Suddenly Miners Are Tearing Up the Seafloor for Critical Metals On that summer morning, I arrived on a red catamaran after rolling over six-foot swells in the South Pacific for two hours, and I clambered up a metal ladder hanging down on the Coco's starboard side. I was there at the invitation of Richard Parkinson, who founded Magellan, a company that specializes in deep-sea operations. Inside the hushed cabin was a young Brazilian named Afhonso Perseguin, his face lit by screens displaying digital readings and colorful topographic charts. I watched on monitors as a robotic arm protruded from the ROV toward a monstrous set of clamshell jaws suspended from a cable that rose all the way up to the ship. Perseguin used the ROV's arm to steer the jaws as a colleague beside him radioed instructions to a winch operator on deck. If you're enjoying this article, consider supporting our award-winning journalism by subscribing. By purchasing a subscription you are helping to ensure the future of impactful stories about the discoveries and ideas shaping our world today. Hydraulics drove the open clamshell into a gray chunk of flat seafloor ringed by rocky mounds and jagged slopes. Small mollusk shells dotted their surface; a crab scuttled out of frame. “Quite amazing, really, isn't it?” murmured John Matheson, a shaven-headed Scot supervising the ROV team. The metal-rich magma ejected over millennia from several such vents—some dormant, some still active like this one—was Magellan's prize. Worldwide, oceanographers have found three distinct types of mineral deposits on the deep seafloor. Manganese crust is an inches-thick, metal-rich pavement that builds up over millions of years as dissolved metallic compounds in seawater gradually precipitate on certain seafloor regions. Polymetallic nodules are softball-size, metal-rich rocks strewn across enormous seafloor fields. Over the past decade several companies have developed detailed but still hypothetical plans to profit from these deposits, hoping to help meet the world's surging demand for the valuable metals necessary for batteries, electric cars, electronics, and many other products. Scientists have warned that these efforts risk destroying unique deep-sea habitats that we do not yet fully understand, and governments have been reluctant to grant exploration licenses in their territorial waters. But from what I saw during my two days and one night onboard the Coco, DSMF was digging in, and a new era of deep-sea mining had all but begun. Holt, one of Magellan's offshore managers, said the aim was to test the physical requirements and environmental impacts of pulling up sulfide deposits. Crew members who had already completed dozens of similar lifts said this loss was an unusual occurrence. The Coco had been bringing up a jaw-load roughly every 12 hours. Just before this latest cache was swung onboard, an Australian marine scientist named Josh Young had been preparing to drop his testing equipment over the ship's side. Using another winch, Young lowered a ring of long plastic cylinders known as Niskin tubes into the surf. Each sampling tube was set to open at a different depth as the ring passed down through the water column for several thousand feet. Peering over his shoulder, I watched an electronic screen reveal the water's temperature, acidity, salinity, density, cloudiness and oxygen content, as well as its oxidizing capacity and conductivity—proxies for water cleanliness—at each depth. Like many offshore projects, the Coco operation was globalization incarnate. Magellan also hired the South African and British deckhands helping Young, plus the ROV team and a number of Malaysian hydrographic surveyors. Up on the ship's bridge, Holt told me this enormously expensive exercise was to better understand the speed and power requirements of this mining technique, which relied on off-the-shelf commercial equipment Magellan had modified for underwater use. His remit was also to quantify the environmental impacts that a future vessel even larger than the 270-foot Coco might generate through similar extraction cycles. “We haven't got huge clouds of sediment that are drifting off down in the current, smothering coral reefs, or all this sort of stuff that people are worried about.” I observed the same 12-hour extraction cycle twice during my time onboard. Holt told me that over nearly two months Magellan's teams were focusing on four separate locations in a wider area collectively designated Solwara 1. He said PNG's Mineral Resources Authority, or MRA, had approved the extraction of about 200 tons of material—from an ore body estimated at more than two million tons—for removal and further testing on shore. As with any mining endeavor, Solwara 1's long-term economic viability would live and die on global metal prices, and in this case the ore's copper concentration was a crucial factor. Two local geologists onboard seemed enthralled by their initial readings. Leaning over the pile of dark-gray rock that had been dumped onto the rear deck—after it had been smashed into pieces by a large drill—Paul Lahari grabbed some samples and carried them into a cramped prefab shipping container that served as a laboratory. “Anything to do with 0.5 or 1 percent, we're already excited,” said the Papua New Guinean, who had decades of onshore and offshore mining experience. He was referring to the typical copper concentrations in ore mined on land. Inside the lab he wielded a small instrument that measures x-ray fluorescence, which he said would reveal the elemental composition of each sample. “That's 10 times more than we get on land,” Lahari said, his voice rising. All 200 tons the Coco recovered and carried onboard would eventually reach an Australian facility, where the rock would be further pulverized. Much smaller samples would then pass through a gauntlet of geochemical tests—heating, fusing, leaching—and the entire batch would be assigned an industry-recognized average copper concentration, or “grade,” alongside a report on the other metals found, including gold. Oceanographers have identified massive sulfide deposits across the Atlantic, Pacific, Indian and Arctic Oceans. Small-scale sample drilling has shown that they often contain similarly high concentrations of copper, alongside zinc and lead. Deposits form close to, if not on, the seafloor surface, meaning there's far less “overburden”—the valueless material that must be removed to access the ore—than in most land-based mines. Other prospectors have been interested in Solwara's potential for years. The country's taxpayers thus became a junior partner with Nautilus. A coastal nation controls resource exploitation in the waters constituting its exclusive economic zone, which reaches 200 nautical miles out from its shoreline in all directions. Any activities in the international waters between nations' economic zones, such as deep-sea mining, are regulated by the International Seabed Authority, or ISA, a body established through a treaty sponsored by the United Nations. A Papua New Guinea governor wrote in a statement that he considered the “presence of any [mining] vessel or activity in the area to be illegal.” Its remaining assets included the mining permit, a few promising core samples, and the three tracked vehicles, only ever tested in shallow waters, that sat rusting on the edge of PNG's capital, Port Moresby. After its insolvency, PNG Prime Minister James Marape told a local newspaper that the country had wasted tens of millions of dollars on a “concept that is a total failure.” In 2020 the head of the MRA ruled out any chance of reviving the Solwara project. In blazing afternoon sunshine, a much smaller skiff ferried me back to a remote, pebbly beach on the PNG island of New Ireland. I wanted to know how PNG's officials and citizens felt about the Coco pulling up their seafloor. A local driver I had hired drove me in the dark over bumpy coastal roads to a guesthouse in the village of Kono. The following morning I sat outside at a rickety wood table, sharing a breakfast of fish, yams and crackers with some of the local men. A Fiji-based environmental campaigner had introduced me to him via an encrypted messaging app. He walked to the home of Kono's chief, Chris Malagan, to discuss what I had told him ahead of a weekly public meeting Malagan presides over, which attracts many of the village's 700 residents. Malagan began that afternoon's meeting underneath large shoreline trees. Nearby, children waded out from the beach to cast lines for small fish in the shallows close to more than a dozen mud and straw huts. Adults sitting among the trees listened intently to Mesulam's description of the Coco's operations, which was based on my eyewitness account. “After all our efforts on campaigning against seabed mining, we thought it was a dead issue now,” he continued, becoming occasionally tearful. “We don't want to be used as guinea pigs for trial and error,” he said. “These metals that are going to be dug out of our ocean will not benefit anyone from here because nobody here is using electric cars.” To better understand the political support and permitting process for deep-sea mining, I left New Ireland on a plane headed to Port Moresby. The capital, with its sprawling neighborhoods, is built around a spectacular natural harbor. He told me neither Nautilus's 25-year environmental permit nor the MRA's subsequently issued mining license for Solwara 1 had ever been made public—despite a constitutionally mandated transparency requirement and a decade-long legal battle waged by good-governance and environmental groups. (Parkinson sent me the cover page of the license, but neither he nor Magellan nor PNG regulators provided a full copy.) Such opaqueness was common in PNG, Bosip told me, but meant it was difficult for local communities to hold international companies to account for potential environmental infractions. “In PNG,” he told me, “the system is such a way that the responses are not forthcoming.” He apparently meant that government ministries, agencies and regulators rarely shared information willingly. A document from the Supreme Court of British Columbia shows that DSMF's listed representatives during those proceedings were Christopher Jordinson, an Australian who'd previously pled guilty to insider trading, and Matthias Bolliger, a Swiss national who was subsequently barred from directorships on the Isle of Man. Documents from the bankruptcy proceedings show the pair are listed as points of contact for DSMF's largest shareholders: Omani tycoon Mohammed Al Barwani, whose family firm owns oil, gas and mining subsidiaries, and Alisher Usmanov, who is among Russia's wealthiest pro-Putin oligarchs. Parkinson told me that in November 2023 he, Bolliger and Jordinson met with New Ireland's governor. I spent days chasing down officials across Port Moresby, trying to get clarity on this approval process. After unanswered e-mails and unreturned phone calls, I finally reached the MRA's managing director, Jerry Garry, by video call. He was in a remote highland region that was slated to host a gold mine, he said, but he told me his officials should be onboard any deep-sea-mining vessel in PNG to monitor operations. PNG's attorney general, Pila Kole Niningi, didn't reply to interview requests. I did reach Fiona Pagla, the PNG Department of Justice's acting director for the national oceans office, who was at a conference in Bali. She told me that she knew nothing about the Coco but that if it was conducting marine scientific research, a committee inside her department should have been asked for approval. Hours later, when I pressed her for details in WhatsApp messages, Pagla replied, “No comment.” The country's environment minister, Simon Kilepa, didn't make himself available for an interview. Prime Minister Marape's chief of staff insisted the premier would not discuss deep-sea mining. The site repeatedly mentioned Nautilus's mining license and environmental permits—still not public—and said PNG would gain from Solwara 1's profits and mining royalties, with benefits for local people “currently being negotiated.” Parkinson had told me soon after I'd left the Coco that Magellan and SM2 were not “cutting corners” and were “operating within the laws of that country.” He had also said the Australian lab readings indicated Solwara 1 is “a credible source of copper.” In response to a request for comment I sent in March by e-mail, DSMF wrote that the results “will be provided to the relevant regulatory authorities in due course, once the analyses by internal and third-party experts are completed.” This past January I finally, and unexpectedly, heard from Julius Chan, a PNG prime minister turned New Ireland governor with a national parliamentary seat. He'd previously said deep-sea miners should engage with islanders to provide confidence that a project wouldn't affect their livelihoods. He wrote in a statement that those involved in Solwara “certainly do not have my government support and approval” and that he considered the “presence of any vessel or activity in the area to be illegal.” He died three weeks later at age 85. In its e-mail response, DSMF wrote, “The Solwara 1 project is compliant with the regulations, having secured a valid mining license as defined in the PNG Mining Act, and is a fully permitted project having met license requirements under relevant Papua New Guinea laws and regulations.” It also noted that “the allowable impacts of mining at Solwara 1 are regulated, managed and conducted in accordance with the Mining Law and Environmental Act (2000).” The Magellan team onboard the Coco had told me it was operating with permission from the MRA, and Parkinson told me before and after my visit to PNG that government officials were aware and supportive of their large-scale extraction tests. Perhaps some people inside the government had not shared details of the Coco's mission as widely as they could have, I reasoned. But when I was onboard, there seemed to be little stopping the Solwara 1 project from scaling up significantly—unless steep capital costs somehow dissuaded deep-pocketed investors or public uproar in PNG forced a rethink among national politicians, who perhaps might have been hoping to recoup the sizable state investment Nautilus once blew through. Norway, the Cook Islands, Japan and Sweden have approved deep-sea mining in their exclusive economic zones. Norway's offshore-resources agency says the country's waters contain manganese crusts, as well as sulfide deposits, and the government had considered awarding exploitation licenses this year. Authorities in the Cook Islands have issued exploration licenses to three operators surveying for polymetallic nodules. Scientists at the University of Tokyo and collaborating institutions recently confirmed a vast nodule field close to Japan's easternmost island, a tiny atoll called Minamitorishima. A consortium of government agencies, academic institutions and private enterprises plans to extract Japan's underwater resources in the decades ahead. With enormous deep-sea regions still unmapped, scientists say similar opportunities exist elsewhere. But after a 2023 study found that some polymetallic nodules emitted enough radiation that inappropriate handling could pose health risks, questions have increased about the wisdom of nodule mining. Citing limited scientific data on long-term environmental impacts, many nations, including Germany, Spain and Chile, have called for a pause. The ISA has granted more than 30 exploration licenses for international waters, some for each of the three kinds of deposits. The authority's new secretary-general, Brazilian oceanographer Leticia Carvalho, took charge in January 2025, promising to end what she considers cozy relations between ISA and potential commercial operators. She has also suggested that the new subsea-mining code should be finalized by late this year. Unlike in the early years of, say, coal mining, environmental scientists are deeply involved in the development of seafloor extraction. A case study involving Japanese state entities digging sulfides at a similar depth, several thousand miles north in the Pacific Ocean, gives some idea of what to expect. Researchers assessed the impact on nearby ocean flora and fauna for three years after a brief mining session. They found that populations of organisms less than a tenth of an inch in size may return to normal levels within a year, but larger species may remain depleted more than three years later. In its statement, DSMF wrote, “Extensive scientific studies have enabled SMS to assess the risks to marine ecosystems and carefully weigh them against the damage caused by terrestrial mining.” The new SMS website says mining in Solwara 1 “will not adversely affect the marine life habitat” and that with recolonization efforts, three years after mining ends, the environment around any vents will “resemble the pre-mining condition of biomass and diversity.” Marine scientists I spoke to questioned that assertion. “It couldn't possibly be.” She says certain species exist only near these vents, and after mining it's “highly likely” those species will become extinct. Throughout the world's deep ocean zones, where scientists estimate thousands of species remain undiscovered, heavy mining equipment may harm organisms that are unable to quickly move out of its way. Leaks from mining equipment or mining water dumped from surface vessels could also threaten open-ocean fisheries, and noise and light pollution could impact reproduction or feeding patterns of species already threatened by other human actions. The juxtapositions I experienced at sea and on land were jarring. The informational asymmetry was striking, too: hydrographers, geologists and environmental scientists with millions of data points designed to gauge surroundings—and profits to be realized thousands of miles away—were set against local residents who seemed to lack access to attested Solwara permits, let alone details of possible environmental drawbacks. For the people who live there, short-term benefits—new local jobs, perhaps, or increased government revenues—might never outweigh stress to the ecosystem and a way of life that depends on it. As this article was going to press, senior PNG officials—including one in the country's Department of Justice—told me the questions I had asked during my reporting had prompted action. In late February the government introduced new mining legislation that, for the first time, includes specific rules for deep-sea mining. The country's Marine Scientific Research Committee, which comprises almost two dozen government entities, passed guidelines that will require future deep-sea-mining licenses to have committee approval. Because the legislation is open to public comment, it is not yet clear whether a new mining law will have retroactive force. If it does, officials told me, DSMF might have to reapply for its environmental permits and mining license and publish a fresh environmental impact assessment. Marx has written for the Wall Street Journal, Vanity Fair, Businessweek, Harpers and Wired, among other publications.

The Nontoxic Cleaner That Kills Germs Better Than Bleach—And You Can Use It on Your Skin Hypochlorous acid is safe enough to spray in your eyes yet more effective than bleach. Rubbing with soapy water and rinsing can physically remove the virus from your hands and send it down the drain but won't effectively kill it. Bleach dismantles norovirus, but you can't spray bleach on skin or food or many other things, and norovirus can live on surfaces for weeks. My dad, a now retired otolaryngologist, had been wondering whether there was something he might put up patients' noses—and his own—to reduce viral load and decrease the chance of COVID infection without, of course, irritating the mucosa or otherwise doing harm. He was imagining a preventive tool, another layer of protection for health-care workers in addition to masks and face shields. It should not be confused with sodium hypochlorite (NaClO), the main active ingredient in household bleach products, even though they both involve chlorine. Sodium hypochlorite is a strong base with a pH of 11 to 13, and when added to water for consumer products it can be irritating and toxic. If you're enjoying this article, consider supporting our award-winning journalism by subscribing. By purchasing a subscription you are helping to ensure the future of impactful stories about the discoveries and ideas shaping our world today. All mammals naturally make hypochlorous acid to fight infection. When you cut yourself, for instance, white blood cells known as neutrophils go to the site of injury, capturing any invading pathogens. Once the pathogen is engulfed, the cell releases biocides, including hypochlorous acid, a powerful oxidant that kills invading microbes within milliseconds by tearing apart their cell membranes and breaking strands of their DNA. Like most disinfectants, it kills pathogens by penetrating their cell walls. But compared with bleach, hypochlorous acid has been shown to be more than 100 times more effective at much lower concentrations, and it works much faster. It doesn't irritate the skin, eyes or lungs. In fact, optometrists use it to clean eyes before procedures, and people have been treating wounds with it for more than a century. Scientists have known about the powers of hypochlorous acid for nearly 200 years. Later in the 19th century, English chemist and physicist Michael Faraday developed a technique for synthesizing HOCl from salt and water via a process called electrochemical activation. Before the advent of antibiotics, hypochlorous acid was a go-to disinfectant. It was used as a wound sanitizer during World War I. They compared the efficacy of sodium hypochlorite (bleach) with that of hypochlorous acid and “found that hypochlorous acid is a more potent germicide than its salts.” They “accordingly devised a method in which the free acid is employed as the antiseptic agent.” For all its benefits, hypochlorous acid solution has one major weakness: it's highly unstable. Within minutes of exposure to light or air hypochlorous acid starts to deteriorate back into salt water, making it useless as a disinfectant. If the solution were to get too acidic, it would start converting into chlorine gas. For decades hypochlorous acid lingered in the background, used as a disinfectant in specific industrial and commercial contexts that could justify a pricey, on-site manufacturing process to create products on demand. But COVID accelerated the need for different methods of disinfection that would be safe, effective and easy to use in a wide range of environments. According to an article in the magazine Health Facilities Management, during the pandemic “many countries introduced continuous HOCl misting and fogging tunnels for entry and exit corridors at mass transit facilities.” Since then, use of HOCl in places such as kitchens, gyms, nursing homes and medical offices has been rising significantly. Hypochlorous acid consumer products are now proliferating, thanks to the development of new manufacturing processes that reportedly make an extended shelf life possible while keeping costs low. Most common are surface sanitizers sold by the bottle and marketed as all-purpose disinfectants for your home, although pure hypochlorous acid isn't really a cleaner—it's not meant to get rid of grime and grease. Like all disinfectants, once hypochlorous acid is applied, it must be left to sit for a period of time. A frustrating thing about the finicky nature of hypochlorous acid is that you can't really decant it from its original bottle into a smaller one without potentially affecting its quality and longevity. When I needed hypochlorous acid that was suitable for air travel, I had to buy a two-ounce bottle of Magic Molecule, an FDA-cleared product launched in 2023. These bottles are conveniently sized but don't last long, and not being able to refill them results in significant plastic waste. Other companies have taken a different approach to the shelf-life problem. Force of Nature also includes vinegar in its formulation, which gives the product cleansing abilities that the company recommends for use on hard surfaces or carpets. Other businesses sell devices that let you add your own salt. In online forums dedicated to fans of hypochlorous acid, members discuss how they use these devices. Some use pH test strips to make sure each batch of hypochlorous acid is within the correct range. Some people, however, are skeptical that at-home machines can consistently make pure HOCl. Last December, troubled by Reddit posters' descriptions of suffering with norovirus, I bought a range of products from Briotech, a company based in Washington State that has been around for years and has coordinated its research with the University of Washington. Briotech sells different concentrations and formulations, including a “skin renew serum” at 0.018 percent concentration (or 180 parts per million) and a stronger gel for taking care of body piercings. Magic Molecule calls its hypochlorous acid an “antimicrobial skin cleanser” under the umbrella of “wound care,” marketing it as a treatment for acne, eczema, rashes, bug bites, and other concerns. It's currently sold online and, as of this year, at the beauty-supply shop Ulta. If I didn't already know about hypochlorous acid, my skepticism radar would have been on highest alert. I might have dismissed hypochlorous acid as just another snake oil. But it's not just the beauty industry showing new interest in HOCl. Research into medical uses for hypochlorous acid has expanded as well. Before the pandemic, it was known that low levels of hypochlorous acid showed some promise in reducing the symptoms of viral and bacterial infections in nasal epithelial cells, but it was unclear how well people would tolerate HOCl administered straight up the nose as an irrigation or a spray. At one hospital in Reading, Pa., for example, 74 COVID-positive patients, all of whom were unvaccinated, completed an experimental course of treatment that involved using a neti pot to rinse their nose with a hypochlorous acid solution for 10 days. Participants used Vashe Wound Solution, a hypochlorous acid that is safely used to treat wounds on skin or eyes and in the mouth. The reported adverse reactions were mild—a sensation of nasal burning, a nosebleed that stopped on its own—and the researcher suggested this application would be safe and effective, albeit one that requires more investigation. Other studies have since shown hypochlorous acid to be effective in reducing symptoms in a range of upper respiratory infections—and, more important, that it does not cause adverse effects. In Europe, Sentinox, an over-the-counter nasal spray containing a low concentration of HOCl (0.005 percent), is already certified as a medical device to reduce the risk of infection from viruses and bacteria, including SARS-CoV-2, by lowering the microbial load in the nose. In a randomized, controlled trial published in 2022, researchers used Sentinox on people with COVID and reported good outcomes with no evidence of safety concerns. I sprayed down my phone case, sink faucets, toothbrush bristles and car steering wheel. I spritzed my face, hands and water bottle multiple times during workouts at the gym. At a restaurant, I watched a server deliver my drink by holding the rim of my glass, so out came the bottle. I refrained from spraying my friend's toddler as I anxiously tracked his germy behavior while he moved across a carpeted airport floor. Here's what happened: I got sick with type A influenza. My husband got it first, and I didn't try to avoid the inevitable. Just after recovering from the flu, I picked up COVID at a large family gathering. Given the nature of airborne respiratory viruses, these events didn't sour me on HOCl. I was diligent about spritzing myself and objects of potential exposure during travel, but it's not like I was excusing myself from dinner conversations to take a huff of the stuff. As of this writing, I have not been sickened by norovirus, and I'd like to believe my judicious use of HOCl has something to do with that. If more people were aware of this molecule, maybe they would swap their Purell bottles and Clorox bleach for a more effective, safer option. (One product called a “norovirus cleanup kit” contains hypochlorous acid.) Hypochlorous acid has been shown to work against avian influenza. If bird flu becomes the next pandemic, HOCl could be one potentially effective mode of virus control that's easily available and cheap to access. Fogging machines could be used to clean surfaces and objects in medical settings, for example. Notably, few of these products are specifically marketed as hand sanitizers, at least in the U.S. (A U.K. company does make a hypochlorous acid sanitizing hand gel approved by European regulatory agencies.) But if the efficacy of the product depends on its long-term stability, how much can you trust a bottle that's lived in your car for six months? Hypochlorous acid sprays now show up in my social feeds, promoted by influencers gushing about their skin-rejuvenating properties. If I hadn't first encountered this disinfectant in academic literature, I might have scrolled right past these ads, dismissing hypochlorous acid as just another snake oil sold to exploit people's fears. Hypochlorous acid might go through rigorous regulatory channels if it's pursued as an intranasal spray that prevents infection by killing viruses before they get into the lungs. Trump was rightly skewered by experts (and many others) for promoting dangerous advice. It goes without saying that bleach, the disinfectant in question, should never be injected into your body. But behind Trump's misinterpretation of whatever medical information had been shared with him prior to that press conference was the seed of an idea: What if a disinfectant could do a type of cleaning, as it were, knocking out virus particles in less than a minute? With norovirus still circulating and the possibility of a bird flu spillover, the potential uses of hypochlorous acid might be worth a closer look. The Next Flu Pandemic Could Be Worse Than COVID If We Don't Heed History. Jen Schwartz is a senior features editor at Scientific American. She produces stories and special projects about how society is adapting—or not—to a rapidly changing world.

Mathematicians' Favorite Shapes Hold the Key to Big Mathematical Mysteries But to mathematicians, shapes encompass a vast universe of surprising forms, from one-dimensional loops to polytopes (geometric objects with flat sides that can exist in any desired dimension). A related category, surfaces—collections of points that form boundaries in 3D space—includes an entire zoo of striking, strange mathematical objects. Some mathematicians love shapes that are deeply connected to the physical world, such as Borromean rings, which are related to regular hair braids, and the permutahedron, which is the basic shape of a zeolite crystal (a material widely used in industrial applications). Others favor more abstract options that represent higher-dimensional realms seemingly divorced from the world we live in. If you're enjoying this article, consider supporting our award-winning journalism by subscribing. By purchasing a subscription you are helping to ensure the future of impactful stories about the discoveries and ideas shaping our world today. My favorite shape is the loop, a circle with all geometric information stripped away, leaving only a free-form one-dimensional object. Surprisingly, we have a good sense of what every possible closed manifold looks like, provided it is one-, two- or three-dimensional or five-or-more-dimensional, but we know little about how four-dimensional manifolds can look. In this framework, the only one-dimensional closed manifold is a loop. The loop is also ubiquitous throughout different fields of topology, often in a very crucial way. For example, the most fruitful and important invariant in topology is arguably the fundamental group, an algebraic object that counts how many ways a loop can be squeezed inside a space. And knot theory is an entire field of math focusing on the question “What are all the ways a loop can be tangled in three-dimensional space?” There is still so much to be learned about loops. This is all metaphor—by “geometric diamond,” I mean it isn't just topological; it has geometry to it, and “diamond” is supposed to make you think of a rigid gemstone. It is a gem, as in a singular, beautiful object, and it is rigid in the sense that you cannot change its geometry—the geometry is unique. “Impossibly hard” is also trying to express this rigidity. Riley showed that the complement of the figure-eight knot has a complete hyperbolic metric—in fact, a unique such metric. [“Hyperbolic” refers to a hyperbola, an open-ended curve.] This means that, for example, it makes sense to ask what its volume is given this unique metric. (It holds approximately 2.03 units of hyperbolic volume.) Soon after, mathematician William Thurston, then at Princeton University, vastly extended Riley's insight, showing that in a certain sense almost all knots have hyperbolic complements. Natural numbers are either composite or prime, depending on whether you can factor them into smaller pieces that then multiply together to give the number you started with. There is a similar situation with knots—instead of multiplication to combine two numbers to make a bigger number, an operation called connect sum combines two knots into a single, bigger knot. People usually care only about prime knots because you can usually understand any composite knot by breaking it up into its prime knot factors first. My favorite shape—and one I think about every day—is called the hyperbolic pair of pants. It is a surface with the shape of a pair of pants, meaning it has three boundary components (a waist and two ankles) and genus 0 (no handle, as opposed to your coffee mug). What makes this shape so special is that to every three lengths a, b and c, we can associate one and only one hyperbolic pair of pants of boundary lengths a, b and c. Thus, the same way that you know how to draw “the rectangle of edges 2 and 3.5,” it makes sense to talk about “the hyperbolic pair of pants of boundaries 1, 6 and 2.4.” You can play and sew hyperbolic pairs of pants together. When you sew two pairs of jeans along their beltlines, an important decision is whether to line up their buttons and, if not, how much to twist. We can construct every hyperbolic surface by sewing together hyperbolic pairs of pants and describe all of them entirely in terms of the boundary lengths and twist angles in this decomposition. They are commonplace because we learn about two-dimensional versions of these shapes as children: triangles, squares, dodecahedrons, and other convex polygons [a polygon is any flat shape made with straight lines; a convex polygon has internal angles that are all less than 180 degrees]. They become complex quickly as one considers higher-dimensional versions of them, called polytopes, and recognizes the myriad pure and applied mathematical connections they have. If one is able to encode data from one mathematical setting as 0/1 coordinates, then the convex hull of those points [the smallest convex shape enclosing the points] describes a polytope. For example, the set of subsets of size 2 over three elements produces the three coordinate points (1,1,0), (1,0,1) and (0,1,1), whose convex hull is a triangle in three-dimensional space. What may be hard to state in one area may suddenly be easier to state using polytopal language. It is these kinds of relationships between various mathematical areas, as well as the pursuit of exploring polytopes in their own right, that keep my attention on these simple yet complicated shapes. One shape that I find really cool is known as the permutahedron (sometimes spelled permutohedron). This is a very symmetrical convex polytope that exhibits many special properties. First, what does it mean for a shape to be convex? Think of it like this: if you pick any two points inside the shape and draw a straight line between them, that line will always stay inside the shape. A convex polytope can be thought of as a shape with flat sides that may exist in any dimension: the zero-dimensional polytopes are points, the one-dimensional polytopes are line segments, and the two-dimensional polytopes are polygons. In three dimensions, we have polyhedra; in general, we have d-polytopes for any dimension d. For example, I like to think about convex polytopes in three dimensions as taking some points, throwing them in space and then sealing them in plastic wrap as tightly as you can. In two dimensions, we can think about points being represented by the heads of nails, wrapping a rubber band around the nails and letting the rubber band snap, creating a polygon. Say you have a set of numbers 1, 2 and 3. You can arrange those three numbers in different orders: (1,2,3), (1,3,2), (2,3,1), and so on. This polytope is actually a truncated octahedron, a shape with 14 sides (six squares and eight regular hexagons). And truncated octahedra can create a space-filling tiling of 3-space. You might have seen this beautifully symmetrical shape in your neighborhood playground; my chemist friend Juliana Velasquez Ochoa of the University of Bologna tells me it is the basic shape in a zeolite crystal. The San Francisco Exploratorium has a pile of identical bright-red permutahedra; when you play with them, you quickly notice that they stack perfectly, tiling [filling] space with no empty space between them. How do we place 24 vertices in space to make the permutahedron Π4? My favorite way is to place them in four-dimensional space. You can just substitute any value n instead of the number 4. (Why don't you try it for n = 3?) So as I alphabetize the stack of final projects of my 18 combinatorics students, I am taking a stroll around Π18 in 18-dimensional space. I love the permutahedron because it is the site of a beautiful, productive dialogue among geometry, algebra and combinatorics [the study of counting, permutations and combinations]. A common joke in my research area is that everyone's favorite surface is the genus 2 surface [a surface with two holes in it] because it's the lowest-genus (closed) hyperbolic surface and, as such, is often the default example drawn in lectures and talks. The Loch Ness monster surface is arguably the “simplest” infinite-type surface, yet its group of topological symmetries known as the mapping class group contains every countable group as a subgroup. Even stronger, there exists a complete hyperbolic metric on the Loch Ness monster surface whose isometry group (the group of geometric symmetries) is G if and only if G is a countable group. So even though the Loch Ness monster surface may appear quite simple in the wild world of infinite-type surfaces, it captures some pretty neat phenomena. I'm a topologist, so I'm enthusiastic about a lot of surfaces and shapes, but probably my favorite surface in the sense of a two-dimensional manifold [a surface that behaves like regular space at the local level] is ℝℙ2, or two-dimensional real projective space. This surface can also be thought of in the following way: Take a Mobius band [essentially a strip of paper twisted once with its ends attached] and a disk. This surface is the first step in an important construction in topology, which is to take the set of lines in all spaces ℝn, for any dimension n, at the same time. (Equivalently, you can take the set of lines in ℝ∞. This space, called ℝℙ∞, has deep connections to many features of topology I like, such as realizing fairly abstract algebraic invariants in terms of maps between spaces, studying vector fields on manifolds and studying the behavior of simple symmetries on spaces. These shapes have amazing ramifications in classical topology. The shapes shown here come from a 1930 paper by Polish mathematician Kazimierz Kuratowski. In it, he discusses peanian continua, which are, roughly speaking, simple closed curves in the plane or Euclidean 2-sphere. A simple closed curve is a continuous curve that doesn't intersect with itself and ends at the same point where it started. Some examples of simple closed curves are shapes represented by circles, ellipses, squares and regular polygons. Kuratowski proved that a peanian continuum containing only a finite number of simple closed curves is homeomorphic [topologically equivalent] to a subset of the plane if and only if it does not contain a topological image of either curve 1 or curve 2. William W. S. Claytor was the third African American to earn a Ph.D. in mathematics. In his 1933 doctoral dissertation, Claytor describes a more general problem that built on Kuratowski's 1930 theorem. Claytor began his problem by focusing on curves 1 and 2. Whereas Kuratowski had restricted the peanian continua to those containing only a finite number of simple closed curves, Claytor imposed no such restriction. I find the three-dimensional representation of 4D objects called ribbon knots very cool. Here's how such a representation is constructed: Take a finite collection of disks, cut slits into them, then add bands between the boundaries of the disks that are allowed to pass through these slits. Therefore, a ribbon knot is an example of the simplest possible type of knot in 4D, and the process of making a ribbon disk gives us a 3D way to construct it. The slice-ribbon conjecture, a major open problem in low-dimensional topology, says every such simple knot in 4D comes from a ribbon disk. I find the shape fascinating because it is a simple construction that underlies a difficult—and impossible to fully visualize—process in 4D space. My favorite shape, the cycloid, has all of these. The resulting curve was named the cycloid by Galileo Galilei, and he is just one of the eminent mathematicians who have been fascinated by it (the list also includes Marin Mersenne, Pierre de Fermat, René Descartes, Blaise Pascal and Isaac Newton). Bizarrely, it's also the solution to another problem about motion. This surface has intrigued mathematicians because of its elegant shape and structural properties. It was discovered in 1744 by Swiss mathematician Leonhard Euler, who proved that the catenoid is a minimal surface, meaning it has the least possible area for a given boundary. This property can be beautifully observed with a soap film, which naturally forms a catenoid when stretched between two circular rings. What makes the catenoid even more special is that besides the plane, it is the only minimal surface that can be obtained as a surface of revolution [a surface created by rotating a curve once around]. Since the 18th century, catenary curves have also been a great source of inspiration in architecture because they distribute forces in a way that makes them ideal for building arches. Catenary arches can be found in many churches and cathedrals, as well as in other architectural masterpieces such as La Pedrera in Barcelona, designed by Antoni Gaudí. Gaudí, a visionary architect, embraced the catenary's natural strength and beauty, incorporating the shape into his designs to create aesthetically stunning and structurally efficient structures. My favorite shape is probably the Borromean rings because they embody many seemingly contradictory properties all at once. They possess a natural symmetry yet cannot be formed from perfect circles. The Borromean rings can also be viewed as a “closed” braid. In this context, they provide the simplest nontrivial example of a so-called Brunnian braid, which becomes “unbraided” as soon as one strand is pulled out. It is somewhat challenging (but always possible) to form braids with this property when using four or more strands, but in fact the most familiar of all braids is Brunnian—the standard hair braid gives rise to the Borromean rings. My own research focuses on symmetries of surfaces, and Brunnian braids play a fundamental role here, arising naturally in algebraic structures that model the motion of points on a plane. Rachel Crowell is a Midwest-based writer covering science and mathematics. Violet Frances began her illustration career at Scientific American in the mid-1990s. Her award-winning work has been featured in publications such as National Geographic, Wired and the Atlantic. Subscribe to Scientific American to learn and share the most exciting discoveries, innovations and ideas shaping our world today. Scientific American maintains a strict policy of editorial independence in reporting developments in science to our readers.

Mathematicians' Favorite Shapes Hold the Key to Big Mathematical Mysteries But to mathematicians, shapes encompass a vast universe of surprising forms, from one-dimensional loops to polytopes (geometric objects with flat sides that can exist in any desired dimension). A related category, surfaces—collections of points that form boundaries in 3D space—includes an entire zoo of striking, strange mathematical objects. Some mathematicians love shapes that are deeply connected to the physical world, such as Borromean rings, which are related to regular hair braids, and the permutahedron, which is the basic shape of a zeolite crystal (a material widely used in industrial applications). Others favor more abstract options that represent higher-dimensional realms seemingly divorced from the world we live in. If you're enjoying this article, consider supporting our award-winning journalism by subscribing. By purchasing a subscription you are helping to ensure the future of impactful stories about the discoveries and ideas shaping our world today. My favorite shape is the loop, a circle with all geometric information stripped away, leaving only a free-form one-dimensional object. Surprisingly, we have a good sense of what every possible closed manifold looks like, provided it is one-, two- or three-dimensional or five-or-more-dimensional, but we know little about how four-dimensional manifolds can look. In this framework, the only one-dimensional closed manifold is a loop. The loop is also ubiquitous throughout different fields of topology, often in a very crucial way. For example, the most fruitful and important invariant in topology is arguably the fundamental group, an algebraic object that counts how many ways a loop can be squeezed inside a space. And knot theory is an entire field of math focusing on the question “What are all the ways a loop can be tangled in three-dimensional space?” There is still so much to be learned about loops. This is all metaphor—by “geometric diamond,” I mean it isn't just topological; it has geometry to it, and “diamond” is supposed to make you think of a rigid gemstone. It is a gem, as in a singular, beautiful object, and it is rigid in the sense that you cannot change its geometry—the geometry is unique. “Impossibly hard” is also trying to express this rigidity. Riley showed that the complement of the figure-eight knot has a complete hyperbolic metric—in fact, a unique such metric. [“Hyperbolic” refers to a hyperbola, an open-ended curve.] This means that, for example, it makes sense to ask what its volume is given this unique metric. (It holds approximately 2.03 units of hyperbolic volume.) Soon after, mathematician William Thurston, then at Princeton University, vastly extended Riley's insight, showing that in a certain sense almost all knots have hyperbolic complements. Natural numbers are either composite or prime, depending on whether you can factor them into smaller pieces that then multiply together to give the number you started with. There is a similar situation with knots—instead of multiplication to combine two numbers to make a bigger number, an operation called connect sum combines two knots into a single, bigger knot. People usually care only about prime knots because you can usually understand any composite knot by breaking it up into its prime knot factors first. My favorite shape—and one I think about every day—is called the hyperbolic pair of pants. It is a surface with the shape of a pair of pants, meaning it has three boundary components (a waist and two ankles) and genus 0 (no handle, as opposed to your coffee mug). What makes this shape so special is that to every three lengths a, b and c, we can associate one and only one hyperbolic pair of pants of boundary lengths a, b and c. Thus, the same way that you know how to draw “the rectangle of edges 2 and 3.5,” it makes sense to talk about “the hyperbolic pair of pants of boundaries 1, 6 and 2.4.” You can play and sew hyperbolic pairs of pants together. When you sew two pairs of jeans along their beltlines, an important decision is whether to line up their buttons and, if not, how much to twist. We can construct every hyperbolic surface by sewing together hyperbolic pairs of pants and describe all of them entirely in terms of the boundary lengths and twist angles in this decomposition. They are commonplace because we learn about two-dimensional versions of these shapes as children: triangles, squares, dodecahedrons, and other convex polygons [a polygon is any flat shape made with straight lines; a convex polygon has internal angles that are all less than 180 degrees]. They become complex quickly as one considers higher-dimensional versions of them, called polytopes, and recognizes the myriad pure and applied mathematical connections they have. If one is able to encode data from one mathematical setting as 0/1 coordinates, then the convex hull of those points [the smallest convex shape enclosing the points] describes a polytope. For example, the set of subsets of size 2 over three elements produces the three coordinate points (1,1,0), (1,0,1) and (0,1,1), whose convex hull is a triangle in three-dimensional space. What may be hard to state in one area may suddenly be easier to state using polytopal language. It is these kinds of relationships between various mathematical areas, as well as the pursuit of exploring polytopes in their own right, that keep my attention on these simple yet complicated shapes. One shape that I find really cool is known as the permutahedron (sometimes spelled permutohedron). This is a very symmetrical convex polytope that exhibits many special properties. First, what does it mean for a shape to be convex? Think of it like this: if you pick any two points inside the shape and draw a straight line between them, that line will always stay inside the shape. A convex polytope can be thought of as a shape with flat sides that may exist in any dimension: the zero-dimensional polytopes are points, the one-dimensional polytopes are line segments, and the two-dimensional polytopes are polygons. In three dimensions, we have polyhedra; in general, we have d-polytopes for any dimension d. For example, I like to think about convex polytopes in three dimensions as taking some points, throwing them in space and then sealing them in plastic wrap as tightly as you can. In two dimensions, we can think about points being represented by the heads of nails, wrapping a rubber band around the nails and letting the rubber band snap, creating a polygon. Say you have a set of numbers 1, 2 and 3. You can arrange those three numbers in different orders: (1,2,3), (1,3,2), (2,3,1), and so on. This polytope is actually a truncated octahedron, a shape with 14 sides (six squares and eight regular hexagons). And truncated octahedra can create a space-filling tiling of 3-space. You might have seen this beautifully symmetrical shape in your neighborhood playground; my chemist friend Juliana Velasquez Ochoa of the University of Bologna tells me it is the basic shape in a zeolite crystal. The San Francisco Exploratorium has a pile of identical bright-red permutahedra; when you play with them, you quickly notice that they stack perfectly, tiling [filling] space with no empty space between them. How do we place 24 vertices in space to make the permutahedron Π4? My favorite way is to place them in four-dimensional space. You can just substitute any value n instead of the number 4. (Why don't you try it for n = 3?) So as I alphabetize the stack of final projects of my 18 combinatorics students, I am taking a stroll around Π18 in 18-dimensional space. I love the permutahedron because it is the site of a beautiful, productive dialogue among geometry, algebra and combinatorics [the study of counting, permutations and combinations]. A common joke in my research area is that everyone's favorite surface is the genus 2 surface [a surface with two holes in it] because it's the lowest-genus (closed) hyperbolic surface and, as such, is often the default example drawn in lectures and talks. The Loch Ness monster surface is arguably the “simplest” infinite-type surface, yet its group of topological symmetries known as the mapping class group contains every countable group as a subgroup. Even stronger, there exists a complete hyperbolic metric on the Loch Ness monster surface whose isometry group (the group of geometric symmetries) is G if and only if G is a countable group. So even though the Loch Ness monster surface may appear quite simple in the wild world of infinite-type surfaces, it captures some pretty neat phenomena. I'm a topologist, so I'm enthusiastic about a lot of surfaces and shapes, but probably my favorite surface in the sense of a two-dimensional manifold [a surface that behaves like regular space at the local level] is ℝℙ2, or two-dimensional real projective space. This surface can also be thought of in the following way: Take a Mobius band [essentially a strip of paper twisted once with its ends attached] and a disk. This surface is the first step in an important construction in topology, which is to take the set of lines in all spaces ℝn, for any dimension n, at the same time. (Equivalently, you can take the set of lines in ℝ∞. This space, called ℝℙ∞, has deep connections to many features of topology I like, such as realizing fairly abstract algebraic invariants in terms of maps between spaces, studying vector fields on manifolds and studying the behavior of simple symmetries on spaces. These shapes have amazing ramifications in classical topology. The shapes shown here come from a 1930 paper by Polish mathematician Kazimierz Kuratowski. In it, he discusses peanian continua, which are, roughly speaking, simple closed curves in the plane or Euclidean 2-sphere. A simple closed curve is a continuous curve that doesn't intersect with itself and ends at the same point where it started. Some examples of simple closed curves are shapes represented by circles, ellipses, squares and regular polygons. Kuratowski proved that a peanian continuum containing only a finite number of simple closed curves is homeomorphic [topologically equivalent] to a subset of the plane if and only if it does not contain a topological image of either curve 1 or curve 2. William W. S. Claytor was the third African American to earn a Ph.D. in mathematics. In his 1933 doctoral dissertation, Claytor describes a more general problem that built on Kuratowski's 1930 theorem. Claytor began his problem by focusing on curves 1 and 2. Whereas Kuratowski had restricted the peanian continua to those containing only a finite number of simple closed curves, Claytor imposed no such restriction. I find the three-dimensional representation of 4D objects called ribbon knots very cool. Here's how such a representation is constructed: Take a finite collection of disks, cut slits into them, then add bands between the boundaries of the disks that are allowed to pass through these slits. Therefore, a ribbon knot is an example of the simplest possible type of knot in 4D, and the process of making a ribbon disk gives us a 3D way to construct it. The slice-ribbon conjecture, a major open problem in low-dimensional topology, says every such simple knot in 4D comes from a ribbon disk. I find the shape fascinating because it is a simple construction that underlies a difficult—and impossible to fully visualize—process in 4D space. My favorite shape, the cycloid, has all of these. The resulting curve was named the cycloid by Galileo Galilei, and he is just one of the eminent mathematicians who have been fascinated by it (the list also includes Marin Mersenne, Pierre de Fermat, René Descartes, Blaise Pascal and Isaac Newton). Bizarrely, it's also the solution to another problem about motion. This surface has intrigued mathematicians because of its elegant shape and structural properties. It was discovered in 1744 by Swiss mathematician Leonhard Euler, who proved that the catenoid is a minimal surface, meaning it has the least possible area for a given boundary. This property can be beautifully observed with a soap film, which naturally forms a catenoid when stretched between two circular rings. What makes the catenoid even more special is that besides the plane, it is the only minimal surface that can be obtained as a surface of revolution [a surface created by rotating a curve once around]. Since the 18th century, catenary curves have also been a great source of inspiration in architecture because they distribute forces in a way that makes them ideal for building arches. Catenary arches can be found in many churches and cathedrals, as well as in other architectural masterpieces such as La Pedrera in Barcelona, designed by Antoni Gaudí. Gaudí, a visionary architect, embraced the catenary's natural strength and beauty, incorporating the shape into his designs to create aesthetically stunning and structurally efficient structures. My favorite shape is probably the Borromean rings because they embody many seemingly contradictory properties all at once. They possess a natural symmetry yet cannot be formed from perfect circles. The Borromean rings can also be viewed as a “closed” braid. In this context, they provide the simplest nontrivial example of a so-called Brunnian braid, which becomes “unbraided” as soon as one strand is pulled out. It is somewhat challenging (but always possible) to form braids with this property when using four or more strands, but in fact the most familiar of all braids is Brunnian—the standard hair braid gives rise to the Borromean rings. My own research focuses on symmetries of surfaces, and Brunnian braids play a fundamental role here, arising naturally in algebraic structures that model the motion of points on a plane. Rachel Crowell is a Midwest-based writer covering science and mathematics. Violet Frances began her illustration career at Scientific American in the mid-1990s. Her award-winning work has been featured in publications such as National Geographic, Wired and the Atlantic. Subscribe to Scientific American to learn and share the most exciting discoveries, innovations and ideas shaping our world today. Scientific American maintains a strict policy of editorial independence in reporting developments in science to our readers.

You've always got to check inside the hidden chamber. When Pavlova and local guide Adrián Beltrán Dimas reached the bottom of the cave, having already explored all that was mapped, they opted to head into an unknown passage through a submerged entrance. The passage led to a previously unseen room in which two engraved shell bracelets sat atop stalagmites, likely as an offering, according to a translated statement from the Mexican National Institute of Anthropology and History (INAH). The explorers also found another bracelet, a giant snail shell, and pieces of black stone discs similar to pyrite mirrors—all of it dated to more than 500 years ago. The bracelets feature S-shaped symbols known as xonecuilli, zigzagging lines,a and circles to create human faces in profile. The archaeologists determined that the stalagmites were manipulated in pre-Hispanic times to give them a more spherical finish, likely to better fit with ritual needs. “Possibly the symbols and representations of characters on the bracelets are related to pre-Hispanic cosmogony regarding creation and fertility,” Cuauhtemoc Reyes Alvarez, INAH archaeologist, said in a statement. The black stone discs resemble others from nearby archaeological regions, such as El Infiernillo, along with ones from distant cultures like Huasteca. Historical reports say extreme cold forced people groups living in the Sierra de Guerrero (located over 7,850 feet above sea level and filled by dense pine and oak forests) to lower altitudes. Little is known about the Tlacotepheuas, other than 16th century historical mentions of their presence. Tim Newcomb is a journalist based in the Pacific Northwest. He covers stadiums, sneakers, gear, infrastructure, and more for a variety of publications, including Popular Mechanics. Ancient Plants May Show the Site of Jesus's Tomb Experts Found an Ancient Altar in the Wrong City A Student Sniffed Out an Ancient Circle of Stones

As the vessel itself is eroded by time, its “digital twin” still offers new insight. Finally, researchers and historians had more than eyewitness accounts to look to so that they might understand what had occurred on the night of April 14, 1912. The last living survivor, Millvina Dean, passed away in 2009. “The future of the wreck is going to continue to deteriorate over time, it's a natural process,” scientist Lori Johnson told IFLScience back in 2019. And today, in combination with modern technology like LiDAR, it's allowing researchers to craft a 3D model of the famous shipwreck to study long after the wreckage itself has deteriorated. The scan was the largest underwater 3D scan ever made, amounting to 16 terabytes of data, according to a new article from National Geographic. The undertaking involved two remote-operated aquatic robots named Romeo and Juliet surveying the site and “taking some 715,000 photos and millions of laser measurements.” This data was then used to create a full-scale digital replica of the wreckage. “The model is so densely detailed,” National Geographic reports, “...a video rendering of it can be projected to life-size in a warehouse, where researchers can walk alongside it and zoom in and out on individual features, like a steam valve from the boiler room, which the scan revealed was left open, possibly to keep an emergency generator running as the ship sank.” One person who found themselves struck by the powerful possibilities of this digitized Titanic was Parks Stephenson, a retired naval officer and Titanic historian. Stephenson had seen the wreckage in person twice, but found it limited from a research standpoint. “You can only see what's immediately in front of you,” he told National Geographic, with regards to seeing through a submersible's “roughly six-inch viewport and camera views.” He describes it as “...like being in a dark room and you have a flashlight that's not very powerful.” “They held the chaos at bay as long as possible, and all of that was kind of symbolized by this open steam valve just sitting there on the stern.” Michale Natale is a News Editor for the Hearst Enthusiast Group. As a writer and researcher, he has produced written and audio-visual content for more than fifteen years, spanning historical periods from the dawn of early man to the Golden Age of Hollywood. Ancient Plants May Show the Site of Jesus's Tomb Time Could Be Flowing in Reverse All Around Us This Strange Stuff May Be Older Than the Cosmos

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. Nature Synthesis (2025)Cite this article Metrics details Molecular daisy chains are mechanically bonded materials with unique properties and compelling structures. Despite the exploration of numerous daisy chain structures, the synthesis of a crystalline mechanically interlocked polymer comprising daisy chain units remains elusive because flexible linkers typically yield amorphous gels, while rigid structures lack processability. Here we combine supramolecular crystallization preorganization with post-insertion of mechanical bonds to address this limitation. We use a C3-symmetric tritopic monomer with ammonium moieties and oligoether arms to generate a preorganized supramolecular honeycomb-like crystalline network via complementary non-covalent interactions, in an aqueous environment. Subsequently, single-crystal-to-single-crystal transformation-directed thiol–ene click chemistry crosslinks terminal alkenes at the end of the oligoether arms using 1,2-ethanedithiol, covalently locking [c2]daisy chain linkages while preserving long-range order. This two-dimensional mechanically interlocked polymer can be exfoliated from its crystals to generate a multilayer counterpart exhibiting a 47-fold stiffness enhancement relative to its bulk parent. Moreover, the trilayer nanosheets preserve the structural integrity with the same hexagonal symmetry as the bulk parent. Our method enables the synthesis of a single-crystalline two-dimensional mechanically interlocked polymer from flexible monomers with precise synthetic control and unlocks the potential of developing mechanically interlocked materials. This is a preview of subscription content, access via your institution Subscribe to this journal Receive 12 digital issues and online access to articles $119.00 per year only $9.92 per issue Buy this article Prices may be subject to local taxes which are calculated during checkout All data that support the findings of this study are available in the Article and Supplementary Information. Crystallographic data for the structures reported in this Article have been deposited at the Cambridge Crystallographic Data Centre, under deposition numbers CCDC 2300835 for D1 and CCDC 2300836 for D2. Copies of the data can be obtained free of charge via https://www.ccdc.cam.ac.uk/structures/. Source data are provided with this paper. Gee, G. & Rideal, E. K. Reaction in monolayers of drying oils I-The oxidation of the maleic anhydride compound of β-elaeostearin. Google Scholar Sakamoto, J., van Heijst, J., Lukin, O. & Schlüter, A. D. Two-dimensional polymers: just a dream of synthetic chemists? Google Scholar Bauer, T. et al. Synthesis of free-standing, monolayered organometallic sheets at the air/water interface. Google Scholar Colson, J. W. & Dichtel, W. R. Rationally synthesized two-dimensional polymers. Google Scholar Nugent, P. et al. Porous materials with optimal adsorption thermodynamics and kinetics for CO2 separation. Google Scholar Akinwande, D., Petrone, N. & Hone, J. Two-dimensional flexible nanoelectronics. Google Scholar Bae, S.-H. et al. Integration of bulk materials with two-dimensional materials for physical coupling and applications. Google Scholar Takata, T., Kihara, N. & Furusho, Y. Polyrotaxanes and polycatenanes: recent advances in syntheses and applications of polymers comprising of interlocked structures. Google Scholar Mena-Hernando, S. & Pérez, E. M. Mechanically interlocked materials. Rotaxanes and catenanes beyond the small molecule. Google Scholar Hart, L. F. et al. Material properties and applications of mechanically interlocked polymers. Google Scholar Okumura, Y. & Ito, K. The polyrotaxane gel: a topological gel by figure-of-eight cross-links. Google Scholar Bissell, R. A., Córdova, E., Kaifer, A. E. & Stoddart, J. F. A chemically and electrochemically switchable molecular shuttle. Google Scholar Kay, E. R., Leigh, D. A. & Zerbetto, F. Synthetic molecular motors and mechanical machines. Google Scholar Feringa, B. L. The art of building small: from molecular switches to motors (Nobel Lecture). Google Scholar Stoddart, J. F. Mechanically interlocked molecules (MIMs)—molecular shuttles, switches, and machines (Nobel Lecture). Google Scholar Harada, A., Li, J. & Kamachi, M. The molecular necklace: a rotaxane containing many threaded α-cyclodextrins. Google Scholar Huang, F. & Gibson, H. W. Polypseudorotaxanes and polyrotaxanes. Google Scholar Harada, A., Hashidzume, A., Yamaguchi, H. & Takashima, Y. Polymeric rotaxanes. Google Scholar Arunachalam, M. & Gibson, H. W. Recent developments in polypseudorotaxanes and polyrotaxanes. Google Scholar Guidry, E. N., Li, J., Stoddart, J. F. & Grubbs, R. H. Bifunctional [c2]daisy-chains and their incorporation into mechanically interlocked polymers. Google Scholar Clark, P. G., Day, M. W. & Grubbs, R. H. Switching and extension of a [c2]daisy-chain dimer polymer. Google Scholar Rotzler, J. & Mayor, M. Molecular daisy chains. Google Scholar Van Raden, J. M., Jarenwattananon, N. N., Zakharov, L. N. & Jasti, R. Active metal template synthesis and characterization of a nanohoop [c2]daisy chain rotaxane. Article PubMed Google Scholar Niu, Z. & Gibson, H. W. Polycatenanes. Google Scholar Gil-Ramírez, G., Leigh, D. A. & Stephens, A. J. Catenanes: fifty years of molecular links. Google Scholar Liu, J. et al. Infinite twisted polycatenanes. Google Scholar Noda, Y., Hayashi, Y. & Ito, K. From topological gels to slide-ring materials. Google Scholar Liu, C. et al. Tough hydrogels with rapid self-reinforcement. Google Scholar Anelli, P. L., Spencer, N. & Stoddart, J. F. A molecular shuttle. Google Scholar Hubin, T. J. & Busch, D. H. Template routes to interlocked molecular structures and orderly molecular entanglements. Google Scholar Beves, J. E., Blight, B. A., Campbell, C. J., Leigh, D. A. & McBurney, R. T. Strategies and tactics for the metal-directed synthesis of rotaxanes, knots, catenanes, and higher order links. Google Scholar Sluysmans, D. & Stoddart, J. F. The burgeoning of mechanically interlocked molecules in chemistry. Trends Chem. Google Scholar Weidmann, J.-L. et al. Poly[2]catenanes and cyclic oligo[2]catenanes containing alternating topological and covalent bonds: synthesis and characterization. Google Scholar Wu, Q. et al. Poly[n]catenanes: synthesis of molecular interlocked chains. Google Scholar Du, R. et al. A highly stretchable and self-healing supramolecular elastomer based on sliding crosslinks and hydrogen bonds. Google Scholar Ikejiri, S., Takashima, Y., Osaki, M., Yamaguchi, H. & Harada, A. Solvent-free photoresponsive artificial muscles rapidly driven by molecular machines. Google Scholar Nakahata, M., Mori, S., Takashima, Y., Yamaguchi, H. & Harada, A. Self-healing materials formed by cross-linked polyrotaxanes with reversible bonds. Google Scholar Choi, S., Kwon, T.-w, Coskun, A. & Choi, J. W. Highly elastic binders integrating polyrotaxanes for silicon microparticle anodes in lithium ion batteries. Google Scholar Li, J. et al. Cationic supramolecules composed of multiple oligoethylenimine-grafted β-cyclodextrins threaded on a polymer chain for efficient gene delivery. Google Scholar Cotí, K. K. et al. Mechanised nanoparticles for drug delivery. Article PubMed Google Scholar Choi, J. W. et al. Ground-state equilibrium thermodynamics and switching kinetics of bistable [2]rotaxanes switched in solution, polymer gels, and molecular electronic devices. Google Scholar Deng, H., Olson, M. A., Stoddart, J. F. & Yaghi, O. M. Robust dynamics. Google Scholar Liu, Y. et al. Weaving of organic threads into a crystalline covalent organic framework. Google Scholar Ma, T. et al. Catenated covalent organic frameworks constructed from polyhedra. Google Scholar Prakasam, T. et al. 2D covalent organic framework via catenation. Google Scholar Fang, L. et al. Mechanically bonded macromolecules. Google Scholar Ashton, P. R. et al. Supramolecular daisy chains. Google Scholar Fang, L. et al. Acid–base actuation of [c2]daisy chains. Google Scholar Bruns, C. J. et al. Redox switchable daisy chain rotaxanes driven by radical–radical interactions. Google Scholar Jiménez, M. C., Dietrich-Buchecker, C. & Sauvage, J.-P. Towards synthetic molecular muscles: contraction and stretching of a linear rotaxane dimer. Google Scholar Cai, K. et al. Radical cyclic [3]daisy chains. Google Scholar Iwaso, K., Takashima, Y. & Harada, A. Fast response dry-type artificial molecular muscles with [c2]daisy chains. Google Scholar Goujon, A. et al. Bistable [c2] daisy chain rotaxanes as reversible muscle-like actuators in mechanically active gels. Google Scholar Zhang, M. et al. Preparation of a daisy chain via threading-followed-by-polymerization. Google Scholar Wang, Y. et al. Mechanically interlocked [an]daisy chain networks. Google Scholar Zhang, Q. et al. Muscle-like artificial molecular actuators for nanoparticles. Google Scholar Du, G., Moulin, E., Jouault, N., Buhler, E. & Giuseppone, N. Muscle-like supramolecular polymers: integrated motion from thousands of molecular machines. Google Scholar Amirsakis, D. G. et al. Diastereospecific photochemical dimerization of a stilbene-containing daisy chain monomer in solution as well as in the solid state. Google Scholar Bruns, C. J. & Stoddart, J. F. Molecular machines muscle up. Google Scholar Gao, L., Zhang, Z., Zheng, B. & Huang, F. Construction of muscle-like metallo-supramolecular polymers from a pillar[5]arene-based [c2]daisy chain. Google Scholar Goujon, A. et al. Controlled sol–gel transitions by actuating molecular machine based supramolecular polymers. Google Scholar Chang, J.-C. et al. Mechanically interlocked daisy-chain-like structures as multidimensional molecular muscles. Google Scholar Samanta, J. et al. An ultra-dynamic anion-cluster-based organic framework. Google Scholar Kade, M. J., Burke, D. J. & Hawker, C. J. The power of thiol-ene chemistry. A Polym. Google Scholar Kory, M. J. et al. Gram-scale synthesis of two-dimensional polymer crystals and their structure analysis by X-ray diffraction. Google Scholar Kissel, P., Murray, D. J., Wulftange, W. J., Catalano, V. J. & King, B. T. A nanoporous two-dimensional polymer by single-crystal-to-single-crystal photopolymerization. Google Scholar Guo, Q.-H. et al. Single-crystal polycationic polymers obtained by single-crystal-to-single-crystal photopolymerization. Article PubMed Google Scholar Kissel, P. et al. A two-dimensional polymer prepared by organic synthesis. Google Scholar Bunck, D. N. & Dichtel, W. R. Bulk synthesis of exfoliated two-dimensional polymers using hydrazone-linked covalent organic frameworks. Google Scholar Gallego, A. et al. Solvent-induced delamination of a multifunctional two dimensional coordination polymer. Google Scholar Dong, J. et al. Free-standing homochiral 2D monolayers by exfoliation of molecular crystals. Google Scholar Zhang, K.-D. et al. Toward a single-layer two-dimensional honeycomb supramolecular organic framework in water. Google Scholar Li, Y.-L. et al. Record complexity in the polycatenation of three porous hydrogen-bonded organic frameworks with stepwise adsorption behaviors. Google Scholar Download references We are grateful for financial support from the National Natural Science Foundation of China (22171232 and 21971211), the ‘Spearhead' and ‘Leading Goose' Research and Development Program of Zhejiang Province (2024SDXHDX0008), the Natural Science Foundation of Anhui Province (2108085MB31), the University Synergy Innovation Program of Anhui Province (GXXT-2021-064), the Excellent Research and Innovation Team Project of Anhui Province (2022AH010001) and Zhejiang Provincial Key Laboratory Construction Project. We extend our gratitude to Z. Chen and Z. Yang from the Instrumentation and Service Centers for Molecular Science and Physical Sciences, respectively at Westlake University for assistance with Raman and nanoindentation measurement as well as the data interpretation. The research was supported by Westlake University HPC Center. We also thank the staff at the SSRF BL17B1 beamline of the National Facility for Protein Science in Shanghai (NFPS), Shanghai Advanced Research Institute, CAS, for providing technical support with X-ray diffraction data collection and analysis. These authors contributed equally: Zheng-Bin Tang, Lifang Bian. Department of Chemistry, Zhejiang University, Hangzhou, China Zheng-Bin Tang Zhejiang Key Laboratory of Precise Synthesis of Functional Molecules, Department of Chemistry, School of Science, School of Engineering, Research Center for Industries of the Future, and Westlake Institute for Optoelectronics, Westlake University, and Westlake Institute for Advanced Study, Hangzhou, China Zheng-Bin Tang, Lifang Bian, Xiaohe Miao, Helei Gao, Lin Liu, Qike Jiang, Lijun Xu, Xiaorui Zheng & Zhichang Liu Institutes of Physical Science and Information Technology, Anhui University, Hefei, China Dengke Shen College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China Andrew C.-H. Sue International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima, Japan Zhichang Liu You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar conceived the idea. conducted experiments, analysed the results and prepared the Supplementary Information. provided insightful discussions on X-ray diffraction measurement. wrote the manuscript. carried out the HRESI-MS measurements. performed the nanoindentation and Raman measurements. provided assistance with AFM measurements. offered support with HRTEM measurement. discussed and revised the manuscript. Correspondence to Zhichang Liu. The authors declare no competing interests. Nature Synthesis thanks the anonymous reviewers for their contribution to the peer review of this work. Primary Handling Editor: Alison Stoddart, in collaboration with the Nature Synthesis team. Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Supplementary Scheme 1, Figs. 1–34, Tables 1 and 2, Refs. 1–8, Experimental details and X-ray crystallographic details. Crystal data for D1, CCDC 2300835. Crystal data for D2, CCDC 2300836. Height profiles and Young's modulus of exfoliated D2 films. Height profiles of the exfoliated nanosheets of D2. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Reprints and permissions Tang, ZB., Bian, L., Miao, X. et al. Synthesis of a crystalline two-dimensional [c2]daisy chain honeycomb network. Download citation Received: 03 May 2024 Accepted: 17 March 2025 Published: 15 April 2025 DOI: https://doi.org/10.1038/s44160-025-00791-x Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative Nature Synthesis (Nat. © 2025 Springer Nature Limited Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. In recent years, increased salt intrusion in surface waters has threatened freshwater availability in coastal regions worldwide. Yet, current future projections of salt intrusion are limited to local regions or changes to single forcing agents. Here, we quantify compounding contributions from changes in river discharge and relative sea level to changing future salt intrusion under a high-emission scenario (Shared Socioeconomic Pathway, SSP3-7.0) for 18 estuaries around the world. We find that the annual 90th percentile future salt intrusion is projected to increase between 1.3% and 18.2% (median 9.1%) in 89% of the studied estuaries worldwide. Our analysis also indicates that, on average, sea-level rise contributes approximately two times more to increasing future salt intrusion than reduced river discharge. We further show that the return levels of present-day 100-year salt intrusion events are projected to increase between 3.2% and 25.2% (median 10.2%) in 83% of the studied estuaries. Estuaries are semi-enclosed bodies of water, where saline ocean and fresh river water meet and mix. Estuaries are considered as highly important socioeconomic areas due to their geological and ecological benefit. Approximately 69% of large cities in the world (22 out of the 32 largest cities) are situated on estuaries1. In recent years, there have been reports about severe salt intrusion events around the world. The US Army Corps of Engineers (USACE) constructed an emergency sill to impede salt intrusion invading the Mississippi River, when New Orleans' municipal drinking water sources were predicted to be contaminated during the city's 132-year historical record drought over the summer and fall of 20232. Similarly, two severe drought events occurred in the Rhine-Meuse Estuary (the Netherlands) in 2018 and 2022, which caused prolonged salt intrusion impacting the freshwater intakes. In 2018, chloride concentration exceeded twice the drinking water norm for 75 consecutive days at the river mouth of the Hollandsche IJssel (the Netherlands) - a strategic river branch for fresh water intake. Except for the year 2018, such severe salt intrusion events only occured 52 days in the decade (2011–2020)3. Many climate studies have demonstrated that, by the end of the 21st century, droughts are projected to increase in frequency, and their intensity is expected to be enhanced in many regions4,5,6. In addition, sea-level rise (SLR) in future climates is also projected to deepen estuaries7. Reduced river discharge decreases export of salt, while SLR enhances salt import by strengthening estuarine circulation and reducing river flow velocity8,9. Increasing water depth due to SLR can alter tidal amplitudes in coastal regions10, with varying effects on salinity depending on estuarine regimes11. In stratified estuaries (exchange flow dominant regime), larger tidal amplitudes weaken estuarine circulation, reducing salt intrusion. Conversely, in well-mixed estuaries (tidal dispersion dominant regime), higher tidal amplitudes enhance tidal dispersion, increasing salt intrusion. Increased ocean salinity imposes stronger baroclinic pressure and allow saline water to intrude further inland12. Enhanced ocean surface stress, driven by wind blowing from the sea toward land, can also amplify estuarine circulation and salt intrusion13. Among these modulations in estuarine dynamics, reduced river discharge and rising water depth due to SLR have been considered as two dominant processes responsible for increasing salt intrusion length in the future14. Here, salt intrusion length is defined as the distance from the mouth to a location where bottom salinity equals to 2 psu. The salt intrusion length is of great interest for multiple stakeholders since it limits water supplies15, and affects biodiversity16 and crop yields17. The potential risk of enhanced salt intrusion under climate change has been quantified using numerical modeling studies7,14,18,19,20,21,22,23,24. However, most previous works mainly focused on changes in only one forcing agent: either river discharge18 or SLR7,19,20,21. This poses challenges in providing a comprehensive understanding of climate change effects on future salt intrusion and quantifying the contribution from each driver. Although studies exist that account for both future river discharge and SLR, these investigate only individual estuaries, and there is a lack of quantification on how climate change affects the statistical properties of future salt intrusion events14,22,23,24. Here, we determine relative changes in future salt intrusion length statistics, as compared to the present day, in 18 estuaries worldwide. The estuaries are selected based on the availability of data that is crucial for the current analysis: estuary geometries, salinity field data at different longitudinal positions, observed multi-year daily river discharge data, and reliable river discharge from a climate model. The estuaries included in this study are from the continents as follows: five (North America), one (South America), six (Europe), three (Africa), two (Asia), and one (Oceania). These sites are representative mid-latitude estuaries, where freshwater availability is expected to become critical issues in the coming decades due to increased salt intrusion driven by more frequent droughts and rising sea-level. All ranges of vertical salinity structures from stratified to partially mixed and well-mixed conditions, are observed in the chosen estuaries. The first aim of our study is to quantify the changes in the statistics of two forcing agents: river discharge and SLR. In this study, SLR consists of absolute and relative contributions. The absolute SLR (ASRL) is caused by steric expansion and the increased ocean volume from ice melt. The regional variability of ASRL was computed by considering gravitational, rotational, and deformational (GRD) effects and changes in the dynamic sea level. The relative SLR (RSLR) considers vertical land motion (VLM), which enables to quantify effective changes of water depth in estuaries. The second goal is to analyze changes in the salt intrusion length statistics due to changes in both forcing agents and how these responses depend on the properties of the considered estuaries. To this end, we obtained daily river discharge for the selected estuaries up to the year 2100 under the high emission scenario (SSP3-7.0) using Community Earth System Model 2 large ensemble simulation results (CESM-LE2, Methods and Supplementary Table S1). We applied a bias correction for the modeled daily river discharge from CESM-LE2 using observed river discharge data using the Quantile Delta Mapping (QDM)25, see Supplementary Fig. Next, we estimated projected regional ASLR due to increasing temperature by post-processing CESM-LE2 results following26 (Methods). The VLM was also quantified for the selected estuaries to compute the RSLR, using data presented in ref. Thereafter, a tidally and width averaged, single channel surface water salt intrusion model was calibrated using salinity field measurements at different longitudinal locations (Methods, Supplementary Note S1). Three consecutive 35-year time windows are defined over the 21st century: present (1996–2030), intermediate future (2031–2065), and long-term future (2066–2100). Smooth transitions in river discharge and RSLR are observed between the intermediate and long-term future in the preliminary analysis. To save computational time, the calibrated salt intrusion model simulations were carried out only for the present (1996–2030) and long-term future (2066–2100) periods under four different combinations among dominant forcing agents: river discharge, ASLR, and VLM (Methods). We first investigate the spatial variability of projected river discharge at the end of the 21st century. Here, low discharge is defined as the annual 10th percentile of the daily river discharge Q10, which is a widely used drought index in hydrology28,29. As seen, CESM-LE2 projects decreasing low discharge magnitude (red in Fig. 1a) in the southern part of North America, northern and southern parts of South America, western and southern Europe, West and South Africa, and some coastal regions of South East Asia, and the western and eastern parts of Australia. Conversely, the magnitude of low discharge is projected to increase (blue in Fig. 1a) along the east and west coasts of a northern part of North America, the middle east of South America, northern Europe, central and eastern Africa, some coastal regions of South East Asia, and central Australia. The projected river discharge by CESM-LE2 is mostly aligned with previous multi-model ensemble mean streamflow projections under the high emission scenario (Representative Concentration Pathway, RCP 8.5)28,29. However, the river discharge projections by CESM-LE2 for the west coast of the USA show the opposite direction of changes (increase) as compared to the multi-model ensemble mean in earlier studies (decrease). This difference is attributed to the fact that CESM branches (CESM1-BGC and CCSM4) show positive biases in future trends of river discharge under RCP 8.5 for these regions30. a The relative changes in the 35-year mean low discharge (Q10) for the future period (2066–2100) compared to present period (1996–2030), where the low discharge is defined as the annual 10th percentile of river discharge. Blue and red areas show projected increase and decrease of Q10 in future, respectively. Grid cells containing \({Q}_{10}^{p} \, < \, 1\,{{{{\rm{m}}}}}^{3}{{{{\rm{s}}}}}^{-1}\) are masked. The basemap is from Natural Earth. b The relative changes in the 10th (orange), 50th (blue), and 90th (purple) percentile of the 35-year mean river discharge between future and present periods, expressed by different subscripts in Q. Here the vertical solid black lines show the ensemble standard deviation of the projected river discharge in CESM-LE2. In both panels, positive and negative ΔQ* are associated with projected decrease and increase of salt intrusion length in the future period. For the selected estuaries, quantification of relative changes in river discharge statistics (the 10th, 50th, and 90th percentiles, expressed by the different subscripts in ΔQ*) are given in Fig. The considered river discharge indices are projected to increase consistently for most of the selected estuaries in North and South America. In addition, the estuaries in southern Europe and Africa show decreasing future river discharge indices. Some estuaries in western Europe and southern Africa also show opposite sign changes in extreme river discharge indices (\(\Delta {Q}_{10}^{*} \, < \, 0\) and \(\Delta {Q}_{90}^{*} \, > \, 0\)), implying enhanced seasonality in a warming climate. The seasonally averaged 35-year mean river discharge are presented for the future and present periods in Supplementary Fig. S2, which supports the enhanced seasonality. RSLR is determined from ASLR and VLM. The parameters δHA and δHVLM are defined as changes in water depth due to ASLR and VLM, respectively, and δHR = δHA − δHVLM. We first quantify future projections of regional δHA, including volume expansion of water column due to steric effects (Steric), ice melt (Glaciers, Greenland, and Antarctica), and changes in dynamic sea level (DSL) (Methods). A uniform increase of water level is assumed for the steric effect contribution. The GRD effects are considered for land ice melt (Supplementary Fig. The GRD effects arise from the fact that ASLR is larger away from ice melting sources due to the reduced gravitational force that pulls the water surface. The contribution due to changes in DSL was also quantified, which was imposed by changes in regional wind stress and large-scale ocean circulation (Supplementary Fig. Figure 2a shows the 35-year mean water surface elevation difference (δHA) between the future and present-day periods. A dipole pattern of δHA is found in the North Atlantic Ocean, which is associated with increased heat and fresh water fluxes, resulting in the weakening of the Atlantic Meridional Overturning Circulation (AMOC)31,32. a Absolute changes of the 35-year mean of water surface elevation between future (2066–2100) and present (1996–2030), δHA. b Changes in water depth due to vertical land motion along global coastlines δHVLM. In a and b, the basemap is from Natural Earth. c Contributions of δHA and δHVLM to the changes in water depth due to relative sea-level rise for each estuary δHR. The horizontal gray solid and dashed lines show the global mean sea-level rise averaged in the future (2066–2100) and zero, respectively. To estimate increases in effective water depth in estuaries, we also considered regional VLM. We employed projected global coastal region VLM data from ref. 27, which utilizes GPS, satellite altimetry, and tide gauges (Methods). The projected VLM accounts for Glacial Isostatic Adjustment (GIA), subsidence due to acquifer withdrawal, and tectonic movements, among many others. 2b presents changes in water depth due to VLM, where positive values (blue) indicate land uplift (which decreases RSLR), while negative values (red) represent land sinking (which increases RSLR). The land uplift in Canada and northern Europe is attributed to GIA rebound, while the land subsidence in East coast of US and western Europe is mainly associated with the GIA forebulge collapse27,33. 2c shows the contributions of ASLR and VLM to changes in the 35-year mean of water surface elevation for the selected estuaries. The temporal evolution of RSLR processes to changing water depth for each estuary is provided in Supplementary Fig. For all the studied estuaries, steric expansion is the dominant contributor to increasing water surface elevation. For most estuaries, contributions from Glaciers and Antarctica are the second and third largest, while contributions from Greenland is less significant. We find that VLM contributions to δHR are less than 15% except for the US coast and Thailand. With the quantified changes in future river discharge and RSLR, we computed salt intrusion length for the selected estuaries using a 2DV salt intrusion model (Methods)34. The salt intrusion model accounts for along-estuary varying width, and assumes a flat channel bed (Supplementary Fig. Measured along-estuary salinity profiles were used to calibrate the salt intrusion model. The root mean square error of the calibrated model ranges from 0.56 to 3.63 psu (median = 1.22 psu, see Supplementary Fig. The relative changes in the 35-year mean of annual salt intrusion length statistics are presented in Fig. 3a (the 90th percentile, \(\Delta {X}_{90}^{*}\)) and Fig. 3b (the 50th percentile, \(\Delta {X}_{50}^{*}\)) under four different combinations among dominant forcing agents. The relative changes in salt intrusion length are defined as \(\Delta {X}_{pct}^{*}=({X}_{pct}^{f}-{X}_{pct}^{p})/{X}_{pct}^{p}\), where the superscript p and f represent the present (1996–2030) and future (2066–2100) periods, and the subscript pct denotes the percentile. The four sets of simulations consider (1) only river discharge changes (δQ), (2) only ASLR (δHA), (3) only RSLR (δHR), and (4) both river discharge changes and RSLR (δQ & δHR). 3 shows that salt intrusion decreases (\(\Delta {X}_{90}^{*}\) and \(\Delta {X}_{50}^{*} \, < \, 0\)) due to increased river discharge in the selected estuaries in the North and South America, and East Africa. For the rest of the studied estuaries, salt intrusion increases (\(\Delta {X}_{90}^{*}\) and \(\Delta {X}_{50}^{*} \, > \, 0\)) because of the reduced river discharge. Ranges of the effects of future river discharge on the relative salt intrusion length are \(-0.41\,\le \Delta {X}_{90}^{*}\le 0.10\) (median = −0.002) and \(-0.36\le \Delta {X}_{50}^{*}\le \,0.28\) (median = 0.01). We find that the magnitude of relative increases in salt intrusion length due to changes in river discharge in this study are smaller as compared to values reported in an earlier study18 for western and southern Europe. The differences originate from the fact that, here, we use a more advanced salt intrusion model that is capable of accounting for converging estuary width. The salt intrusion model is less sensitive to changes in river discharge when using converging estuary width in the along-estuary direction. a Relative changes of the 35-year mean of annual 90th percentile salt intrusion length between the future (2066–2100) and present (1996–2030) periods. Four combinations among the considered forcing agents are investigated: (1) only river discharge changes (δQ), (2) only absolute sea-level rise is imposed (δHA), (3) only relative sea-level rise is imposed (δHR), and (4) both river discharge changes and relative sea-level rise are considered (δQ & δHR). The vertical black solid lines represent one ensemble standard deviation from different realizations of climate conditions in the Community Earth System Model 2 large ensemble simulations (CESM-LE2). b The same as a, but for relative changes of 35-year mean of annual 50th percentile salt intrusion length. In both panels, positive and negative ΔX* show projected increase and decrease of salt intrusion length in the future period. The salt intrusion length consistently increases due to ASLR, as an increase in water depth enhances salt intrusion, ranging from \(0.017\le \Delta {X}_{90}^{*}\le 0.25\) (median = 0.069) and \(0.019\,\le \Delta {X}_{50}^{*}\le 0.28\) (median = 0.076). By including the VLM, future salt intrusion increases range from \(0.021\le \Delta {X}_{90}^{*}\le 0.26\) (median = 0.071) and \(0.024\le \Delta {X}_{50}^{*}\le 0.30\) (median = 0.076). The result indicates that the contribution of VLM to changes in future salt intrusion length is insignificant. We find that the effect of RSLR on future salt intrusion length exceeds that due to changes in river discharge. This holds when we consider only estuaries with increasing \(\Delta {X}_{90}^{*}\) due to the reduced magnitude of low discharge (estuaries: g–k, m, n, q, r). For those estuaries, changes in salt intrusion lengths are \(0.018\le \Delta {X}_{90}^{*}\le 0.096\) (median = 0.035) and \(0.049\le \Delta {X}_{90}^{*}\le 0.098\) (median = 0.066) when isolated δQ and δHR are considered, respectively. Our analysis of the decomposed contributions of future forcing highlights the importance of RSLR on increasing salt intrusion length at the end of the 21st century. Compound changes in river discharge and RSLR (δQ & δHR case) lead to \(-0.23\le \Delta {X}_{90}^{*}\le 0.18\) (median = 0.079) and \(-0.15\le \Delta {X}_{50}^{*}\le 0.35\) (median = 0.072). We further computed changes in the return periods and levels of extreme salt intrusion events. We first calculated return periods and levels using the 35-year annual maximum timeseries \({X}_{max}^{A}\) for the present and future periods (the triangle and circle markers in Fig. Next, Generalized Extreme Value (GEV) distribution functions were fitted to the return period curves for each period (gray dashed and orange solid lines for present and future). Here, 100-year events were considered as typical extreme events (blue vertical line). The extreme return levels were defined as extrapolated \({X}_{max}^{A}\) that corresponds to the 100-year return periods based on the fitted GEV distribution functions (i.e., \({X}_{max}^{A}\) where gray dashed and orange solid curves intersect with the vertical blue line). The extreme return levels for the present and future are denoted as \({X}_{p}^{yr100}\) and \({X}_{f}^{yr100}\), respectively (red horizontal dashed and solid lines, respectively). Pangani was taken as an example to visualize the changes in return period curves where we observed the largest relative increases in the future 100-year return level (Fig. The same plots for all the remaining estuaries are presented in Supplementary Fig. The following results focus only on the future simulations in which all the changes in forcings are considered, including the river discharge and RSLR (δQ & δHR case). We find − 0.28 ≤ ΔXyr100* ≤ 0.25 (median 0.095) for all the studied estuaries and 0.032 ≤ Δ Xyr100* ≤ 0.25 (median 0.10) for the 83% of the estuaries (15 out of 18) showing increasing future 100-year return levels. The changed future return periods for the extreme events were computed by finding points where \({X}_{p}^{yr100}\) intersect with future return curves (i.e., the red horizontal dashed lines meet with the orange solid lines in Fig. It is found that such future return periods are projected to decrease to 3.2 years for 6 estuaries on average (a,b,d,n,p,r in Supplementary Fig. For 9 estuaries (c,g–k,m,o,q in Supplementary Fig. S9), the salt intrusion length belonging to a future 2-year return level is larger than ones corresponding to the extreme event under present-day conditions, as is seen from the orange circles always being above the red horizontal dashed lines. For 3 estuaries (e,f,l in Supplementary Fig. S9), return levels in future are projected to be reduced because of increasing magnitude of low discharge. Our results show that events that are considered as extreme in the present-day would occur much more frequent under changes in river discharge and increasing water depth in the future climate. a An example of return periods and levels computed from the 35-year annual maximum timeseries \({X}_{max}^{A}\) for Pangani (Tanzania) for present (1996–2030) and future (2066–2100). Here, gray triangles and orange circles show estimated return periods. The corresponding gray dashed and orange solid lines are the fitted curves using the generalized extreme value distribution function. The shaded areas present 95% confidence interval computed by the bootstrapping method. The blue vertical line demarks the 100-year return period, defined as an extreme event. The horizontal red dashed and solid lines represent return levels corresponding to the extreme events for the present (\({X}_{p}^{yr100}\)) and future (\({X}_{f}^{yr100}\)), respectively. The same plots for all the studied estuaries are presented in Supplementary Fig. The vertical black solid lines show uncertainties associated with 95% confidence interval using the bootstrapping method. Our analysis provides future projections of the global-scale salt intrusion length under the high emission scenario (SSP3-7.0) using CESM-LE2 with two dominant future forcing agents: river discharge and RSLR. We show that the 35-year mean annual 90th percentile salt intrusion length is projected to range from 1.3% to 18.2% (median 9.1%) in 89% of the studied estuaries (16 out of 18). We also quantify that return levels of 100-year events are intensified in the future by 3.2−25.2% (median 10.2%) in 83% of the studied estuaries (15 out of 18). A systematic decomposition of the effects of changes in river discharge and water depth on future salt intrusion length allows to investigate the relative importance of the two forcings. We find that increasing water depth due to RSLR and decreasing river discharge are responsible for increasing salt intrusion length from 4.9% to 9.6% (median 6.6%) and from 1.7% to 9.6% (median 3.5%), respectively. This indicates that increasing water depth due to RSLR contributes to increasing future salt intrusion length approximately twice as much than decreasing river discharge. We stress that the factor two greater contribution by RSLR is from averaged salt intrusion length simulation results among the studied estuaries, and the relative importance of each forcing can vary significantly. To better understand why our simulation results show greater contributions from elevating water depth to increasing salt intrusion length, we examined this based on the reduced-complexity steady state tidally-averaged salt budget equation (Eq. As shown in Supplementary Note S2, salt intrusion length scales as X ~ HmQn. Here, m = 2 and n = −1/3 for stratified estuaries (exchange flow dominant regime, Eq. S17), while m = 1 and n = −1 for well-mixed estuaries (tidal dispersion dominant regime, Eq. These scaling relations highlight that X is six times more sensitive to changes in H as compared to changes in Q (∣m/n∣ = 6) for stratified estuaries. For well-mixed estuaries, X similarly responds to changes in H and Q (∣m/n∣ = 1). This implies that X is expected to respond 1-6 times more sensitively to changes in H as compared to changes in Q for partially-mixed estuaries. S10, most of the studied estuaries are classified as partially-mixed estuaries (Supplementary Note 3 and Fig. The increased mean and extreme surface water salt intrusion length are expected to pose significant socio-economic challenges in coastal regions in the coming decades. For instance, when saline ocean water intrudes more frequently farther upstream, freshwater intakes are more likely to be contaminated. Increases in salinity and an extended salt intrusion length can affect agricultural landscape, reducing crop yields or forcing farmers to grow salt-tolerant species17. In addition, a higher drinking water salinity has been shown to elevate the risks of cardiovascular and kidney health problems39. Failure to adapt to these new agricultural conditions in a timely manner can lead to substantial economic loss and food shortage17. Our findings imply that these surface water salinization problems are projected to worsen in many estuaries worldwide. Although our study provided a global-scale view on how changing water depth and river discharge affect salt intrusion, further improvements can be made for future projections. Incorporating realistic bottom topography will be an important step forward in capturing local estuarine dynamics and salt intrusion processes. When the water depth is increased, inhomogeneous residual circulation patterns emerge depending on the bathymetric characteristics40. This modulated residual circulation can influence local salt transport and salt intrusion length. Furthermore, the rate of local sedimentation build-up and erosion due to future coastal and fluvial morphodynamics can be characterized41. With this additional contribution, we can better quantify the effective change of water depth in estuaries. In addition, anthropogenic water regulation (e.g., reservoir operation and water withdrawal) is a significant source of uncertainties for projections of river discharge and salt intrusion. Changing dynamics of tides10, winds13, and ocean salinity12 in estuaries can play a role in future salt intrusion by influencing mixing and stratification. The proposed framework in this study can be applied to any other estuaries if essential observations for the analysis are available: estuary geometries, longitudinal salinity measurements, multi-year daily river discharge data from observation, and reliable modeled river discharge from a climate model. We acknowledge that our analysis focuses on relatively large mid-latitude estuaries, where all the necessary data are publicly accessible. To provide a more comprehensive view of future salt intrusion processes in other estuaries, collective efforts to make necessary salinity and hydrological data publicly available will be crucial. Such data-sharing efforts with additional modeling work can help better understand future salt intrusion processes that are not addressed in this study, such as those occurring in fjords. CESM is a fully coupled global climate model simulating ocean, land, atmospheric, and sea-ice processes, and their feedbacks. In this study, we projected future river discharge and sea-level rise under the SSP3-7.0 based on the CESM2 large ensemble simulation results, CESM-LE2 (n = 69). Here n is the total number of ensemble members considered, where consistent data are publicly available for daily river discharge, monthly air surface temperature, and monthly precipitation. The SSP3-7.0 represents the medium to high end of emission scenario, proposed in the Coupled Model Intercomparison Project Phase 6 (CMIP6). Following priority protocols in CMIP6, CESM-LE2 focused on the SSP3-7.0 due to large computational costs. A nominal horizontal spatial resolution of 1° was used for periods 1850–2100 in all the simulations. More detailed descriptions of CESM-LE2 are documented at https://www.cesm.ucar.edu/community-projects/lens242. The modeled daily river discharge consists of contributions from surface and groundwater, and ice melt runoff computed in the land surface model in CESM-LE2. The accumulated total runoff on the land surfaces is routed to river networks with spatially varying river flow velocities using Manning's equation, based on heterogeneous roughness, hydraulic radius, and water surface slopes in land grid cells43,44. The modeled river discharge is abstracted depending on irrigation demands in land grid cells, but flow regulations by reservoirs are not considered45. We adjusted systematic biases observed in the modeled river discharge using the Quantile Delta Mapping (QDM) method25. The QDM method that was used to correct the modeled river discharge is elaborated in detail in ref. Comparisons between seasonally averaged river discharge from CESM-LE2 and observations (before and after the bias correction) are provided in Supplementary Fig. Changes of the seasonally averaged river discharge in CESM-LE2 between present (1996–2030) and future (2066–2100) are also given in Supplementary Fig. Locations and measurement periods of the observed river discharge are summarized in Supplementary Table S1. Future sea-level rise (2066–2100) was projected by post-processing the modeled air surface and oceanic temperature, and snowfall results in CESM-LE2, following the methods outlined in ref. In these methods, the global mean sea-level rise (GMSLR) consists of four major contributions: (1) steric expansion, and ice melt from the (2) Antarctica and (3) Greenland ice sheets as well as (4) glaciers. Here, the steric expansion was quantified by vertically integrating specific volume anomalies over the full depth of the water column46, which is associated with volume expansion of the water column due to changes in density by varying temperature, pressure, and salinity. The SLR due to the melting Antarctica ice sheet was calculated based on surface mass balance47 and basal melt48, using snowfall over the continent and oceanic temperatures adjacent to the continental shelves. The contribution by the Greenland ice sheet was computed based on a mass balance between snowfall and surface melt49. The contribution by the glaciers was calculated using power law relations between sea-level rise and global mean surface temperature anomalies47. Nineteen glacier regions in the Randolph Glacier Inventory were considered, excluding glaciers in the Antarctica and sub-Antarctica regions. Because we projected future salt intrusion length for estuaries at the global scale, it was crucial to consider spatial variability in the sea-level rise projection. Two sources of spatial variability were quantified in our analysis. First, we computed Gravitational, Rotational, and Deformation (GRD) effects induced by decreasing ice mass50. The GRD effects are induced by reduced gravitational force due to decreased ice mass that pulls water surface, resulting in greater SLR away from ice melting sources (Supplementary Fig. Second, we also characterized spatial patterns in changes of dynamic sea-level changes (DSL) that are associated with varying regional wind stresses and large-scale ocean circulations over the 21st century (Supplementary Fig. Decadal changes of DSL are calculated based on a climate model output (variable name SSH) in CESM-LE2. Temporal evolution of different contributors to ASLR for each estuary is provided in Supplementary Fig. We assumed that SLR processes are relatively slow as compared to changes in daily river discharge. To create consistent temporal resolution of SLR as daily river discharge, we linearly interpolated annual ASLR due to steric expansion and ice melt with GRD as well as monthly DSL into daily changes. To quantify relative sea-level changes, we employed projected VLM along global coastlines that is presented in ref. Therein, VLM was reconstructed from 1995 to 2020 by combining direct VLM observation from Global Navigation Satellite Systems (GNSS)51 and an indirect VLM predictions that are based on tide gauges52 and altimetry data. Potential nonlinear VLM processes (e.g. glacial isostatic adjustment, tectonic activity, surface mass loading changes, and local natural or anthropogenic effects) were considered in space and time in the reconstruction. The quantified statistical properties of VLM trends and uncertainties in the reconstruction were used to project VLM up to the year 215027. Changes in water depth due to VLM are presented along global coastlines in Fig. The temporal evolution of VLM up to the year 2100 is shown for each investigated estuary in Supplementary Fig. Similar to ASLR, we linearly extrapolated the VLM trends into daily-scale changes. In this study, we assumed uniform water depth, allowing along-estuary varying width from the mouth to inland. To construct the converging estuary width, we fitted an exponential function to directly measured data in field campaigns53 and Google Earth34. For estuaries, in which width data was unavailable from the literature, we employed remotely sensed data from satellite images (Global River Widths from Landsat, GRWL)54. We divided estuaries into segments, where the index i is an integer, numbering the segments. The index i = 0 is the estuary segment adjacent to the mouth and increasing i indicates segments away from the mouth to inland. Here, x is the along-estuary coordinate with the origin x = 0 at the estuary mouth and negative upstream. The constant coefficients Bs,i, Ls,i, and Lc,i represent the largest estuary width facing seaward, streamwise estuary length, and convergence length at each segment, respectively. The characteristics of estuary geometries used in our analysis are summarized in Supplementary Table S2. Comparisons between the observed estuary width and Eq. (1) are provided in Supplementary Fig. We computed two-dimensional salinity structures in the along-estuary and vertical coordinates (2DV) using a time-dependent, width and tidally averaged single channel salt intrusion model. The 2DV salt intrusion model solves the mass, momentum, and salt balances with parameterized horizontal and vertical eddy viscosity and diffusivity34,55. The salt balance describes the temporal changes in salinity due to seaward salt flux caused by advection by river flow and landward salt flux by density driven exchange flow and horizontal mixing induced by tidal disperson. The solution methods for the 2DV salt intrusion model are given in ref. We ran spin-up simulations for 1 year for the present (the year 1995) and future (the year 2065). Next, we conducted simulations for 35 years in the periods 1996–2030 (present) and 2066–2100 (future) using time series of river discharge, SLR, and VLM. The effects of changes in river discharge and RSLR on salt intrusion length at the end of the 21st century were systematically investigated by switching on/off future forcings. When considering changes in river discharge alone (blue vertical bar, δQ in Fig. 3), we used river discharge time series from 1996–2030 and 2066–2100 for the present and future periods, while imposing ASLR time series from 1996–2030 for both periods. When examining the impact of ASLR only (red vertical bar, δHA in Fig. 3), we employed the ASLR time series from 1996–2030 and 2066–2100 for the present and future periods, while using river discharge time series from 1996–2030 for both periods. For VLM contributions, we added VLM to ASLR timeseries (yellow vertical bar, δHR in Fig. To analyze the combined contributions of river discharge and RSLR to future salt intrusion length (cyan vertical bar, δQ & δHR in Fig. Salinity measurements were available in different time scales, which were needed for the model calibration. First, we utilized one-day snapshots of salinity field s(x) collected during dry seasons. Second, we used salinity timeseries measured at multiple spatial locations s(x, t) with daily (or monthly) temporal resolutions (Supplementary Table S4). For consistent model calibration, if applicable, we used time-averaged longitudinal salinity profiles over the month when the seasonally averaged river discharge is the lowest, denoted as \({{s}}_{dry}(x)={\langle s(x,t)\rangle }_{dry}\). Here, 〈 ⋅ 〉 is a time-averaging operator, and subscript dry indicates a period of interest, which was the driest month. The period of interest (dry seasons) was aligned with the purpose of our analysis to project changes in the potentially largest salt intrusion length for the future. When the vertical locations of salinity measurements were inconsistent among the data sources, we assumed the data to represent the depth-averaged salinity fields. If salinity data were collected at one vertical location and the measurement depth was reported, we extracted salinity profiles from the 2DV salt intrusion model at the corresponding vertical locations for the calibration. Two constants for horizontal eddy diffusivity ch and vertical eddy viscosity cv were used as primary calibrating parameters in the 2DV salt intrusion model. We generated 200 - 400 combinations of cv and ch using the stochastic gradient descent method56. These combinations of cv and ch allowed to obtain the minimum root mean square errors of longitudinal salinity profiles between observation and model results, while keeping the absolute difference between modeled and observed X minimal. It was ensured that values of the ensemble-averaged cv and ch were independent of the number of combinations. If the ocean boundary salinity socn, which is a forcing parameter of the model, is not directly measured in observations, socn was also determined together with cv and ch following the same procedure. The ensemble averaged cv and ch from the combinations were defined as the calibrated eddy viscosity and diffusivity parameters. The corresponding ensemble standard deviations were defined as uncertainties associated with 2DV salt intrusion model calibrations (Supplementary Table S3). All the data sources are given in Supplementary Table S4. The raw and processed data used and generated in this study have been deposited in Zenodo (https://doi.org/10.5281/zenodo.14837324). The basemap used in all figures in this paper is available at https://www.naturalearthdata.com/. All the scripts and raw and processed data that reproduce the figures in this paper have been deposited in Zenodo (https://doi.org/10.5281/zenodo.14837324). Valle-Levinson, A., Contemporary Issues in Estuarine Physics. Miller, P. & Hiatt, M. Hydrometeorological drivers of the 2023 Louisiana water crisis. Wullems, B. J., Brauer, C. C., Baart, F. & Weerts, A. H. Forecasting estuarine salt intrusion in the Rhine-Meuse delta using an LSTM model. Global changes in drought conditions under different levels of warming. Global drought and severe drought-affected populations in 1.5 and 2 C warmer worlds. Responses of estuarine salinity and transport processes to potential future sea-level rise in the Chesapeake Bay. MacCready, P. & Geyer, W. R. Advances in estuarine physics. Geyer, W. R. & MacCready, P. The estuarine circulation. The impact of future sea-level rise on the global tides. Matsoukis, C., Amoudry, L. O., Bricheno, L. & Leonardi, N. Numerical investigation of river discharge and tidal variation impact on salinity intrusion in a generic river delta through idealized modelling. & Lwiza, K. M. Factors driving bottom salinity variability in the Chesapeake Bay. Jongbloed, H., Schuttelaars, H. M., Dijkstra, Y. M., Donkers, P. B. Influence of wind on subtidal salt intrusion and stratification in well-mixed and partially stratified estuaries. Bellafiore, D. et al. Saltwater intrusion in a Mediterranean delta under a changing climate. Dynamic mechanism of an extremely severe saltwater intrusion in the Changjiang Estuary in February 2014. Jassby, A. D. et al. Isohaline position as a habitat indicator for estuarine populations. Loc, H. H. et al. How the saline water intrusion has reshaped the agricultural landscape of the Vietnamese Mekong Delta, a review. Lee, J., Biemond, B., de Swart, H. & Dijkstra, H. A. Increasing risks of extreme salt intrusion events across European estuaries in a warming climate. A. N. & Dutta, D. Assessing impacts of sea-level rise on river salinity in the Gorai river network, Bangladesh. Chua, V. P. & Xu, M. Impacts of sea-level rise on estuarine circulation: An idealized estuary and San Francisco Bay. Assessment of sea-level rise impacts on salt-wedge intrusion in idealized and Neretva River Estuary. Yang, Z., Wang, T., Voisin, N. & Copping, A. Estuarine response to river flow and sea-level rise under future climate change and human development. & Freire, P. Saltwater intrusion in the upper Tagus Estuary during droughts. Projections of salt intrusion in a mega-delta under climatic and anthropogenic stressors. Bias correction of GCM precipitation by quantile mapping: how well do methods preserve changes in quantiles and extremes? Ocean eddies strongly affect global mean sea-level projections. Regional variations in relative sea-level changes influenced by nonlinear vertical land motion. van Vliet, M. T. Global river discharge and water temperature under climate change. Global change in streamflow extremes under climate change over the 21st century. The future of sediment transport and streamflow under a changing climate and the implications for long-term resilience of the San Francisco Bay Delta. Bouttes, N., Gregory, J. M., Kuhlbrodt, T. & Smith, R. The drivers of projected North Atlantic sea-level change. Exploring the drivers of global and local sea-level change over the 21st century and beyond. Hammond, W. C., Blewitt, G., Kreemer, C. & Nerem, R. S. GPS imaging of global vertical land motion for studies of sea-level rise. Biemond, B., de Swart, H. E., Dijkstra, H. A. & Dìez-Minguito, M. et al. Estuarine salinity response to freshwater pulses. Monismith, S. G., Kimmerer, W., Burau, J. R. & Stacey, M. T. Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay. MacCready, P. Toward a unified theory of tidally-averaged estuarine salinity structure. Chen, S.-N. Asymmetric estuarine responses to changes in river forcing: A consequence of nonlinear salt flux. Ralston, D. K. & Geyer, W. R. Response to channel deepening of the salinity intrusion, estuarine circulation, and stratification in an urbanized estuary. Xeni, C. et al. Epidemiological evidence on drinking water salinity and blood pressure: a scoping review. Valentim, J. M. et al. Sea-level rise impact in residual circulation in Tagus estuary and Ria de Aveiro lagoon. Hou, X., Xie, D., Feng, L., Shen, F. & Nienhuis, J. H. Sustained increase in suspended sediments near global river deltas over the past two decades. Rodgers, K. B. et al. Ubiquity of human-induced changes in climate variability. Tesfa, T. K. et al. A subbasin-based framework to represent land surface processes in an Earth system model. Evaluating global streamflow simulations by a physically based routing model coupled with the Community Land Model. Taranu, S. I. et al. Bridging the gap: a new module for human water use in the Community Earth System Model version 2.2.1. Richter, K., Riva, R. & Drange, H. Impact of self-attraction and loading effects induced by shelf mass loading on projected regional sea-level rise. et al. Sea level change. Technical report, PM Cambridge University Press (2013). Projecting Antarctica's contribution to future sea-level rise from basal ice shelf melt using linear response functions of 16 ice sheet models (LARMIP-2). Fettweis, X. et al. Estimating the Greenland ice sheet surface mass balance contribution to future sea-level rise using the regional atmospheric climate model MAR. Frederikse, T., Landerer, F. W. & Caron, L. The imprints of contemporary mass redistribution on local sea-level and vertical land motion observations. Blewitt, G., Kreemer, C., Hammond, W. C. & Gazeaux, J. MIDAS robust trend estimator for accurate GPS station velocities without step detection. Holgate, S. J. et al. New data systems and products at the permanent service for mean sea-level. Gisen, J., Savenije, H. & Nijzink, R. Revised predictive equations for salt intrusion modelling in estuaries. Allen, G. H. & Pavelsky, T. M. Global extent of rivers and streams. Kiefer, J., Wolfowitz, J. Stochastic estimation of the maximum of a regression function. This work is financially supported by NWO Domain Applied and Engineering Sciences (2022/TTW/01344701, Perspective Program SALTISolutions, H.A.D.) and Deltares's strategic research initiative -Liveable Deltas in a Changing World' (11209189-029, Salt Intrusion around the World under influence of Climate Change, W.K.). The authors appreciate Dutch National Supercomputer (Snellius) for the computational resources. The authors are also grateful to Dr. Tim Hermans for his valuable insight on the analysis of vertical land motion and Avelon Gerritsma for her exploratory activities in the inception phase of the project. Jiyong Lee, Bouke Biemond, René M. van Westen, Huib E. de Swart & Henk A. Dijkstra Daan van Keulen, Ymkje Huismans & Wouter M. Kranenburg Department of Hydraulic Engineering, Delft University of Technology, Delft, The Netherlands Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar contributed to salt intrusion modeling analysis and reviewed the paper. contributed to creating estuary geometry data. contributed to discussions and reviewed the paper. contributed to the sea-level rise projection analysis and reviewed the paper. designed the study and contributed to data analysis, and reviewed the paper. provided financial support and computational resources, designed the study, contributed to data analysis, and reviewed the paper. The authors declare no competing interests. Nature Communications thanks Christian Ferrarin, Braulio Juárez and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available. Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. Lee, J., Biemond, B., van Keulen, D. et al. Global increases of salt intrusion in estuaries under future environmental conditions. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. Dysregulated protein degradation via the ubiquitin-proteasomal pathway can induce numerous disease phenotypes, including cancer, neurodegeneration, and diabetes. While small molecule-based targeted protein degradation (TPD) and targeted protein stabilization (TPS) platforms can address this dysregulation, they rely on structured and stable binding pockets, which do not exist to classically “undruggable” targets. Here, we expand the TPS target space by engineering “deubiquibodies” (duAbs) via fusion of computationally-designed peptide binders to the catalytic domain of the potent OTUB1 deubiquitinase. In human cells, duAbs effectively stabilize exogenous and endogenous proteins in a DUB-dependent manner. Using protein language models to generate target-binding peptides, we engineer duAbs to conformationally diverse target proteins, including key tumor suppressor proteins p53 and WEE1, and heavily-disordered fusion oncoproteins, such as PAX3::FOXO1. We further encapsulate p53-targeting duAbs as mRNA in lipid nanoparticles and demonstrate effective intracellular delivery, p53 stabilization, and apoptosis activation, motivating further in vivo translation. The ubiquitin-proteasomal pathway regulates critical processes, including protein folding, DNA repair, and cell differentiation, thus helping to maintain proteostasis1. Dysregulation of this pathway—such as improper degradation of tumor suppressors or mutant, misfolded proteins—can lead to severe pathogenic phenotypes, such as cancer, neurodegenerative disease, cystic fibrosis, and diabetes2,3,4,5. Therefore, there is a need for proteome editing tools that are capable of correcting this dysregulation by selectively removing ubiquitin from target proteins. While the controllable installation of ubiquitin has been extensively exploited in the form of targeted protein degradation (TPD) strategies such as PROTACs and molecular glues1, only recently has the reverse process, targeted protein stabilization (TPS), gained attention6. The current state-of-the-art TPS modality, termed deubiquitinase-targeting chimeras or DUBTACs, is analogous to PROTACs: they recruit endogenous deubiquitinases (DUBs), but still rely on the arduous design of chemical linkers and existence of small-molecule warheads, which do not exist for classically “undruggable” proteins due to their conformational disorder and lack of putative or cryptic binding site accessibility6. Due to the labor-intensive and time-consuming process of designing de novo binders—whether small molecules or biologics—for target proteins7, achieving a truly programmable TPS system currently remains unrealized. In recent years, our team has described a unique TPD strategy that involves genetically fusing target-specific short “guide” peptides, designed via sequence-based algorithms, to the ubiquitin conjugation domain of the human E3 ubiquitin ligase, CHIP8,9,10,11,12. Without the requirement of a stable target structure, this programmable design process results in chimeric proteins called “ubiquibodies” (uAbs) for TPD which can target a conformationally varied array of target proteins8,9,10,11,12. Here, we design the analogous platform for TPS, termed deubiquibodies (duAbs), by fusing computationally-designed peptide guides to the catalytic domain of the potent OTUB1 deubiquitinase. Utilizing pre-existing binders, our first-generation fusion duAb architecture effectively stabilizes exogenous and endogenous proteins in a DUB-dependent manner following ectopic expression in human cells. We showcase the inherent programmability of duAbs by swapping in target-binding peptides designed via recent generative protein language models (pLMs), SaLT&PepPr, PepPrCLIP, and PepMLM10,11,12. These peptide-guided duAbs stabilize their intended target substrates, including the transcription factors β-catenin and FOXP3, the tumor suppressors WEE1 and p53, and a disordered fusion oncoprotein PAX3::FOXO1. As a final step toward in vivo translation, we deliver p53-targeting duAbs as mRNA in lipid nanoparticles (LNPs), and demonstrate effective intracellular delivery, p53 stabilization, and apoptosis induction. Recently, Kanner et al. fused the OTUD1 deubiquitinase domain to yellow fluorescent protein-targeting nanobodies (YFP Nbs) to create enDUBO1 constructs that stabilize target-YFP fusion proteins (Fig. We hypothesized that DUB domains exhibiting more potent deubiquitinase activity may improve TPS. To evaluate potential effectors for recruitment, Poirson et al., conducted a proteome-scale induced proximity screen to rank both ubiquitinating and deubiquitinating enzymes in terms of catalytic activity14. They isolated a subset of deubiquitinases, including OTUB1 and UCHL1, as well as a SUMOlase, UBC9, with potent stabilization activity (Supplementary Table 1)14. Of note, OTUB1 is the endogenous deubiquitinase recruited by DUBTACs (Fig. A Building from prior work13, a YFP nanobody (YFP Nb) was linked to potent deubiquitinase catalytic domains using different linker candidates. B KCNQ1-YFP stabilization by YFP Nb-based stabilizers in HEK293T cells determined by flow cytometric analysis. Cells were co-transfected with a pcDNA3-Nedd4L vector in the presence or absence of 4 μM PR-619 DUB inhibitor as indicated. Data are the average of independent replicates (n = 3). (C) KCNQ-YFP stabilization by YFP Nb-based stabilizers, specifically comparing the YFP Nb-L2-OTUB1 fusion with the OTUB1 C91S and OTUB1 D88A/C91S/H265A (ASA) mutants. Cells were co-transfected with a pcDNA3-Nedd4L vector. Data are the average of individual replicates (n = 3). For B, C, normalized cell fluorescence was calculated by dividing the percentage of YFP+ cells in a sample by that of (-) DUB with no DUB inhibitor for control cells. Samples with p value representations above their respective bars reflect comparisons between the control and that sample; all other p value notations compare those specific samples. Please refer to source data for numeric p values. Using known domain annotations of these proteins in UniProt15, we isolated the catalytic domains of each enzyme and fused them to the aforementioned YFP Nbs via either the GAPGSG linker (used for enDUBO1) termed L113 or the flexible GSGSG linker already used in the uAb architecture termed L2 (Supplementary Table 1 and 2). To evaluate these designs, we employed a reporter fusion between the potassium ion channel protein, KCNQ1, and YFP, which was co-transfected in HEK293T cells with KCNQ1's E3 ubiquitin ligase, Nedd4L13,16. We also sought to determine whether our DUB fusions acted in a DUB-dependent manner by employing the pan-DUB inhibitor PR-61917. Importantly, we observed that addition of PR-619 at a standard concentration (4 μM) abrogated stabilization, confirming the DUB-dependent mechanism of these stabilizer constructs (Fig. To further establish this mechanism, we investigated whether direct OTUB1 catalytic activity affected KCNQ1-YFP stabilization by mutating the catalytic cysteine-91 (C91), as well as the complete OTUB1 catalytic triad with aspartic acid-88 (D88) and histidine-265 (H265)18,19..We demonstrate that our OTUB1 C91S and D88A/C91S/H265A (ASA) mutants18 did not yield changes to KCNQ1-YFP expression (Fig. We next explored whether the OTUB1 catalytic domain could be guided to target proteins via short peptide binders (Fig. As first candidates, we chose the β-cat_SnP_7 and β-cat_SnP_8 peptides derived from our SaLT&PepPr algorithm, both of which exhibit nanomolar binding affinity to β-catenin10. Our hypothesis was that by fusing these peptides to OTUB1, we would induce stabilization of β-catenin in HEK293T cells, which possess an intact Wnt signaling pathway20. We demonstrate that, when fused to β-cat_SnP_7 via L2, the OTUB1 catalytic domain induces statistically significant stabilization of β-catenin-sfGFP proteins and outperformed other DUB fusions (Fig. We again show that employing the pan-DUB inhibitor PR-619 inhibits DUB-dependent stabilization of β-catenin-sfGFP, as expected. In a similar manner, we exhibit that linking β-cat_SnP_7 to OTUB1 C91S and ASA mutants impedes β-catenin-sfGFP stabilization (Fig. We additionally demonstrate potent duAb activity within 48–72 h post transfection by monitoring β-catenin-sfGFP expression (Fig. We corroborated these results by co-transfecting the β-cat_SnP_7-L2-DUB fusions into HEK293T cells alongside TOP-GFP, a fluorescent reporter that serves as a reliable readout of β-catenin–dependent transcriptional activity (Fig. Cells transfected with β-cat_SnP_7-L2-OTUB1 exhibited significantly higher Wnt signaling than either untransfected cells or cells transfected with our other DUB fusion candidates (Fig. A Instead of using a YFP Nb, which is not a therapeutically relevant binder, target-specific peptides can instead be leveraged for a more programmable method of protein stabilization. B β-catenin-sfGFP stabilization in HEK293T cells comparing the four different DUB domain candidates linked to βcat_SnP_710 measured by flow cytometric analysis. Cells were transiently transfected in the presence or absence of 4 μM PR-619 DUB inhibitor. Data are the average of independent replicates (n = 3). C β-catenin-sfGFP stabilization by βcat_SnP_7-linked stabilizers, specifically comparing the βcat_SnP_7-L2-OTUB1 fusion with the OTUB1 C91S and OTUB1 ASA mutants. Data are the average of individual replicates (n = 3). D Time-course experiment demonstrates that potent duAb activity can be achieved within three days of treatment. Data was collected by extracting treated HEK293T cells at t = 6, 12, 24, 36, 48, and 72 h post transfection. E TOP-GFP assay for quantifying Wnt signaling in HEK293T cells21. Stabilization of endogenous β-catenin results in higher levels of Wnt signaling and increased GFP levels, measured by flow cytometry. Data are the average of independent replicates (n = 3). F TOP-GFP signals in HEK293T cells measured by flow cytometric analysis. Cells were transiently transfected in the presence or absence of 4 μM PR-619 DUB inhibitor. Data are the average of independent replicates (n = 3). G TOP-GFP signals in HEK293T cells comparing the βcat_SnP_7-L2-OTUB1 fusion with the OTUB1 C91S and OTUB1 ASA mutants measured by flow cytometric analysis. Cells were transiently transfected, and data are the average of independent replicates (n = 3). For B, G, normalized cell fluorescence was calculated by dividing the percentage of sfGFP+ cells in a sample by that of (-) DUB with no DUB inhibitor for control cells. Samples with p value representations above their respective bars reflect comparisons between the control and that sample; all other p value notations compare those specific samples. H Nano LC-MS/MS analysis of total proteins collected from HEK293T cells co-transfected with plasmids encoding β-catenin-sfGFP and either βcat_SnP_7-L2-OTUB1 or polyG-L2-OTUB1. Data was log2-transformed, and a t-test was performed to generate a volcano plot of differentially abundant proteins. Most notably, both exogenous β-catenin-sfGFP (CTNNB1GFP) and endogenous β-catenin (CTNNB1) were among the few proteins that were abundantly present in the β-catenin-stabilizing duAb samples over the non-targeting duAb control. I Overexpressed β-catenin-sfGFP (CTNNB1GFP) abundances comparing non-targeting vs. β-catenin-stabilizing duAb treatment in HEK293T cells. J Endogenous β-catenin (CTNNB1) abundances comparing non-targeting vs. β-catenin-stabilizing duAb treatment in HEK293T cells. Please refer to source data for numeric p values. Finally, to assess the specificity of our peptide-guided OTUB1 system, we performed one-dimensional liquid chromatography-tandem mass spectrometry (1D-LC-MS/MS) analysis on total proteins harvested from HEK293T cells overexpressing β-catenin-sfGFP, with treatment of either our non-targeting, polyG-L2-OTUB1 fusion or our β-cat_SnP_7-L2-OTUB1 fusion (Fig. Quantifying the abundances of approximately 9300 proteins, our analysis demonstrated increased levels of both β-catenin-sfGFP and endogenous β-catenin (Fig. In comparison, there were minimal changes in the abundance of other proteins. However, we posit that increased “off-target” protein abundance may likely be attributed to downstream functional changes as a result of β-catenin stabilization. For example, Axin 2 (ACTN2), a known regulator of Wnt signaling22, was upregulated, as was NEIL1, which initiates colorectal cancer phenotypes by destabilizing DNA damage23. Together, these results establish our peptide-guided OTUB1 system, which we henceforth refer to as deubiquibodies or “duAbs”, as a potent and accurate system for TPS. Next, we sought to demonstrate duAb programmability by designing peptides to diverse target proteins. As many disease-related proteins are conformationally disordered, we decided to leverage protein language models trained to design peptide binders provided only input sequences, rather than 3D structures (Fig. We first focused our attention on FOXP3, a classically undruggable transcription factor that plays a central role in the development and function of regulatory T cells (Tregs)24. FOXP3 is naturally regulated by the CHIP E3 ubiquitin ligase, which is expressed in HEK293T cells25. We applied the SaLT&PepPr interface-prediction algorithm to isolate guide peptides from its well-known interacting partner, NFAT (Supplementary Table 2)25,26 and subsequently tested the corresponding peptide-guided duAbs in a FOXP3-mCherry HEK293T stable cell line. Our results demonstrate that SaLT&PepPr-derived duAbs induce statistically significant stabilization of FOXP3-mCherry in a DUB-dependent manner, outperforming a duAb composed of a previously-designed P60D2A FOXP3-targeting peptide (Fig. A Programmable target stabilization via language model-derived peptides. Cellular mCherry fluorescence was measured by flow cytometry in independent replicates (n = 3). Normalized cell fluorescence was calculated by dividing the percentage of mCherry+ cells in a sample by that of control cells expressing a duAb vector expressing a non-specific poly-glycine (polyG) control peptide sequence. C Stabilization of endogenous WEE1 in protein extracts of HepG2 cells analyzed by immunoblotting. Cells were transiently transfected with a pcDNA3 plasmid encoding a polyG-OTUB1 control or one of the peptide-guided OTUB1 constructs as indicated. Transient transfection with an empty pcDNA3 plasmid served as an additional control. Blots were probed with anti-WEE1 and anti-GAPDH antibodies and are representative of biological replicates (n = 3) and technical replicates (n = 2) with similar results. D Stabilization of endogenous PAX3::FOXO1 in protein extracts of RH4 cells analyzed by immunoblotting. RH4 cells were transiently transfected with a pcDNA3 plasmid encoding one of the candidate duAbs while transfection with a polyG peptide-guided duAb served as a control. Blots were probed with anti-FOXO1 and anti-GAPDH antibodies and are representative of biological replicates (n = 3). For all immunoblots in (C) and (D), an equivalent amount of protein was loaded in each lane. Molecular weight (MW) ladder is indicated at left. Intensity of target protein bands was calculated via densitometry and normalized to intensity of GAPDH loading control and then normalized to polyG-OTUB1 control. Data are the average of biological replicates and technical replicates (n = 3 for WEE1 and PAX3::FOXO1). The p values above each bar in the fold stabilization and densitometry analyses represent the comparison between the control (polyG-OTUB1, no DUB inhibitor) and the respective sample; all other p value notations compare the specified samples. Please refer to source data for numeric p values. All structures were predicted via the AlphaFold3 server, and the shading was done according to AlphaFold's confidence metric, plDDT, as follows: Very low (plDDT <50) = Orange, Low (70 > plDDT > 50) = Yellow, Confident (70 > plDDT > 90) = Light Blue, Very high (plDDT > 90) = Light Blue. Encouraged by the stabilization of FOXP3, we next focused our attention on WEE1, an inhibitor of tumor growth in non-cancerous eukaryotic somatic cells. Specifically, WEE1 acts as a kinase to phosphorylate the cyclin-dependent kinase (CDK1)–cyclin B1 complex28. This phosphorylation hinders cell cycle advancement in the S and G2 phases of mitosis28. WEE1 has been shown to be regulated by the ubiquitin-proteasomal pathway in hepatocellular carcinoma cell lines and that treatment with a proteasome inhibitor or DUBTAC leads to WEE1 stabilization in these cells6,29,30. To target WEE1 for duAb-mediated stabilization, we designed six WEE1-specific peptides via a de novo peptide design algorithm, PepPrCLIP (Supplementary Table 2)12. The resulting guide peptides were each fused to OTUB1 in our duAb plasmid and tested in HepG2 hepatocellular carcinoma cells. Immunoblot analysis with an anti-WEE1 antibody revealed that each of the peptide-guided duAbs induced statistically significant stabilization of endogenous WEE1 (Fig. Fusion oncoproteins drive pediatric cancers, such as EWS::FLI1 for Ewing sarcoma, exhibit a “Goldilocks” phenomenon, where suppression of their ubiquitination can induce fusion oncoprotein overdose and cancer cell death31. However, pharmacologically stabilizing these proteins is highly difficult, as these proteins exhibit almost complete structural disorder with no discernable binding pockets (Fig. To overcome this structural disorder, we used the recently developed peptide generator, PepMLM, which only requires the target sequence as input and outperforms structure-based RFDiffusion11, to generate ten PAX3::FOXO1-targeting, the predominant driver of pediatric alveolar rhabdomyosarcoma (ARMS)33. After transfecting plasmids encoding these peptide-guided duAbs into fusion-positive RH4 ARMS cells, we observed stable increases in the levels of PAX3::FOXO1 fusion oncoprotein for five of the duAb designs (Fig. Finally, we sought to stabilize p53, a key tumor suppressor protein that regulates cell cycle arrest, apoptosis, and DNA repair in response to cellular stress and DNA damage34. The ability to stabilize p53 with duAbs would ensure its availability to suppress tumor formation and growth by maintaining genomic integrity and inhibiting malignant cell proliferation (Fig. 4B), thus we designed eight peptides using PepMLM11. As p53 is destabilized via ubiquitination in human cervical carcinoma, amongst many other cancers, we transfected HeLa cells with plasmid DNA encoding eight different duAb designs36. Immunoblot analysis revealed that two duAbs, p53_pMLM_4 and p53_pMLM_5, exhibited potent duAb-dependent stabilization as evidenced by significant increases in endogenous p53 levels (Fig. A Programmable design of p53-targeting duAbs, encapsulation and delivery via mRNA-encapsulated lipid nanoparticles (LNPs), and downstream apoptosis activation. B Stabilization of endogenous p53 in protein extracts of HeLa cells analyzed by immunoblotting. HeLa cells were transiently transfected with a pcDNA3 plasmid encoding one of the candidate duAbs while transfection with a polyG peptide-guided duAb served as a control. An equivalent amount of protein was loaded in each lane. Blots were probed with anti-p53 and anti-GAPDH antibodies and are representative of biological replicates (n = 3). C Stabilization of endogenous p53 in protein extracts of HeLa cells after the best p53-stabilizing duAb (p53_pMLM_4-OTUB1) was delivered via LNPs analyzed by immunoblotting. HeLa cells were transiently transfected with LNPs encapsulating p53_pMLM_4-duAbs encoded as mRNA (loaded 1 μg and 2 μg, respectively) while transfection with luciferase-encoding mRNA-LNP served as a control. An equivalent amount of protein was loaded in each lane. Blots were probed with anti-p53 and anti-Vinculin antibodies and are representative of biological replicates (n = 3). D Increase in apoptosis hallmark cleaved-PARP-1 (Cl-PARP-1) in protein extracts of HeLa cells after the best p53-stabilizing duAb (p53_pMLM_4-OTUB1) was delivered via LNPs analyzed by immunoblotting. HeLa cells were transiently transfected with LNPs encapsulating p53_pMLM_4-duAbs encoded as mRNA (loaded 1 μg and 2 μg, respectively) while transfection with luciferase-encoding mRNA-LNP served as a control. An equivalent amount of protein was loaded in each lane. Blots were probed with anti-Cl-PARP-1 and anti-Vinculin antibodies and are representative of biological replicates (n = 3). For all immunoblots in (B–D), an equivalent amount of protein was loaded in each lane. Molecular weight (MW) ladder is indicated at left. Intensity of target protein bands was calculated via densitometry and normalized to intensity of GAPDH and Vinculin loading controls and then normalized to applicable controls (polyG-OTUB1 for (B) and luciferase LNP for (C) and (D)). Data are the average of biological replicates and technical replicates (n = 3 for p53 and Cl-PARP-1). Please refer to source data for numeric p values. The structure for p53 was predicted via the AlphaFold3 server, and the shading was done according to AlphaFold's confidence metric, plDDT, as follows: very low (plDDT <50) = orange, low (70 > plDDT > 50) = yellow, confident (70 > plDDT > 90) = light blue, very high (plDDT > 90) = light blue. Previous studies have shown successful LNP-mediated delivery of genetically encodable TPD modalities as mRNA37,38,39,40,41. Thus, we encapsulated our top p53 stabilizer – p53_pMLM_4-duAb – in LNPs, delivered them in HeLa cells, and showed via immunoblot analysis that we can similarly stabilize endogenous p53 levels (Fig. We further evaluated downstream functional effects via PARP-1 cleavage, which has been shown to be a hallmark of apoptosis activation (Fig. 4A)42, and exhibited significant cleaved-PARP-1 expression upon treatment of our p53-stabilizing duAbs (Fig. In total, these results motivate further in vivo translation of the duAb platform for therapeutic applications. In this work, we have demonstrated that our genetically encodable duAbs represent a modular platform for rescuing ubiquitinated proteins, particularly those that are otherwise “undruggable” by conventional small molecule-based strategies. While we see evidence of target stabilization via OTUD1 and OTUB1 domains, we did not observe this same effect for UBC9 and UCHL1. These results can be corroborated with studies that describe UBC9 as a SUMO-conjugating enzyme rather than a hydrolase43,44. In comparison, while UCHL1 is a potent deubiquitinase that is well expressed across different cell types, it primarily targets mono-ubiquitinated proteins and binds weakly to polyubiquitinated proteins due to the structure of its active site45,46. Additionally, while OTUD1's catalytic domain has been leveraged previously13, its performance was not as strong as the OTUB1 catalytic domain in our study; this may be attributed to its facilitation of K63-deubiquitination rather than K48-deubiquitination, which plays a role in autophagy and pathways other than ubiquitin-proteasome regulation47,48. As duAbs are ~290 amino acids in length (Supplementary Table 1), their intracellular delivery, at first glance, poses a challenge for therapeutic application. However, with the rapid advancements of targeted LNP platforms49, duAbs can be readily encapsulated as mRNA and delivered to specific tissues of interest37,39, as opposed to DUBTACs, which like PROTACs, may home to any tissue, risking potential side effects and toxicity50. Here, we designed LNPs to deliver p53-targeting duAbs, which not only induced p53 stabilization but also activated downstream apoptosis. Interestingly, we noticed that increasing the level of mRNA payload did not increase p53 stabilization efficiency. This may be due to a hook effect, where increasing the amount of payload overdetermined thresholds may lead to lower levels of translated protein51. Nonetheless, with further optimization, duAbs delivered via LNPs could provide a targeted and tunable approach for TPS, minimizing off-target effects while maximizing therapeutic efficacy in disease-specific contexts. Finally, as a genetically encoded tool, peptide-guided duAbs, alongside uAbs, could serve as a powerful platform for proteome-wide target modulation, enabling combinatorial screening of protein activation and inhibition, similar to CRISPRa and CRISPRi for genetic screening52. With advances in pLM architectures, our language model-generated peptides can be further optimized to selectively bind post-translational and mutant isoforms of target proteins53,54,55, and fused to diverse PTM domains, including kinases, phosphatases, acetylases, and deglycosylases7. In total, this study represents a next step towards this eventual goal of a fully programmable proteome editing system. The β-cat_SnP_7 peptide10, β-cat_SnP_8 peptide10, P60D2A peptide27, and YFP nanobodies13 were described in previous works and obtained from respective manuscript metadata. Binding peptides designed in this study were either generated by the previously-described SaLT&PepPr algorithm10 (https://huggingface.co/ubiquitx/saltnpeppr) via input of an interacting partner sequence, by the de novo PepPrCLIP algorithm12 (https://huggingface.co/ubiquitx/pepprclip) via input of the target protein sequence, or by the target sequence-conditioned PepMLM algorithm11 (https://huggingface.co/ChatterjeeLab/PepMLM-650M)11. All binder sequences can be found in Supplementary Table 2. All duAb plasmids were generated from the standard pcDNA3 vector, harboring a cytomegalovirus (CMV) promoter. An Esp3I restriction site was introduced immediately upstream of the OTUB1 catalytic domain and flexible GSGSG linker via the KLD Enzyme Mix (NEB, Cat # M0554S) following PCR amplification with mutagenic primers (Azenta). For duAb assembly, oligos for candidate peptides were annealed and ligated via T4 DNA Ligase (NEB, Cat # M0202S) into the Esp3I-digested duAb backbone. Assembled constructs were transformed into 50 μL NEB Turbo Competent Escherichia coli cells (NEB, Cat # C2984H), and plated onto LB agar supplemented with the appropriate antibiotic for subsequent sequence verification of colonies and plasmid purification (Azenta). The HEK293T and HeLa cell lines were maintained in Dulbecco's Modified Eagle's Medium (DMEM, Gibco Cat # 11995073) supplemented with 100 units/mL penicillin, 100 mg/mL streptomycin (Gibco, Cat # 15140122), and 10% fetal bovine serum (FBS, Gibco, Cat # A5670402). The hepatocellular carcinoma cell line, HepG2, was maintained in Eagle's Minimum Essential Medium (EMEM, Sigma Aldrich Cat # M2279-500ML) supplemented with 100 units/mL penicillin, 100 mg/mL streptomycin, and 10% fetal bovine serum (FBS). The alveolar rhabdomyosarcoma cell line, RH4, was maintained in RPMI 1640 supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, and 10% fetal bovine serum (FBS). The RH4 cell line was a generous gift from Dr. Corinne Linardic. For duAb screening in reporter cell lines, pcDNA-duAb (500 ng) plasmids were transfected into cells as triplicates (2 × 105/well in a 24-well plate) with Lipofectamine 2000 (Invitrogen, Cat # 11668027) in Opti-MEM (Gibco, Cat # 31985062). After 2 days post transfection, 4 μM PR-619 (DUB inhibitor, MedChemExpress, Cat # HY-13814) was added to applicable cells (with equivalent volume of media added to non-treated cells), and subsequently cells were harvested within 24 hours post-treatment and analyzed on a Attune NxT Flow Cytometer (ThermoFisher) for GFP fluorescence (488-nm laser excitation, 530/30 filter for detection) and mCherry fluorescence (561-nm laser excitation, 620/15 filter for detection). 10,000 events were gated for data analysis based on default FSC/SSC parameters for the analyzed cells. Cells expressing eGFP and mCherry were gated, and these were normalized to a sample transfected with a non-targeting duAb using the FlowJo software (https://flowjo.com/). Representative flow cytometry gating strategies are indicated in Supplementary Fig. For endogenous target screening in cell lines, pcDNA-duAb (800 ng) plasmids were transfected into cells as duplicates (3 × 105/well in a 12-well plate) with Lipofectamine 2000 (Invitrogen) in Opti-MEM (Gibco). Cells were harvested after 72 h for subsequent cell fractionation and immunoblotting. For target-reporter packaging, HEK293T cells were seeded in a 6-well plate and transfected at ~50% confluency. For each well, 0.5 μg pMD2.G (Addgene #12259), 1.5 μg psPAX2 (Addgene #12260) and 0.5 μg of the target-mCherry reporter transfer vector were transfected with Lipofectamine 3000 (Invitrogen) according to the manufacturer's protocol. The medium was exchanged 8 hours post transfection, and the viral supernatant was harvested at 48 and 72 hours post transfection. The viral supernatant was concentrated to 100x in 1× DPBS using Lenti-X Concentrator (Clontech, Cat # 631232) according to the manufacturer's instructions, and stored at −80 °C for further use. For target-reporter cell line generation, 1 × 105 HEK293T cells were mixed with 20 μL of the concentrated virus in a 6-well plate. Media was changed 24 h post transduction. Antibiotic selection was started 36 h post transduction by adding 2 μg/mL puromycin (Sigma, Cat # P8833). Cells were harvested for sorting at 5 days post antibiotic selection, and a single cell of mCherry positive was plated in a 96-well plate. Genomic PCR was performed after cell growth to validate the genotype of the monoclonal cell line. HEK293T cells were maintained in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, and 10% FBS. Target-sfGFP (1 μg) + pcDNA3-duAb (1 μg) plasmids were transfected into cells as triplicates (5 × 105/well in a 6-well plate) with Lipofectamine 2000 (Invitrogen) in Opti-MEM (Gibco). After 72 h post transfection, cells were harvested and washed four times with 500 μL 1× cold PBS. The cell pellets were resuspended in 300 μL Pierce RIPA buffer (ThermoFisher, Cat # 89900) and incubated on ice for 30 min. The homogenates were treated with 20% (w/v) SDS in triethylammonium bicarbonate buffer, pH 8.5 (Sigma Aldrich, Cat # T7408), followed by probe sonication and heating at 80 °C for 5 min. The supernatants were collected after centrifugation and the concentrations were determined using detergent-compatible Bradford assay. From each sample, 20 μg was reduced and alkylated, and digested with trypsin using an S-trap micro device. Peptide eluents were lyophilized, and after reconstitution, equal volumes of each sample were mixed to make an SPQC pool. Approximately 1 μg of each sample, and three replicates of the SPQC pool were analyzed by 1D-LCMS/MS. Samples were analyzed using a M-Class UPLC system (Waters) coupled to an Exploris 480 high resolution accurate tandem mass spectrometer (ThermoFisher) via a Nanospray Flex Ion source and processed using Spectronaut 16. The p values were calculated by performing a Student's t-test on log2fc values. For the TOP-GFP assay, 2 × 105 HEK293T cells/well were seeded on a 24-well plate 20–24 h prior to transfection. On the day of transfection, each well received the following plasmids: TOP-GFP plasmid (Addgene #35489) and a duAb plasmid. A total of 500 ng of plasmid DNA in a ratio of TOP-GFP:duAb plasmids = 1:1 was mixed with Lipofectamine 2000 reagent (Invitrogen) in serum-free Opti-MEM medium (Gibco) and added dropwise to each well after incubation at room temperature for 20 min. After 72 h of incubation, cells were harvested and analyzed similarly as mentioned for duAb screening. Viable, single cells were gated, and normalized EGFP cell fluorescence was calculated as compared to a sample transfected with a non-targeting duAb, using the FlowJo software (https://flowjo.com/). mRNA with ARCA cap and poly(A) tail additions for p53_pMLM_4-OTUB1 was synthesized via in vitro transcription using the HiScribe T7 ARCA mRNA Kit (NEB, Cat # E2060S). The mRNA was then concentrated and cleaned of impurities using the RNEasy MinElute Cleanup Kit (Qiagen, Cat # 74204). CleanCap® FLuc mRNA (NEB, Cat # L7602-100) was used as a control. Lipid nanoparticles (LNPs) were prepared by diluting DLIN-MC3-DMA (MedKoo Biosciences, Cat # 555308), DSPC (Avanti Polar Lipids, Cat # 850365P-500mg), Cholesterol (Sigma Aldrich, Cat # C3045), and DMG-PEG2000 (NOF American Corporation, Cat # GM-020) in ethanol using standard molar ratios 50:10:38.5:1.5, respectively. The prepared mRNA for p53_pMLM_4-OTUB1 and luciferase were diluted in 10 mM citrate buffer (ThermoFisher, Cat # J61249.AP) in a 2:1 volume ratio with the lipid mixture, and mRNA was loaded in a 1:20 mass ratio with the lipid, respectively, in a NanoAssemblr™ Spark™ nanoparticle formulation system (Cytiva, Cat # NIS0001). After LNP production, they were transfected into HeLa cells 48 h post-seeding and were extracted 72 h post transfection for immunoblot analysis. On the day of harvest, cells were detached by addition of 0.05% trypsin-EDTA and cell pellets were washed twice with ice-cold 1× PBS. Cells were then lysed and subcellular fractions were isolated from lysates using a 1:100 dilution of protease inhibitor cocktail (Millipore Sigma, Cat # P8340) in Pierce RIPA buffer (ThermoFisher, Cat # 89900). Specifically, the protease inhibitor cocktail-RIPA buffer solution was added to the cell pellet, the mixture was placed at 4 °C for 30 min followed by centrifugation at 15,000 rpm for 10 min at 4 °C. The supernatant was collected immediately to pre-chilled PCR tubes and quantified using the Pierce BCA Protein Assay Kit (ThermoFisher, Cat # 23227). Twenty micrograms lysed protein was mixed with 4× Bolt™ LDS Sample Buffer (ThermoFisher, Cat # NP0007) with 5% β-mercaptoethanol (Millipore Sigma, Cat # M3148) in a 3:1 ratio and subsequently incubated at 95 °C for 10 min prior to immunoblotting, which was performed according to standard protocols. Briefly, samples were loaded at equal volumes into Bolt™ Bis-Tris Plus Mini Protein Gels (ThermoFisher, Cat # NW04125BOX) and separated by electrophoresis. iBlot™ 2 Transfer Stacks (Invitrogen) were used for membrane blot transfer, and following a 1 h room-temperature incubation in 5% milk-TBST, proteins were probed with rabbit anti-WEE1 antibody (Abcam, Cat # ab137377; diluted 1:1000), mouse anti-p53 antibody (Santa Cruz Biotechnology, Cat # sc-126; diluted 1:1000), rabbit anti-FOXO1 antibody (Cell Signaling Technology, Cat # 2880S; diluted 1:1000), rabbit anti-Cl-PARP-1 (Cell Signaling Technology, Cat # 5625 T, diluted 1:750), rabbit anti-Vinculin (Invitrogen, Cat # 700062; diluted 1:2000), or mouse anti-GAPDH (Santa Cruz Biotechnology, Cat # sc-47724; diluted 1:10,000) for overnight incubation at 4 °C. The blots were washed three times with 1X TBST for 5 min each and then probed with a secondary antibody, donkey anti-rabbit IgG (H + L), horseradish peroxidase (HRP) (Abcam, Cat # ab7083, diluted 1:5000) or goat anti-mouse IgG (H + L) Poly-HRP (ThermoFisher, Cat # 32230, diluted 1:5000) for 1–2 h at room temperature. Following three washes with 1× TBST for 5 min each, blots were detected by chemiluminescence using a BioRad ChemiDoc™ Touch Imaging System (Biorad). Densitometry analysis of protein bands in immunoblots was performed using ImageJ software as described here: https://imagej.nih.gov/ij/docs/examples/dot-blot/. Briefly, bands in each lane were grouped as a row or a horizontal “lane” and quantified using FIJI's gel analysis function. Intensity data for the duAb bands was first normalized to band intensity of either GAPDH or Vinculin in each lane then to the average band intensity for empty duAb vector control cases across replicates. All structures were predicted via the AlphaFold3 server (https://alphafoldserver.com/), and the shading was done according to AlphaFold's confidence metric, plDDT, as follows: Very low (plDDT <50) = Orange, Low (70 > plDDT > 50) = Yellow, Confident (70 > plDDT > 90) = Light Blue, Very high (plDDT > 90) = Light Blue. Sample sizes were not predetermined based on statistical methods but were chosen according to the standards of the field (three independent biological replicates for each condition), which gave sufficient statistics for the effect sizes of interest. All data were reported as average values with error bars representing standard deviation (SD). The p value representations above each bar in the fold stabilization and densitometry analyses are indicative of comparisons between the control and the respective sample; all other p value notations are between the specified samples. No data were excluded from the analyses. The experiments were not randomized. The investigators were not blinded to allocation during experiments and outcome assessment. Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article. All data needed to evaluate the conclusions in the paper are present in the paper and supplementary tables. Raw and processed data underlying graphical figures (including raw immunoblots) are provided as Source Data, which can be found in our Zenodo depository: https://doi.org/10.5281/zenodo.15121468. The duAb cloning vector (#232089) has been deposited to Addgene: https://www.addgene.org/232089/. Source data are provided with this paper. & Jia, D. Targeted protein degradation: mechanisms, strategies and application. Sabapathy, K. & Lane, D. P. Therapeutic targeting of p53: all mutants are equal, but some mutants are more equal than others. Ward, C. L., Omura, S. & Kopito, R. R. Degradation of CFTR by the ubiquitin-proteasome pathway. Rao, G., Croft, B., Teng, C. & Awasthi, V. Ubiquitin-proteasome system in neurodegenerative disorders. Costes, S. et al. β-cell dysfunctional ERAD/ubiquitin/proteasome system in type 2 diabetes mediated by islet amyloid polypeptide-induced UCH-L1 deficiency. Henning, N. J. et al. Deubiquitinase-targeting chimeras for targeted protein stabilization. Chen, T., Hong, L., Yudistyra, V., Vincoff, S. & Chatterjee, P. Generative design of therapeutics that bind and modulate protein states. Portnoff, A. D., Stephens, E. A., Varner, J. D. & DeLisa, M. P. Ubiquibodies, synthetic E3 ubiquitin ligases endowed with unnatural substrate specificity for targeted protein silencing. Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions. Brixi, G. et al. SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders. Chen, T. et al. PepMLM: Target sequence-conditioned generation of peptide binders via masked language modeling. Bhat, S. et al. De novo design of peptide binders to conformationally diverse targets with contrastive language modeling. Kanner, S. A., Shuja, Z., Choudhury, P., Jain, A. & Colecraft, H. M. Targeted deubiquitination rescues distinct trafficking-deficient ion channelopathies. Poirson, J. et al. Proteome-scale discovery of protein degradation and stabilization effectors. UniProt: the universal protein knowledgebase in 2023. The KCNQ1 potassium channel is down-regulated by ubiquitylating enzymes of the Nedd4/Nedd4-like family. Hsu, F.-S. et al. PR-619, a General inhibitor of deubiquitylating enzymes, diminishes cisplatin resistance in urothelial carcinoma cells through the suppression of c-Myc: an in vitro and in vivo study. Seo, S. U. et al. Phosphorylation of OTUB1 at Tyr 26 stabilizes the mTORC1 component, Raptor. Wu, Q., Huang, Y., Gu, L., Chang, Z. & Li, G.-M. OTUB1 stabilizes mismatch repair protein MSH2 by blocking ubiquitination. Tan, C. W., Gardiner, B. S., Hirokawa, Y., Smith, D. W. & Burgess, A. W. Analysis of Wnt signaling β-catenin spatial dynamics in HEK293T cells. Differential WNT activity in colorectal cancer confers limited tumorigenic potential and is regulated by MAPK signaling. Cao, J.-H. et al. NEIL1 drives the initiation of colorectal cancer through transcriptional regulation of COL17A1. Hori, S. FOXP3 as a master regulator of Treg cells. Barbi, J., Pardoll, D. M. & Pan, F. Ubiquitin-dependent regulation of Foxp3 and Treg function. Wu, Y. et al. FOXP3 controls regulatory T cell function through cooperation with NFAT. Lozano, T. et al. Blockage of FOXP3 transcription factor dimerization and FOXP3/AML1 interaction inhibits T regulatory cell activity: sequence optimization of a peptide inhibitor. Ghelli Luserna di Rorà, A., Cerchione, C., Martinelli, G. & Simonetti, G. A WEE1 family business: regulation of mitosis, cancer progression, and therapeutic target. Hashimoto, O. et al. Inhibition of proteasome-dependent degradation of Wee1 in G2-arrested Hep3B cells by TGF beta 1. Cruz, L., Soares, P. & Correia, M. Ubiquitin-specific proteases: players in cancer cellular processes. Seong, B. K. A. et al. TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma. Defining the condensate landscape of fusion oncoproteins. Linardic, C. M. PAX3-FOXO1 fusion gene in rhabdomyosarcoma. Kastenhuber, E. R. & Lowe, S. W. Putting p53 in context. Lavin, M. F. & Gueven, N. The complexity of p53 stabilization and activation. Wesierska-Gadek, J., Schloffer, D., Kotala, V. & Horky, M. Escape of p53 protein from E6-mediated degradation in HeLa cells after cisplatin therapy. Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR-Cas gene editing. Ghosal, S. et al. Nanoparticle-mediated delivery of peptide-based degraders enables targeted protein degradation. Riley, R. S. et al. Ionizable lipid nanoparticles for in utero mRNA delivery. Chan, A. et al. Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins. Programmable protein degraders enable selective knockdown of pathogenic β-catenin subpopulations in vitro and in vivo. The 89-kDa PARP1 cleavage fragment serves as a cytoplasmic PAR carrier to induce AIF-mediated apoptosis. Knipscheer, P. et al. Ubc9 sumoylation regulates SUMO target discrimination. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1. Bishop, P., Rocca, D. & Henley, J. M. Ubiquitin C-terminal hydrolase L1 (UCH-L1): structure, distribution and roles in brain function and dysfunction. Mevissen, T. E. T. et al. OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis. Hou, X., Zaks, T., Langer, R. & Dong, Y. Lipid nanoparticles for mRNA delivery. Chen, Y. et al. Proteolysis-targeting chimera (PROTAC) delivery system: advancing protein degraders towards clinical translation. Patel, N. et al. Development and characterization of an in vitro cell-based assay to predict potency of mRNA-LNP-based vaccines. Kampmann, M. CRISPRi and CRISPRa screens in mammalian cells for precision biology and medicine. & Chatterjee, P. PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks. & Chatterjee, P. moPPIt: generation of motif-specific binders with protein language models. Vincoff, S. et al. FusOn-pLM: a fusion oncoprotein-specific language model via adjusted rate masking. We thank the Colecraft Lab at Columbia University for providing enDUBO1 and KCNQ1-YFP constructs. We also thank Dr. Matthew Foster and Marlene Violette at the Duke Proteomics and Metabolomics Core Facility for assistance with proteomics experiments and analysis. We further thank Dr. Qianben Wang and Dr. Zhifen Cui at Duke University for allowing usage of the NanoAssemblr Spark for lipid nanoparticle formulation and providing technical expertise. The research was supported by institutional startup funds to the lab of P.C. from Duke University, as well as the Wallace H. Coulter Foundation, The Hartwell Foundation, and NIH grants 3U54CA231630-01A1S4 and 1R21CA278468-01. The SaLT&PepPr and PepPrCLIP algorithms were provided and developed in conjunction with UbiquiTx, Inc. These authors contributed equally: Lauren Hong, Tianzheng Ye, Tian Z. Wang. Department of Biomedical Engineering, Duke University, Durham, NC, USA Lauren Hong, Tian Z. Wang, Divya Srijay, Howard Liu, Lin Zhao, Rio Watson, Sophia Vincoff, Tianlai Chen, Kseniia Kholina, Shrey Goel & Pranam Chatterjee Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA Department of Computer Science, Duke University, Durham, NC, USA Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar You can also search for this author inPubMed Google Scholar built constructs, conducted transfections, carried out Western blotting and flow cytometry experiments, and performed data analyses, with assistance from T.Z.W., D.S., and R.W. conducted p53 LNP experiments with assistance from H.L. developed fluorescent reporter cell lines. designed guide peptides, with assistance from K.K. All authors reviewed and edited the paper. conceived, designed, directed, and supervised the study. are listed as inventors on US Patent Application 63/541,921: “Peptide-Guided Protein Stabilizers and Uses Thereof”. are co-founders of UbiquiTx, Inc., which commercializes genetically encoded proteome editing technologies, and are co-inventors of duAb patents. 's interests are reviewed and managed by Duke University in accordance with their conflict-of-interest policies. 's interests are reviewed and managed by Cornell University in accordance with their conflict-of-interest policies. Nature Communications thanks Marc Güell, Matylda Izert-Nowakowska and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available. Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. Programmable protein stabilization with language model-derived peptide guides. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.