to intercept the key futile.

One of the most well-known QKD protocols is the BB84 protocol, proposed by Charles Bennett and Gilles Brassard in 1984. The protocol uses polarized photons to transmit the encryption key between two parties, Alice and Bob. By encoding the key in the polarization states of the photons, Alice and Bob can detect any eavesdropping attempts by a third party, Eve. If Eve tries to intercept the key, her measurement will disturb the quantum state of the photons, alerting Alice and Bob to her presence.

In addition to providing unparalleled security, quantum cryptography also offers several other advantages over classical encryption methods. For instance, it is immune to brute-force attacks, which involve systematically trying every possible key combination to decrypt a message. This is because the security of quantum cryptography is based on the fundamental laws of physics, rather than the computational complexity of the encryption algorithm. Furthermore, quantum cryptography is future-proof, as it is resistant to attacks from quantum computers, which are expected to render many classical encryption schemes obsolete.

Despite its numerous benefits, the widespread adoption of quantum cryptography faces several challenges. One of the main hurdles is the limited range of QKD systems, which currently stands at around 100 kilometers. This is due to the fact that photons are prone to being absorbed or scattered as they travel through optical fibers, leading to a loss of signal. To overcome this issue, researchers are exploring the use of quantum repeaters, which can extend the range of QKD systems by amplifying the signal without disturbing the quantum state of the photons.

Another challenge is the high cost and complexity of implementing quantum cryptography systems. The technology requires specialized equipment, such as single-photon detectors and sources, which can be expensive and difficult to maintain. However, as research in the field progresses and the technology matures, it is expected that the cost and complexity of quantum cryptography systems will decrease, making them more accessible to a wider range of users.

In conclusion, quantum cryptography represents a major breakthrough in the field of secure communication, offering unparalleled security and immunity to brute-force attacks and quantum computing threats. While there are still challenges to overcome, such as limited range and high implementation costs, the potential benefits of quantum cryptography are immense. As cyber threats continue to evolve and grow in sophistication, the need for robust security measures will only become more urgent. In this context, quantum cryptography is poised to play a crucial role in safeguarding our digital infrastructure and ensuring the confidentiality of our communications.

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This 17-year-old works to make quantum mainstream – Indiatimes.com

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Shraddha Aangiras was in the 8th grade when her father showed her a TEDx video of Shohini Ghose, a quantum physicist. Shraddha was immediately spellbound. I was really fascinated that something could be zero and one at the same time. I had been coding for a while by then, so I could wrap my head around most things, but with quantum, I couldnt. So she started googling more and more, and she landed upon articles that were easy to read. But I wanted to learn more. So, I downloaded this introductory book, Quantum Computation and Quantum Information, because it was really preliminary. And when I opened it, I saw maths symbols that I had never seen before. Thats when the 8th grader realised she needed to up her maths game. So, in a year, she taught herself undergraduate maths and physics, only to realise at the end of it that she didnt actually need to know so much. I had learned a lot of theory but not the required industry skills I was aiming for. I realised I spent an entire year learning something that wasnt necessary. A clearer path for me to go ahead would have been great. Shraddha is now 17, and a student at RV PU Collegein Bengaluru, with one overriding mission make quantum computing more accessible to students. She partnered with One Million for One Billion (1M1B) under The Purpose Academy programme to start a quantum career accelerator programme called Quetzal that is open to all undergraduate STEM students in India. Shraddha presented her work on Quetzal at UC Berkeley recently. At Quetzal, well train undergraduate students across India in fundamental quantum computing for two weeks. This programme will have learning days as well as mission days. On learning days, well teach them through lectures, as well as hands-on labs, to ensure the students have an industry perspective. Mission days will be in between these learning days, to not onlytest how well students learn, but also to check their consistency, says Shraddha. The programme will then select the top students and connect them with quantum computing internships. The plan is to have two groups of a thousand students each, and to provide 100 internships. Engineering students who join the programme can expect to learn about qubits, quantum circuits and quantum algorithms. It will primarily revolve around learning Qiskit, IBMs open-source software development kit (SDK). Qiskit is great to have in your portfolio as an intern, Shraddha says.

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The multiverse is doomed and even Spider-Man and The Flash can’t save it – Yahoo Entertainment

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Clockwise from Top Left: The Flash (Warner Bros.) Spider-Man: Across The Spider-Verse (Sony), Doctor Doom And The Multiverse Of Madness (Marvel), Ant-Man And The Wasp: Quantumania (Marvel)

Has Guardians of the Galaxy Vol. 3 saved the Marvel Cinematic Universe? Movie-goers loved itthe film is expected to earn around $800 million worldwide, and the Rotten Tomatoes audience score came in at 94 percent. Critics were 82 percent positive, and they liked it a lot better than Ant-Man And The Wasp: Quantumania (RT critics score: a miserable 47 percent), or Dr. Strange In The Multiverse Of Madness (74 percent), or Eternals (with another 47 percent critics score, proving misery loves company).

By most measures, then, GOTG3 is a major Marvel comeback. There must be champagne and high-fives all around over at Marvel Films, am I right? Not if Kevin Feige is as smart as they say. Because what GOTG3 really confirms is that the multiversethe whole organizing principle behind the still-emergent Marvel Phase Four multi-film story arcis box office poison.

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You remember the multiverse. Its a plot device strip-mined for the MCU from old print comics and launched in the Loki TV series on Disney+. It involves ideas borrowed by way of a seventh-grade education in string theory, Einsteins Theory of Relativity, and quantum physics, and its all about parallel universes crowding each other out of existence.

If youre like most viewers, you actively disliked the multiverse in the fulsomely named Dr. Strange In The Multiverse Of Madness and you truly hated it by the time the equally tongue-twisting Ant-Man And The Wasp: Quantumania arrived. Possibly thats because, in the MCU, the multiverse has approximately two functions: it liberates whatever pickup squad of CG artists Marvel has deployed to treat art direction like something Peter Max dreamed up while experimenting with LSD, and its mostly a way to lower the dramatic stakes.

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Think about it: If theres potentially another Iron Man out there in the multiverse, and he could be played by Robert Downey Jr., how resonant is Tony Starks big death scene in Avengers: Endgame? When Ant-Man and company spend an entire movie taking down a Big Bad like Kang the Conqueror, how much should we care if five minutes later the end credits scene reminds us Kang variants are stocked up like Campbells soup cans in the multiversal limbo-land they call home?

The Spider-Verse movies are standalone animated features which, despite a few knowing gags, arent supposed to be part of the MCU, and theyre produced by Sony, not Marvel. In fact, Sony was allegedly warned by Kevin Feige during prep on Into The Spider-Versenotto get ahead of itself by transforming the Spider-Verse into a setup comparable to anything in the MCU. And remember: the Spider-Verse movies are, amongst other things, comedies, using the multiverse premise to make gags about talking pigs.

Thats a flashing warning light writ large. An old Hollywood adage is that parodies and satires mark the end of a cycle, in the way Blazing Saddles came out when the Western was dying. Abbott And Costello Meet Frankenstein literally finished off the very first cinematic universe: the Universal horror franchise of the 1930s and 40s, gunned down by the rat-a-tat slapstick of the schtickmeisters behind Whos On First?

But The Flash you sayand there are reasons to treat the upcoming Ezra Miller Flash feature as a different kind of multiverse saga for the DCEU. For one thing, in the larger sphere of superhero comics, The Flash is considered to be the great hero-protagonist of the whole multiverse premise. Flash Of Two Worlds is a 1961 Flash storyline widely acknowledged as the birth of the multiverse gimmick. In it, the 1960s Barry Allen comic book Flash uses super-speeding molecules to vibrate himself onto Earth-2, where he teams up with the 1940s Jay Garrick Flash.

The Flash was also the prime mover in what comics aficionados still believe to be the greatest multiverse arc of them all (as well as a pioneer of the crossover event, an approach Marvel Films rode to the bank in MCU Phases One through Three). Marv Wolfman and George Perezs 1985 DC Comics masterwork Crisis On Infinite Earths never made it to the movie screen, but it was tributed in a big way by DCs TV Arrowverse, especially on (you guessed it) the CW version of The Flash.

Its instructive to take a closer look at how DC comics utilized the multiverse, though. In Flash Of Two Worlds, the multiverse was a nifty pseudo-scientific bridge between two continuities: the original 1940s Golden Era DC Flash books and the rebooted and more enduringly popular Barry Allen variant (the one Ezra Miller is playing).

That teaming opened a floodgate, because DC now had access to its entire dead roster of pre-Comics Code super avengers, to use as plot devices in the contemporary lineup. Over time, there were storylines involving the often scarier and more violent early DC characters like Sandman, The Spectre, or even the Earth-2 Batman (you know, the homicidal one with the guns) as story devices in current continuities.

Eventually, it all got out of hand, so a part of Marv Wolfmans pitch when he conceived Crisis On Infinite Earths was about housecleaning; at the end of the saga, the five DC universes had merged into one, taking out a lot of dead weight superhero characters (and the Barry Allen Flash) in the process. The closest analogy may be Spider-Man: No Way Homea multiverse Marvel movie essentially disconnected from any larger story strategy, created to harmonize Sonys various non-MCU Spider-Man projects with the current MCU.

A spring cleaning emphasis does not indicate DC is betting the farm on the multiverse the way Marvel has. After Guardians Of The Galaxy Vol. 3, though, it would be surprising if Marvel isnt at least re-evaluating its multiverse strategyif it hasnt already. GOTG3 is an old-fashioned closerthe capstone to a trilogy of movies in the way Return Of The Jedi or The Dark Knight Rises also were.

When the GOTG3 storyline ends, our troop of space mercenaries has splintered, and while there may be more adventures to come, the original collectives race appears to have been run and there dont seem to be multitudes of Star Lords waiting for their cue. And thats really how it should be. Because admit it. Youre already sick of the multiverseand that means its not the sort of thing to build the future of an entire cinematic universe on.

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Physics of Time Travel: A Scientific Perspective – Mirage News

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For centuries, humans have been intrigued by the concept of time travel. Its a theme deeply embedded in our literature, movies, and collective imagination. But can it ever be more than just fantasy?

In this article, well dive into what modern physics suggests about the potential for time travel.

To understand time travel, we first need to grasp the concept of space-time, a term popularized in the early 20th century by physicist Albert Einstein. In his theory of relativity, Einstein suggested that space and time are interwoven into a single four-dimensional fabric known as space-time. Objects with mass or energy cause this fabric to curve, creating what we perceive as gravity.

Einsteins equations also suggest the existence of wormholes, which are theoretical bridges or shortcuts through space-time. In theory, a wormhole could link two different points in time as well as space, providing a potential mechanism for time travel. However, wormholes remain purely theoretical, and if they do exist, they are likely to be extremely unstable.

The concept of the arrow of time, established by British astronomer Arthur Eddington, states that time only flows in one direction forward. This concept is reinforced by the second law of thermodynamics, which states that the total entropy (or disorder) of an isolated system can never decrease over time. This implies that reversing or halting the flow of time would violate this fundamental law of physics.

However, at the quantum level, many of the laws of physics are time-symmetric, meaning they would operate the same way if time were flowing backward. This discrepancy between the macroscopic and quantum realms adds another layer of complexity to our understanding of time and whether it could ever be traversed in a non-linear way.

Einsteins theory of relativity also introduced the phenomenon of time dilation, which is the closest thing to time travel thats been experimentally confirmed. According to the theory, time passes at different rates for objects moving relative to each other or experiencing different gravitational fields.

This has been experimentally verified numerous times. For example, atomic clocks flown in airplanes or placed at high altitudes tick slightly slower compared to those on Earths surface. Although this isnt time travel in the sense often depicted in fiction, it does demonstrate that time is not absolute but relative and dependent on velocity and gravity.

A significant challenge to the idea of time travel is the grandfather paradox. This thought experiment asks what would happen if a person were to go back in time and kill their grandfather before their parent was born. This would seemingly create a contradiction, as the time traveler could never have existed to travel back in time in the first place.

Some physicists suggest that the principles of quantum mechanics might resolve such paradoxes. The many-worlds interpretation of quantum mechanics proposes that each possible outcome of a quantum event happens in a different universe. Applying this to time travel, it might be that any action a time traveler takes merely creates a new timeline or universe, avoiding any contradictions in their original timeline.

While time travel remains firmly in the realm of science fiction, the complex theories and principles of modern physics suggest that our understanding of time is far from complete. Wormholes, time dilation, and quantum mechanics all point to a universe where time might not be as straightforward as our everyday experience suggests.

But even if time travel is theoretically possible, practical implementation is another story entirely. The energy requirements and technological capabilities needed to manipulate space-time or stabilize wormholes are far beyond our current reach.

The dream of time travel inspires us to push the boundaries of human knowledge and capability. Whether or not we ever manage to achieve it, the pursuit expands our understanding of the universe and our place within it.

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Quantum Spin Liquids: The Future of Superconductors – EnergyPortal.eu

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Quantum spin liquids (QSLs) have been a topic of intense research and interest in the field of condensed matter physics for the past few decades. These exotic states of matter have the potential to revolutionize our understanding of superconductivity and pave the way for a new generation of technological applications. In this article, we will explore the fascinating world of quantum spin liquids and discuss their potential impact on the future of superconductors.

At the heart of quantum spin liquids lies the concept of quantum entanglement, a fundamental principle of quantum mechanics that allows particles to be instantaneously connected regardless of the distance between them. In a QSL, the magnetic moments or spins of electrons become entangled with one another, leading to a highly correlated and entangled state of matter. This entanglement gives rise to unique and intriguing properties that set QSLs apart from other forms of matter.

One of the most striking features of quantum spin liquids is their ability to maintain long-range quantum entanglement even at high temperatures. This is in stark contrast to conventional superconductors, which rely on the formation of Cooper pairs of electrons to achieve superconductivity, a phenomenon that typically occurs only at extremely low temperatures. The resilience of QSLs to thermal fluctuations makes them promising candidates for the development of high-temperature superconductors, which could have far-reaching implications for energy transmission, transportation, and other technological applications.

Another remarkable property of quantum spin liquids is their inherent resistance to magnetic order. In most materials, the spins of electrons tend to align themselves in a regular pattern when subjected to a magnetic field, a phenomenon known as magnetic ordering. However, in a QSL, the spins remain in a disordered and fluctuating state even in the presence of a magnetic field. This absence of magnetic order is a direct consequence of the strong quantum entanglement between the spins, which prevents them from settling into a fixed arrangement.

The study of quantum spin liquids has also led to the discovery of new types of elementary particles, known as anyons. Unlike conventional particles such as electrons and protons, which are classified as fermions or bosons, anyons exhibit unique quantum properties that are intermediate between the two. The existence of anyons in QSLs has been predicted theoretically, and recent experimental evidence has provided strong support for their presence in these exotic states of matter. The discovery of anyons opens up new avenues for research in quantum computing, as they have the potential to be used as building blocks for quantum bits or qubits, the fundamental units of quantum information.

The potential applications of quantum spin liquids in the realm of superconductivity are vast and varied. The development of high-temperature superconductors could revolutionize the way we generate, transmit, and store electrical energy, leading to significant improvements in energy efficiency and a reduction in greenhouse gas emissions. Moreover, the unique properties of QSLs could be harnessed for the development of advanced materials with tailored magnetic and electronic properties, opening up new possibilities in the fields of electronics, spintronics, and quantum computing.

In conclusion, quantum spin liquids represent a fascinating and promising frontier in the study of condensed matter physics. Their unique properties, stemming from the intricate interplay of quantum entanglement and magnetic interactions, have the potential to reshape our understanding of superconductivity and pave the way for a new generation of technological applications. As research in this area continues to advance, we can expect to witness exciting breakthroughs and discoveries that will undoubtedly have a profound impact on our lives and the world around us.

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Interview: Three Books That Make Tess Gunty Angry – The New York Times

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An incomplete list: Claudia Rankine, Anne Carson, Maggie Nelson, Yuri Herrera, Zadie Smith, Diane Williams, Valeria Luiselli, Olga Tokarczuk, Rachel Kushner, Elena Ferrante, Ben Lerner, Carmen Maria Machado, Joy Williams, Hanif Abdurraqib, Nuar Alsadir, Robin Coste Lewis, Natalie Diaz, Ocean Vuong, Sharon Olds, Morgan Parker, Tommy Pico, Terrance Hayes, Ada Limn, Tracy K. Smith, Annie Baker, Amy Herzog, Paula Vogel, Svetlana Alexievich, Rachel Aviv, Ed Yong, Matthew Desmond, Alexandra Kleeman, Susan Choi, Chris Ware, Tommy Orange, Javier Zamora, Jenny Offill, Annie Ernaux, Anne Enright, Lydia Davis, Raven Leilani, Mark Z. Danielewski, Jennifer Egan, George Saunders. I cant believe I get to share a time period with all of these people.

Whats the last book you read that made you cry?

Calling a Wolf a Wolf, by Kaveh Akbar, specifically the penultimate poem: I Wont Lie This Plague of Gratitude. Akbar alchemizes pain into beauty line after line, but it was an unexpected evocation of hope that made me cry. In this poem, the speaker is thunderstruck by a newfound plague of gratitude. The speaker says: Not long ago I was hard to even/hug ... I had to learn to love people one at a time/singing hey diddle diddle will you suffer me/a little ... now I am cheery/and Germanic like a drawer full/of strudel. Akbars describing a small psychological sanctuary a relief, permanent or fleeting, from everything that has haunted the speaker until now. The poem plunged me into that first miraculous flash of hope you enjoy after a long storm of bad brain chemistry. The moment you remember that it can be enjoyable to simply exist.

The last book that made you furious?

So many come to mind. I guess Im often furious? Im currently reading three impeccably researched works of nonfiction that are informing previously amorphous concerns. Poverty, by America, by Matthew Desmond, investigates structurally engineered poverty. One of the many memorable facts that this book delineates is that America spends over twice as much on tax benefits for the upper class as it does on national defense. Empire of Pain, by Patrick Radden Keefe, makes me enraged about the Sackler family, of course, but more generally about how vulnerable American health care and pharmaceutical systems are to bad actors worse, poorly regulated capitalism incentivizes bad actors to do harm. The Alignment Problem, by Brian Christian, makes me furious about the myopic tech boys currently pursuing immortality and godlike dominance by attempting to summon the existential threat of artificial general intelligence into the world. They are facilitated by an absence of legal restrictions and the primeval excuse that if We dont do it first, They will.

What book might people be surprised to find on your shelves?

My family is always shocked by how many books on neuroscience and quantum physics Ive amassed. They like to remind me that I am bad at science. Probably most surprising is that Im still under the delusion that I will someday read all 1,500 pages of The Matter With Things, by Iain McGilchrist a blend of neuroscience, metaphysics and epistemology about the hemispheres of the brain and the nature of consciousness. I think you start levitating as soon as you finish it.

Whats the best book youve ever received as a gift?

When I graduated college, my good friend Alex gave me a beautiful, professionally bound copy of the novella I wrote for my thesis. He even got a mutual friend to blurb it. The novella itself is a catastrophe a cluttered story about four characters from different centuries saddled with shared omniscient narration who meet in a Purgatory that resembles postindustrial Indiana. Eventually, it collapses into metafictional chaos. Flawed as the project is, I had transferred my 21-year-old spirit into its pages, and Alex knew that if I could hold a leatherbound copy of this effort in my hands, if I could see my name engraved in gold on the spine, some psychological chasm between the life I had and the life I wanted would begin to close. For years, as I submitted my fiction and accumulated rejections, losing faith that I would ever publish, I would catch a glimpse of this book on my shelf, and its presence would nourish me. It remains one of the most cherished gifts Ive ever received.

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Events Calendar School of Mathematics and Statistics Colloquium … – Carleton University

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When Information Theory Meets Algebra and Topology

In recent years, a few surprising connections have arisen between information theory, algebra, and topology. This talk is in a similar vein. We will discuss a certain correspondence between Shannon entropy and continuous functions on topological simplices that satisfy an equation akin to the Leibniz rule from Calculus. The correspondence relies heavily on a particular operad, which is an abstract tool with origins in algebraic topology. A broad goal for this talk is to unwind this result and to share why the confluence of these ideas is both unexpected yet intriguing.

Speaker Bio:

Headshot of SpeakerTai-Danae Bradley is currently a research mathematician at Sandbox AQ and a visiting professor of mathematics at The Masters University where she helps run the Math3ma Institute. She finished her PhD in mathematics in spring 2020 at the CUNY Graduate Center under the supervision of John Terilla and spent some time as a postdoctoral researcher at X, the Moonshot Factory (Google X). Her research interests lie in the intersection of quantum physics, machine intelligence, and category theory.

Links: https://www.sandboxaq.com/ https://www.masters.edu/ https://math3ma.institute/ https://qcpages.qc.cuny.edu/~jterilla/

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Graphene and Quantum Computing: A Match Made in Heaven – CityLife

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Graphene and Quantum Computing: A Match Made in Heaven

Graphene, a single layer of carbon atoms arranged in a hexagonal lattice, has been hailed as a wonder material since its discovery in 2004. This ultra-thin, ultra-strong material has the potential to revolutionize industries ranging from electronics to medicine. One area where graphenes unique properties could have a particularly profound impact is in the realm of quantum computing.

Quantum computing is an emerging field that seeks to harness the strange and powerful properties of quantum mechanics to perform calculations far beyond the capabilities of classical computers. While still in its infancy, quantum computing has the potential to revolutionize fields such as cryptography, drug discovery, and artificial intelligence. However, the development of practical quantum computers has been hampered by a number of technical challenges, including the need for materials that can support and manipulate delicate quantum states.

This is where graphene comes in. Graphenes remarkable electronic properties make it an ideal candidate for use in quantum computing. For one, graphene is an excellent conductor of electricity, with electrons able to move through the material with very little resistance. This property could be used to create ultra-fast, low-power quantum computing devices.

Moreover, graphenes two-dimensional structure gives it unique quantum properties. Electrons in graphene behave as if they have no mass, allowing them to move at extremely high speeds and follow the rules of quantum mechanics rather than classical physics. This means that graphene could potentially be used to create quantum bits, or qubits, the fundamental building blocks of quantum computers.

Qubits are the quantum equivalent of classical bits, which represent information as either a 0 or a 1. However, qubits can exist in a superposition of both 0 and 1 simultaneously, allowing quantum computers to perform many calculations at once. This parallelism is what gives quantum computers their immense potential for solving complex problems.

One of the key challenges in building a quantum computer is maintaining the delicate quantum states of qubits. Quantum states are easily disturbed by their environment, leading to errors in calculations. This phenomenon, known as decoherence, is a major obstacle to the development of practical quantum computers.

Graphenes unique properties could help address this issue. The materials two-dimensional structure means that it can be easily integrated with other materials, such as superconductors, which are essential for maintaining quantum states. Additionally, graphenes high electron mobility could be used to create devices that can manipulate and control qubits with high precision.

Recent research has demonstrated the potential of graphene for quantum computing applications. In one study, scientists at the Massachusetts Institute of Technology (MIT) were able to create a graphene-based device that could control the flow of electrons with a high degree of precision. This device, known as a valleytronics system, could potentially be used to create qubits that are less susceptible to decoherence.

In another study, researchers at the University of Cambridge were able to use graphene to create a new type of qubit that is both more stable and more easily controlled than existing designs. This topological qubit could be a major step forward in the development of practical quantum computers.

While there is still much work to be done, it is clear that graphene has the potential to play a crucial role in the development of quantum computing. The marriage of these two cutting-edge fields could lead to breakthroughs that were once thought to be the stuff of science fiction. As researchers continue to explore the potential of graphene and quantum computing, we may be on the cusp of a new era of technological innovation that will reshape our world in ways we can only begin to imagine.

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How generative AI language models are unlocking the secrets of DNA – Big Think

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Large language models (LLMs) learn from statistical associations between letters and words to predict what comes next in a sentence and are trained on large amounts of data. For instance, GPT-4, which is the LLM underlying the popular generative AI app ChatGPT, is trained on several petabytes (several million gigabytes) of text.

Biologists are leveraging the capability of these LLMs to shed new light on genetics by identifying statistical patterns in DNA sequences. DNA language models (also called genomic or nucleotide language models) are similarly trained on large numbers of DNA sequences.

DNA as the language of life is an oft-repeated clich. A genome is the entire set of DNA sequences that make up the genetic recipe for any organism. Unlike written languages, DNA has few letters: A, C, G, and T (representing the compounds adenine, cytosine, guanine, and thymine). As simple as this genomic language might seem, we are far from uncovering its syntax. DNA language models can improve our understanding of genomic grammar one rule at a time.

What makes ChatGPT incredibly powerful is its adaptability to a wide range of tasks, from generating poems to copy editing an essay. DNA language models are versatile too. Their applications range from predicting what different parts of the genome do to predicting how different genes interact with each other. By learning genome features from DNA sequences, without the need for reference genomes, language models could also potentially open up new methods of analysis.

A model trained on the human genome, for example, was able to predict sites on RNA where proteins are likely to bind. This binding is important in the process of gene expression the conversion of DNA into proteins. Specific proteins bind to RNA, limiting how much of it is then further translated into proteins. In this way, these proteins are said to mediate gene expression. To be able to predict these interactions, the model needed to intuit not just where in the genome these interactions will take place but also how the RNA will fold, as its shape is critical to such interactions.

The generative capabilities of DNA language models also allow researchers to predict how new mutations may arise in genome sequences. For example, scientists developed a genome-scale language model to predict and reconstruct the evolution of the SARS-CoV-2 virus.

In recent years, biologists have realized that parts of the genome previously termed junk DNA interact with other parts of the genome in surprising ways. DNA language models offer a shortcut to learn more about these hidden interactions. With their ability to identify patterns across long stretches of DNA sequences, language models can also identify interactions between genes located on distant parts of the genome.

In a new preprint hosted on bioRxiv, scientists from the University of California-Berkeley present a DNA language model with the ability to learn genome-wide variant effects. These variants are single-letter changes to the genome that lead to diseases or other physiological outcomes and generally require expensive experiments (known as genome-wide association studies) to discover.

Named the Genomic Pre-trained Network (GPN), it was trained on the genomes of seven species of plants from the mustard family. Not only can GPN correctly label the different parts of these mustard genomes, it can also be adapted to identify genome variants for any species.

In another study published in Nature Machine Intelligence, scientists developed a DNA language model that could identify gene-gene interactions from single-cell data. Being able to study how genes interact with each other at single-cell resolution will reveal new insights into diseases that involve complex mechanisms. This is because it allows biologists to pin variations between individual cells to genetic factors that lead to disease development.

Language models can have problems with hallucination whereby an output sounds sensible but is not rooted in truth. ChatGPT, for example, could hallucinate health advice that is essentially misinformation. However, for protein design, this creativity makes language models a useful tool for designing completely new proteins from scratch.

Scientists are also applying language models to protein datasets in an effort to build on the success of deep learning models like AlphaFold in predicting how proteins fold. Folding is a complex process that enables a protein which starts off as a chain of amino acids to adopt a functional shape. Because protein sequences are derived from DNA sequences, the latter determine how the former fold, raising the possibility that we may be able to discover everything about protein structure and function from gene sequences alone.

Meanwhile, biologists will continue to use DNA language models to extract more and better insights from the large amounts of genome data available to us, across the full range and diversity of life on Earth.

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DNA sucked into air filters can reveal what plants and animals are … – Lincoln Journal Star

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NEW YORK DNA is all around us even in the air we breathe. Now scientists found that air quality monitoring stations which pull in air to test for pollution also pick up lots of DNA that can reveal what plants and animals have been in the area.

The method could help solve the tricky challenge of keeping tabs on biodiversity, according to a recent study in the journal Current Biology.

The findings suggest biodiversity data has been collected "on massive scales literally for decades and nobody's noticed," said study author Elizabeth Clare, a biologist at Canada's York University.

As animals and plants go through their life cycles, they leave little bits of themselves in the environment scales, fur, feathers, pollen that carry their genetic signature.

Scientists have long known this kind of environmental DNA floats around in water and used it to track what species are swimming in lakes and rivers. It's been harder to get a genetic picture of what's roaming around on land, said Kristine Bohmann, who studies environmental DNA at the University of Copenhagen and was not involved with the latest study.

Air sampling filters stationed in June 2023 at the Auchencorth Moss research facility in Scotland.

In 2021, both Bohmann and Clare worked on similar projects to see whether they could pull animal DNA from the air. After setting up vacuum pumps in local zoos, the teams were able to sequence DNA from dozens of species.

"You can actually, in a Ghostbuster kind of way, vacuum DNA out of the air," Bohmann said.

Then researchers wanted to try that on a bigger scale.

For this latest study, Clare and her team tested air filters from two monitoring stations, one in London and one in Scotland, that are part of a national network to test for pollution.

After extracting DNA from pieces of the filter disks, the scientists were able to identify more than 180 different kinds of plants and animals, said study author Joanne Littlefair, a biologist at Queen Mary University of London.

The filters picked up on a wide range of wildlife, including grasses, fungi, deer, hedgehogs and songbirds along with "the ubiquitous pigeon," Littlefair said.

Now, the team hopes this method could track ecosystems all over the world. Even though biodiversity decline is a global issue, it's hard to test for on a large scale, Clare said.

It's easy to use systems that are already in place, pointed out James Allerton, an air quality scientist at the UK's National Physical Laboratory. Many countries have networks set up to monitor air quality, and some of them store their old filters for years or even decades an archive that could help show how ecosystems have changed over time.

More research is needed to see if the data from these filters can show real biodiversity trends over time, said Fabian Roger, who has been working on a similar project at ETH Zurich in Switzerland. Still, it's exciting that an existing system could be "co-opted" to monitor wildlife, he wrote in an email.

Alyssa Bennett, small mammals biologist for the Vermont Department of Fish and Wildlife, inspects a dead bat in a cave in Dorset, Vt.

Laura Kloepper, right, a visiting assistant professor at the University of New Hampshire, carries out research with students in a bat cave May 2 in Dorset, Vt.

Researchers shine light on clusters of bats roosting in a cave in Dorset, Vt., on May 2. Scientists studying bat species hit hard by the fungus that causes white nose syndrome, which has killed millions of bats across North America, say more bats that hibernate at the Vermont cave are tolerating the disease and passing protective traits on to their young.

Alyssa Bennett, small mammals biologist for the Vermont Department of Fish and Wildlife, points to a bat in a cave in Dorset, Vt., on May 2. Scientists studying bat species hit hard by the fungus that causes white nose syndrome, which has killed millions of bats across North America, say there is a glimmer of good news for the disease. Experts say more bats that hibernate at a cave in Vermont, the largest bat cave in New England, are tolerating the disease and passing protective traits on to their young.

Bats roost in a cave in Dorset, Vt., on May 2. Scientists studying bat species hit hard by the fungus that causes white nose syndrome, which has killed millions of bats across North America, say there is a glimmer of good news for the disease. Experts say more bats that hibernate at a cave in Vermont, the largest bat cave in New England, are tolerating the disease and passing protective traits on to their young.

Laura Kloepper, a visiting assistant professor at the University of New Hampshire in the Department of Biological Sciences and the Center for Acoustics Research and Behavior Lab, carries out research in a bat cave in Dorset, Vt., on May 2. Scientists studying bat species hit hard by the fungus that causes white nose syndrome, which has killed millions of bats across North America, say there is a glimmer of good news for the disease.

Bats roost in a cave May 2 in Dorset, Vt., where some of the mammals are tolerating a deadly disease and passing protective traits on to their young.

Alyssa Bennett, small mammals biologist for the Vermont Department of Fish and Wildlife, reaches toward roosting bats in a cave in Dorset, Vt., on May 2. Scientists studying bat species hit hard by the fungus that causes white nose syndrome, which has killed millions of bats across North America, say there is a glimmer of good news for the disease. Experts say more bats that hibernate at a cave in Vermont, the largest bat cave in New England, are tolerating the disease and passing protective traits on to their young.

Alyssa Bennett, small mammals biologist for the Vermont Department of Fish and Wildlife, stretches the wings of a dead bat in a cave in Dorset, Vt.

Alyssa Bennett, small mammals biologist for the Vermont Department of Fish and Wildlife, holds a dead bat in a cave in Dorset, Vt., on May 2, 2023. Scientists studying bat species hit hard by the fungus that causes white nose syndrome, which has killed millions of bats across North America, say there is a glimmer of good news for the disease. Experts say more bats that hibernate at a cave in Vermont, the largest bat cave in New England, are tolerating the disease and passing protective traits on to their young.

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DNA sucked into air filters can reveal what plants and animals are ... - Lincoln Journal Star

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