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Sailing history is rife with tales of monster-sized rogue waves — huge, towering walls of water that seemingly rise up from nothing to dwarf, then deluge, vessel and crew. Rogue waves can measure eight times higher than the surrounding seas and can strike in otherwise calm waters, with virtually no warning. Now a prediction tool developed by MIT engineers may give sailors a 2-3 minute warning of an incoming rogue wave, providing them with enough time to shut down essential operations on a ship or offshore platform. The tool, in the form of an algorithm, sifts through data from surrounding waves to spot clusters of waves that may develop into a rogue wave. Depending on a wave group’s length and height, the algorithm computes a probability that the group will turn into a rogue wave within the next few minutes. “It’s precise in the sense that it’s telling us very accurately the location and the time that this rare event will happen,” says Themis Sapsis, the American Bureau of Shipping Career Development Assistant Professor of Mechanical Engineering at MIT. “We have a range of possibilities, and we can say that this will be a dangerous wave, and you’d better do something. That’s really all you need.” Sapsis and former postdoc Will Cousins have published their results this week in the Journal of Fluid Mechanics. Like many complex systems, the open ocean can be represented as a chaotic mix of constantly changing data points. To understand and predict rare events such as rogue waves, scientists have typically taken a leave-no-wave-behind approach, in which they try to simulate every individual wave in a given body of water, to give a high-resolution picture of the sea state, as well as any suspicious, rogue-like activity. This extremely detailed approach is also computationally expensive, as it requires a cluster of computers to solve equations for each and every wave, and their interactions with surrounding waves. “It’s accurate, but it’s extremely slow — you cannot run these computations on your laptop,” Sapsis says. “There’s no way to predict rogue waves practically. That’s the gap we’re trying to address.” Sapsis and Cousins devised a much simpler, faster way to predict rogue waves, given data on the surrounding wave field. In previous work, the team identified one mechanism by which rogue waves form in unidirectional wave fields. They observed that, while the open ocean consists of many waves, most of which move independently of each other, some waves cluster together in a single wave group, rolling through the ocean together. Certain wave groups, they found, end up “focusing” or exchanging energy in a way that eventually leads to an extreme rogue wave. “These waves really talk to each other,” Sapsis says. “They interact and exchange energy. It’s not just bad luck. It’s the dynamics that create this phenomenon.” In their current work, the researchers sought to identify precursors, or patterns in those wave groups that ultimately end up as rogue waves. To do this, they combined ocean wave data available from measurements taken by ocean buoys, with nonlinear analysis of the underlying water wave equations. Sapsis and Cousins used the statistical data to quantify the range of wave possibilities, for a given body of water. They then developed a novel approach to analyze the nonlinear dynamics of the system and predict which wave groups will evolve into extreme rogue waves. They were able to predict which groups turned rogue, based on two parameters: a wave group’s length and height. The combination of statistics and dynamics helped the team identify the length-scale of a critical wave group, which has the highest likelihood of evolving into a rogue wave. Using this, the team derived a simple algorithm to predict a rogue wave based on incoming data. By tracking the energy of the surrounding wave field over this length-scale, they could immediately calculate the probability of a rogue wave developing. “Using data and equations, we’ve determined for any given sea state the wave groups that can evolve into rogue waves,” Sapsis says. “Of those, we only observe the ones with the highest probability of turning into a rare event. That’s extremely efficient to do.” Sapsis says the team’s algorithm is able to predict rogue waves several minutes before they fully develop. To put the algorithm into practice, he says ships and offshore platforms will have to utilize high-resolution scanning technologies such as LIDAR and radar to measure the surrounding waves. “If we know the wave field, we can identify immediately what would be the critical length scale that one has to observe, and then identify spatial regions with high probability for a rare event,” Sapsis says. “If you are performing operations on an aircraft carrier or offshore platform, this is extremely important.” “The approach is original — it is fast, easy to implement, and it does not require computational power,” says Miguel Onorato, professor of physics at the University of Turin, who was not involved in the research. “Tests in wave basins and field measurements data are needed in order to establish reliability of the tool in realistic conditions.” This research was supported in part by the Office of Naval Research, the Army Research Office, and the American Bureau of Shipping.

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For those of you who take sandcastle building very seriously, listen up: MIT engineers now say you can trust a very simple equation to calculate the force required to push a shovel — and any other “intruder”— through sand. The team also found that the same concept, known as the resistive force theory, can generate useful equations  for cohesive materials like muds. Aside from calculating the elbow grease needed to carve out a beachside moat, the researchers say the equation can be used to optimize the way vehicles drive over gravel and soil, such as rovers navigating the Martian landscape. It can also help illuminate the ways in which animals such as lizards and worms burrow through earth. Resistive force theory (RFT) is not new and in fact was proposed in the 1950s to describe the way in which objects move through viscous fluids such as water (on small scales) and honey. It was only much later that scientists thought to apply the same idea to granular material such as sand; they found the theory predicted the force required to move objects through grains even better than its analog for fluids. The reason for this has been a mystery, particularly since predicting granular versus fluid behavior is notoriously difficult. Ken Kamrin, associate professor of mechanical engineering at MIT, says scientists have regarded granular RFT as “somewhat like magic,” unsure of what makes the concept work so spot-on for sand. In a paper published today in Nature Materials, Kamrin, along with former MIT postdoc Hesam Askari, have essentially solved this mystery. They report that they have identified a mechanical explanation for why the equation works so well for granular materials. Now, they say that scientists have reason to trust the resistive force theory to give accurate force estimates through sand, and even pastier materials like mud and gels. “People observed this concept worked but didn’t know why, and that’s really shaky ground for scientists — is it just a coincidence?” Kamrin says. “Now we can explain the backbone of the granular resistive force theory, so you can close your eyes and have confidence that it’s going to work. It gives us some fleeting hope that we might be able to design something that more efficiently moves, swims, or drives over sand.” Granular RFT works like this: Imagine you are working with a shovel, buried at a certain depth in the sand. You want to know how much to push on the shovel, to move it in a particular direction. To answer this question, you first need to do some experiments with a small, square plate, made from the same material as your shovel. Push the plate through sand, starting from all possible orientations and moving in all possible directions. During each test, measure the amount of force it takes to move the plate. According to the theory, you can think of the shovel as an assemblage of similar small plates. To estimate the force required to move the shovel, simply imagine each plate is on its own and add up all the tiny, individual forces of each plate, at each specific location and orientation along the shovel. As it turns out, this theory works remarkably well for granular materials, and somewhat well in fluids. “If something is working well, it would be nice to know why,” Kamrin says. “There may be a large set of problems you might solve if you knew why the intrusion problem is so easy to figure out in sand.” Kamrin set out to write the simplest equation he could think of that would represent granular flows, to see whether the equation, and the mechanical relationships it defines, could also reproduce the simplified picture assumed in resistive force theory. If so, he reasoned, the equation — also called a continuum model — could give a mechanical explanation for why RFT works, and furthermore, validate the theory. The equation he came up with is a variant of a standard model, based on Coulomb’s yield criterion, a simple criterion that determines whether granular material will flow or not. Imagine a collection of sand compressed between your hands. Coulomb’s equation states that in order to slide one hand against the other the shear stress — akin to the force applied to slide your hands — divided by the surrounding pressure — squeezing the sand together — must equal something called the friction coefficient. If this ratio reaches the friction coefficient (determined by the sand’s properties), your hand will move. Kamrin added one more ingredient to the equation: a separation rule, to account for the fact that sand, in general, does not stick together. For example, if you move a shovel through sand, it will create a temporary hole behind the shovel that is immediately refilled with in-falling sand — a realistic phenomenon that Kamrin says is important to include, to accurately represent sand flow, particularly in “intrusion” scenarios such as pushing a shovel through sand. Kamrin and Askari applied their continuum model in finite element simulations in which they simulated a simple plate moving through granular media in many ways. The simulation was designed to mimic actual experiments performed by others. They found that both the flow of the grains and the force against the plate matched what others had observed in their experiments. The team then simulated more complex objects, such as a circle and a diamond, moving through sand, using first their continuum model and then RFT with their previous plate simulations serving as the RFT inputs. Both simulations produced nearly identical results and predicted the same force value needed to move both objects. When the researchers pushed the simulation to model three-dimensional objects, both the continuum model and RFT again generated the same answers. “The agreement is unbelievably good,” Kamrin says. “It turns out RFT happens to work really well, thanks to an interesting property in the Coulomb continuum model.” Interestingly, this simplification does less well in predicting the force applied to an object through fluid. When Kamrin and Askari modeled an object — in this case, a simple garden hoe — through fluid, the force from the viscous flow equations was inherently incompatible with the sum of forces from separate small plates.  When the material model was switched to the granular model, the total force exactly matched what a sum of small independent plate forces would give. “In some sense, this is a litmus test,” Kamrin says. “In the end, it proves the granular continuum model perfectly agrees with the resistive force theory in a class of representative problems.” To see if RFT could make accurate predictions in any other material besides grains, the researchers “went through the Rolodex of materials that have modeling equations,” and found using a similar test that indeed, RFT could also apply to certain cohesive materials like pastes, gels, and mud. Kamrin says now scientists can rely on RFT to help solve many traction-related problems. But could the equation also help one get out of, say, quicksand? “Let’s put it this way: Either way, you need to do a bit of work to figure out how to push yourself out of quicksand,” Kamrin says. “But in the right circumstances RFT divides the amount of work by a whole lot. You don’t have to solve differential equations anymore. Just give me a couple charts and a piece of paper and a pen, and I can calculate my way out of a sticky situation.” “Now that we know that RFT is a consequence of plasticity, scaling relations can be developed to understand pros and cons of different vehicle running gear and animal appendages, like, how do large and small tires compare? How do flipper-like feet versus long skinny feet compare? How do different body shapes affect sand-swimming performance?” says Daniel Goldman, associate professor of physics at Georgia Tech, who was not involved in the research. “There are still many aspects of these interactions that are not yet tested against RFT, like situations when animals step into material that their feet have previously disturbed, but Ken's work can lead to predictions that we can test.” This research was supported, in part, by the Army Research Office.

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Research at Indiana Univ. has identified a genetic mechanism that is likely to drive mutations that can lead to cancer. The study, published today in the Proceedings of the National Academy of Sciences, finds the enzyme APOBEC3G -- a known trigger for mutations that occur as benign tumor cells transform into cancerous malignancies that spread throughout the body -- appears to cause these harmful changes by mutating genes during the replication of DNA. The research, conducted in the bacteria Escherichia coli, was supported in part by IU's $6.2 million grant to investigate bacterial evolution from the U.S. Army Research Office. Patricia Foster, the principal investigator on the grant and a professor in the IU Bloomington College of Arts and Sciences' Department of Biology, is senior author on the study. The study also received support from the Wayne State University School of Medicine, whose researchers provided expertise on APOBEC3G and helped analyze the data. All experiments were carried out at IU. "Many tumors accumulate mutations during their growth, which leads to the subsequent characteristics that permit metastasis," Foster said. "Based upon the results revealed in bacteria in our study, we believe that the APOBEC family of enzymes create some of these mutations specifically during the rapid growth of these tumors." The results could have implications for personalized medicine, a growing movement to tailor treatments and therapies based upon individualized genetic information. For example, since it is possible to identify tumors potentially vulnerable to the enzyme by using current DNA sequencing technology, a physician treating these tumors might want to explore temporarily suppressing expression of this enzyme, she said. An important organism for studying genes, E. coli allows scientists to observe genetic changes over thousands of generations in a relatively short time span. The results apply to humans as well as bacteria since the basic mechanisms of DNA replication are the same across all species. Normally, the APOBEC family of enzymes plays an important role in the human immune system by driving changes in immune cells that aid in defense against viruses, possibly including the HIV/AIDS virus. But IU scientists found the harmful influence of the enzyme family arises from the complex way that two halves of every double-stranded DNA molecule must unravel to replicate during cellular division -- splitting into two temporarily single-stranded DNA chains thousands of "links" in length to serve as templates for the new copy. These links are the four chemicals, or nucleobases, that comprise all DNA: cytosine, or C; guanine, or G; adenine, or A; and thymine, or T. As these paired chemicals are split in half to be copied, one of the two single-stranded bits of DNA -- known as the lagging strand template -- is highly vulnerable to genetic mutation, Foster said. This "gap in the armor" occurs because the enzyme that builds a new string of DNA -- known as a DNA polymerase -- must repeatedly traverse the nucleobases in the lagging strand template thousands of times during the course of replication, stopping further down the chain from the base pair previously inserted on the past loop along the chemical chain. Each of these polymerase "hops" creates a long stretch of DNA that temporarily remains as a single strand. The complex process -- driven by the fact that the two DNA strands are oriented in opposite directions and polymerases copy in only a single direction -- introduces more opportunities for errors in the lagging strand template compared to the continuous, step-by-step process that replicates the other half of the split strand of DNA, called the leading strand template. "We're talking about thousands of bases exposed without a complimentary strand throughout the whole replication cycle," Foster said. "If I were going to design an organism, I would make two types of copying enzymes, one that could go each way. But that's not how it works; no organism has ever evolved a more efficient way to replicate DNA." The mechanism by which the APOBEC family of enzymes drives mutation is cytosine deamination, in which a cytosine -- the "C" nucleobase -- transforms into uracil, one of the four bases in RNA that doesn't play a role in DNA replication. But the presence of uracil during DNA replication can cause an error when a thymine -- the "T" nucleobase -- replaces a cytosine. APOBEC enzymes specifically target the C's in single-stranded DNA for deamination. The disruptive effect of the enzyme on genetic replication in the study was observed in a strain of E. coli whose ability to remove the dangerous uracils had been switched off. To conduct the experiment, Foster's lab observed the effect of APOBEC3G on approximately 50 identical lineages of E. coli over the course of nearly 100 days, with each day encompassing 20 to 30 bacterial generations. Over time, a unique pattern of nucleotides was detected in the mutated DNA, a chain of three cytosine molecules, or C-C-C, the same genetic signature found in other studies of the enzyme family. And these mutations were four times more likely to be found on the lagging-strand template than on the leading-strand template. "These results strongly suggest that these mutations occur as APOBEC3G attacks cytosines during DNA replication, while they're most exposed on the lagging strand template," Foster said. "This basic mechanism appears to be the same in bacteria and in human tumors cells."

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Abstract: A University of Oklahoma-led team of physicists believes chip-based atomic physics holds promise to make the second quantum revolution--the engineering of quantum matter with arbitrary precision--a reality. With recent technological advances in fabrication and trapping, hybrid quantum systems are emerging as ideal platforms for a diverse range of studies in quantum control, quantum simulation and computing. James P. Shaffer, professor in the Homer L. Dodge Department of Physics and Astronomy, OU College of Arts and Sciences; Jon Sedlacek, OU graduate student; and a team from the University of Nevada, Western Washington University, The United States Naval Academy, Sandia National Laboratories and Harvard-Smithsonian Center for Astrophysics, have published research important for integrating Rydberg atoms into hybrid quantum systems and the fundamental study of atom-surface interactions, as well as applications for electrons bound to a 2D surface. "A convenient surface for application in hybrid quantum systems is quartz because of its extensive use in the semiconductor and optics industries," Sedlacek said. "The surface has been the subject of recent interest as a result of it stability and low surface energy. Mitigating electric fields near 'trapping' surfaces is the holy grail for realizing hybrid quantum systems," added Hossein Sadeghpour, director of the Institute for Theoretical Atomic Molecular and Optical Physics, Harvard-Smithsonian Center for Astrophysics. In this work, Shaffer finds ionized electrons from Rydberg atoms excited near the quartz surface form a 2D layer of electrons above the surface, canceling the electric field produced by rubidium surface adsorbates. The system is similar to electron trapping in a 2D gas on superfluid liquid helium. The binding of electrons to the surface substantially reduces the electric field above the surface. "Our results show that binding is due to the image potential of the electron inside the quartz," said Shaffer. "The electron can't diffuse into the quartz because the rubidium adsorbates make the surface have a negative electron affinity. The approach is a promising pathway for coupling Rydberg atoms to surfaces as well as for using surfaces close to atomic and ionic samples." ### A paper on this research was published in the American Physics Society's Physical Review Letters. The OU part of this work was supported by the Defense Advanced Research Projects Agency Quasar program by a grant through the Army Research Office, the Air Force Office of Scientific Research and the National Science Foundation. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

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When an airplane begins to move faster than the speed of sound, it creates a shockwave that produces a well-known “boom” of sound. Now, researchers at MIT and elsewhere have discovered a similar process in a sheet of graphene, in which a flow of electric current can, under certain circumstances, exceed the speed of slowed-down light and produce a kind of optical “boom”: an intense, focused beam of light. This entirely new way of converting electricity into visible radiation is highly controllable, fast, and efficient, the researchers say, and could lead to a wide variety of new applications. The work is reported today in the journal Nature Communications, in a paper by two MIT professors — Marin Soljačić, professor of physics; and John Joannopoulos, the Francis Wright Davis Professor of physics — as well as postdoc Ido Kaminer, and six others in Israel, Croatia, and Singapore. The new finding started from an intriguing observation. The researchers found that when light strikes a sheet of graphene, which is a two-dimensional form of the element carbon, it can slow down by a factor of a few hundred. That dramatic slowdown, they noticed, presented an interesting coincidence. The reduced speed of photons (particles of light) moving through the sheet of graphene happened to be very close to the speed of electrons as they moved through the same material. “Graphene has this ability to trap light, in modes we call surface plasmons,” explains Kaminer, who is the paper’s lead author. Plasmons are a kind of virtual particle that represents the oscillations of electrons on the surface. The speed of these plasmons through the graphene is “a few hundred times slower than light in free space,” he says. This effect dovetailed with another of graphene’s exceptional characteristics: Electrons pass through it at very high speeds, up to a million meters per second, or about 1/300 the speed of light in a vacuum. That meant that the two speeds were similar enough that significant interactions might occur between the two kinds of particles, if the material could be tuned to get the velocities to match. That combination of properties — slowing down light and allowing electrons to move very fast — is “one of the unusual properties of graphene,” says Soljačić. That suggested the possibility of using graphene to produce the opposite effect: to produce light instead of trapping it. “Our theoretical work shows that this can lead to a new way of generating light,” he says. Specifically, he explains, “This conversion is made possible because the electronic speed can approach the light speed in graphene, breaking the ‘light barrier.’” Just as breaking the sound barrier generates a shockwave of sound, he says, “In the case of graphene, this leads to the emission of a shockwave of light, trapped in two dimensions.” The phenomenon the team has harnessed is called the Čerenkov effect, first described 80 years ago by Soviet physicist Pavel Čerenkov. Usually associated with astronomical phenomenon and harnessed as a way of detecting ultrafast cosmic particles as they hurtle through the universe, and also to detect particles resulting from high-energy collisions in particle accelerators, the effect had not been considered relevant to Earthbound technology because it only works when objects are moving close to the speed of light. But the slowing of light inside a graphene sheet provided the opportunity to harness this effect in a practical form, the researchers say. There are many different ways of converting electricity into light — from the heated tungsten filaments that Thomas Edison perfected more than a century ago, to fluorescent tubes, to the light-emitting diodes (LEDs) that power many display screens and are gaining favor for household lighting. But this new plasmon-based approach might eventually be part of more efficient, more compact, faster, and more tunable alternatives for certain applications, the researchers say. Perhaps most significantly, this is a way of efficiently and controllably generating plasmons on a scale that is compatible with current microchip technology. Such graphene-based systems could potentially be key on-chip components for the creation of new, light-based circuits, which are considered a major new direction in the evolution of computing technology toward ever-smaller and more efficient devices. “If you want to do all sorts of signal processing problems on a chip, you want to have a very fast signal, and also to be able to work on very small scales,” Kaminer says. Computer chips have already reduced the scale of electronics to the points that the technology is bumping into some fundamental physical limits, so “you need to go into a different regime of electromagnetism,” he says. Using light instead of flowing electrons as the basis for moving and storing data has the potential to push the operating speeds “six orders of magnitude higher than what is used in electronics,” Kaminer says — in other words, in principle up to a million times faster. One problem faced by researchers trying to develop optically based chips, he says, is that while electricity can be easily confined within wires, light tends to spread out. Inside a layer of graphene, however, under the right conditions, the beams are very well confined. “There’s a lot of excitement about graphene,” says Soljačić, “because it could be easily integrated with other electronics” enabling its potential use as an on-chip light source. So far, the work is theoretical, he says, so the next step will be to create working versions of the system to prove the concept. “I have confidence that it should be doable within one to two years,” he says. The next step would then be to optimize the system for the greatest efficiency. This finding “is a truly innovative concept that has the potential to be the key toward solving the long-standing problem of achieving highly efficient and ultrafast electrical-to-optical signal conversion at the nanoscale,” says Jorge Bravo-Abad, an assistant professor at the Autonomous University of Madrid, in Spain, who was not involved in this work. In addition, Bravo-Abad says, “the novel instance of Čerenkov emission discovered by the authors of this work opens up whole new prospects for the study of the Čerenkov effect in nanoscale systems, without the need of sophisticated experimental set-ups. I look forward to seeing the significant impact and implications that these findings will surely have at the interface between physics and nanotechnology.” The research was supported by the U.S. Army Research Laboratory and the U.S. Army Research Office, through the Institute for Soldier Nanotechnologies at MIT. The team included researchers Yichen Shen, Ognjen Ilic, and Josue Lopez at MIT; Yaniv Katan at Technion, in Haifa, Israel; Hrvoje Buljan at the University of Zagreb in Croatia; and Liang Jie Wong at the Singapore Institute of Manufacturing Technology.

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