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Scooped by Dr. Stefan Gruenwald!

Rules devised for building artificial protein molecules from scratch

Rules devised for building artificial protein molecules from scratch | Amazing Science |

By following certain rules, scientists can prepare architectural plans for building artificial protein molecules not found in the real world. Based on these computer renditions, previously non-existent proteins can be produced from scratch in the lab. The principles to make this happen have now been elucidated in detail.

Dr. Nobuyasu Koga and Dr. Rie Tatsumi-Koga, a husband-and-wife scientific team in Dr. David Baker's lab at the University of Washington Protein Design Institute led the effort. The project benefited from hundreds of thousands of computer enthusiasts around the world who adopted Rosetta@home for simulating designed proteins. In this project, protein molecules start as an unstable, high energy chain of amino acids. This chain then begins folding into various shapes to try to achieve a stable, low energy state. The end result is its distinctive molecular structure.


Rosetta@home volunteers helped the project team to plot this energy landscape from protein structure predictions. "The structural options become fewer as the interactions that stabilize the protein selectively favor one folding pattern over others," explained Koga. "This decline in conformation options to eventually achieve a unique, ordered structure is called a funnel-shaped energy landscape," he said, drawing a tornado-like figure on a whiteboard. The researchers came up with guidelines for robustly generating this type of energy landscape.


According to Tatsumi-Koga, these rules require the interactions among the residues in the protein's amino acid chain to consistently favor the same folded conformation in forming its molecular shape. This is made possible, for example, by defining whether a specific unit will form a "right-handed" orientation or its mirror image, and disfavor others. The researchers, she said, synthesized the proteins they had originally designed and tested "in silico" (on the computer) and physically characterized them through "in vitro" (laboratory test tube) experiments. They also compared the molecular structures of the computer models with these laboratory-derived proteins to see how well they matched. Koga stressed that the project looked strictly at protein structure. He smiled as he said his group was striving toward a "platonic ideal," a reference to Plato's theory of perfect forms. During this project, the researchers achieved a library of five ideal structures, but since filing their report have added several more. To make them accessible to other scientists, the designs have been deposited in the Research Collaboratory for Structural Bioinformatics and the lab analysis of their chemical structure was put in the Biological Magnetic Resonance Database.

The team was not attempting to create specific new proteins that could carry out particular activities. However, their design principles and methods, according to their report, should allow the ready creation of a wide range of robust, stable, building blocks for the next generation of engineered functional proteins. Such proteins would be custom-made for the task, instead of repurposed from proteins with unrelated functions. The hope is that engineered proteins will be useful for drug and vaccine development, especially for formidable viruses like HIV or rapidly changing ones, like the flu. Proteins designed to exact specifications might also prove therapeutically useful in cleaving mutated genes, and for speeding up chemical reactions important in industry and environmental reclamation.

Ronan Delisle's curator insight, October 21, 2014 5:39 AM

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DNA directly imaged with electron microscope for the first time

DNA directly imaged with electron microscope for the first time | Amazing Science |

It's the most famous corkscrew in history. Now an electron microscope has captured the famous Watson-Crick double helix in all its glory, by imaging threads of DNA resting on a silicon bed of nails. The technique will let researchers see how proteins, RNA and other biomolecules interact with DNA.


The structure of DNA was originally discovered using X-ray crystallography. This involves X-rays scattering off atoms in crystallised arrays of DNA to form a complex pattern of dots on photographic film. Interpreting the images requires complex mathematics to figure out what crystal structure could give rise to the observed patterns.


The new images are much more obvious, as they are a direct picture of the DNA strands, albeit seen with electrons rather than X-ray photons. The trick used by Enzo di Fabrizio at the University of Genoa, Italy, and his team was to snag DNA threads out of a dilute solution and lay them on a bed of nanoscopic silicon pillars.


The team developed a pattern of pillars that is extremely water-repellent, causing the moisture to evaporate quickly and leave behind strands of DNA stretched out and ready to view. The team also drilled tiny holes in the base of the nanopillar bed, through which they shone beams of electrons to make their high-resolution images. The results reveal the corkscrew thread of the DNA double helix, clearly visible. With this technique, researchers should be able to see how single molecules of DNA interact with other biomolecules.

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SABRE engine passes milestone tests

SABRE engine passes milestone tests | Amazing Science |

The team from UK firm Reaction Engines announced this morning that the SABRE engine technology, which could power a reusable spaceplane known as Skylon capable of entering orbit without additional rockets, had been proven in tests evaluated by the European Space Agency (ESA).


Reaction Engines has been testing the SABRE heat exchanger and anti-frost system using a standard jet turbine engine. The company called the technology, which could also lead to supersonic flights from Europe to Australia in four hours, ‘the biggest breakthrough in aerospace propulsion since the invention of the jet engine’.

Via Szabolcs Kósa
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NASA: MESSENGER Probe Finds New Evidence for Water Ice at Mercury's Poles

NASA: MESSENGER Probe Finds New Evidence for Water Ice at Mercury's Poles | Amazing Science |

New observations by the MESSENGER spacecraft provide compelling support for the long-held hypothesis that Mercury harbors abundant water ice and other frozen volatile materials in its permanently shadowed polar craters.


Three independent lines of evidence support this conclusion: the first measurements of excess hydrogen at Mercury's north pole with MESSENGER's Neutron Spectrometer, the first measurements of the reflectance of Mercury's polar deposits at near-infrared wavelengths with the Mercury Laser Altimeter (MLA), and the first detailed models of the surface and near-surface temperatures of Mercury's north polar regions that utilize the actual topography of Mercury's surface measured by the MLA.

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Engineers pave the way towards 3D printing of personal electronics

Engineers pave the way towards 3D printing of personal electronics | Amazing Science |

Scientists are developing new materials which could one day allow people to print out custom-designed personal electronics such as games controllers which perfectly fit their hand shape.


The University of Warwick researchers have created a simple and inexpensive conductive plastic composite that can be used to produce electronic devices using the latest generation of low-cost 3D printers designed for use by hobbyists and even in the home. The material, nicknamed ‘carbomorph’, enables users to lay down electronic tracks and sensors as part of a 3D printed structure – allowing the printer to create touch-sensitive areas for example, which can then be connected to a simple electronic circuit board.


So far the team has used the material to print objects with embedded flex sensors or with touch-sensitive buttons such as computer game controllers or a mug which can tell how full it is. The next step is to work on printing much more complex structures and electronic components including the wires and cables required to connect the devices to computers.


The research was led by Dr. Simon Leigh in the School of Engineering at the University of Warwick. Dr. Leigh said: “It’s always great seeing the complex and intricate models of devices such as mobile phones or television remote controls that can be produced with 3D printing, but that’s it, they are invariably models that don’t really function. “We set about trying to find a way in which we could actually print out a functioning electronic device from a 3D printer.

“In the long term, this technology could revolutionalise the way we produce the world around us, making products such as personal electronics a lot more individualised and unique and in the process reducing electronic waste.


“Designers could also use it to understand better how people tactilely interact with products by monitoring sensors embedded into objects. “However, in the short term I can see this technology having a major impact in the educational sector for example, allowing the next generation of young engineers to get hands-on experience of using advanced manufacturing technology to design fairly high-tech devices and products right there in the classroom.”


The printed sensors can be monitored using existing open-source electronics and freely available programming libraries. A major advantage of using 3D printing is that sockets for connection to equipment such as interface electronics can be printed out instead of connected using conductive glues or paints.

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Unexpected data from the Large Hadron Collider suggest the collisions may be producing a new type of matter

Unexpected data from the Large Hadron Collider suggest the collisions may be producing a new type of matter | Amazing Science |
Collisions between protons and lead ions at the Large Hadron Collider (LHC) have produced surprising behavior in some of the particles created by the collisions. The new observation suggests the collisions may have produced a new type of matter known as color-glass condensate.


When beams of particles crash into each other at high speeds, the collisions yield hundreds of new particles, most of which fly away from the collision point at close to the speed of light. However, the Compact Muon Solenoid (CMS) team at the LHC found that in a sample of 2 million lead-proton collisions, some pairs of particles flew away from each other with their respective directions correlated.


"Somehow they fly at the same direction even though it's not clear how they can communicate their direction with one another. That has surprised many people, including us," says MIT physics professor Gunther Roland, whose group led the analysis of the collision data along with Wei Li, a former MIT postdoc who is now an assistant professor at Rice University.


The MIT heavy-ion group, which includes Roland and MIT physics professors Bolek Wyslouch and Wit Busza, saw the same distinctive pattern in proton-proton collisions about two years ago. The same flight pattern is also seen when ions of lead or other heavy metals, such as gold and copper, collide with each other.


Those heavy-ion collisions produce a wave of quark gluon plasma, the hot soup of particles that existed for the first few millionths of a second after the Big Bang. In the collider, this wave sweeps some of the resulting particles in the same direction, accounting for the correlation in their flight paths.


It has been theorized that proton-proton collisions may produce a liquid-like wave of gluons, known as color-glass condensate. This dense swarm of gluons may also produce the unusual collision pattern seen in proton-lead collisions, says Raju Venugopalan, a senior scientist at Brookhaven National Laboratory. Venugopalan and his former student Kevin Dusling theorized the existence of color-glass condensate shortly before the particle direction correlation was seen in proton-proton collisions. While protons at normal energy levels consist of three quarks, they tend to gain an accompanying cluster of gluons at higher energy levels. These gluons exist as both particles and waves, and their wave functions can be correlated with each other. This "quantum entanglement" explains how the particles that fly away from the collision can share information such as direction of flight path, Venugopalan says. The correlation is "a very tiny effect, but it's pointing to something very fundamental about how quarks and gluons are arranged spatially within a proton," he says.

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Beyond machines, the IBM SyNAPSE project: Can a computer be made to think like a human?

Beyond machines, the IBM SyNAPSE project: Can a computer be made to think like a human? | Amazing Science |

Researchers at IBM have been working on a cognitive computing project called Systems of Neuromorphic Adaptive Plastic Scalable Electronics (SyNAPSE). By reproducing the structure and architecture of the brain—the way its elements receive sensory input, connect to each other, adapt these connections, and transmit motor output—the SyNAPSE project models computing systems that emulate the brain's computing efficiency, size and power usage without being programmed.

IBM is combining principles from nanoscience, neuroscience and supercomputing as part of a multi-year cognitive computing initiative. The Defense Advanced Research Projects Agency (DARPA) has awarded approximately US$21 million in new funding for phase 2 of the SyNAPSE project. For this project, a world-class, multi-dimensional team has been assembled, consisting of IBM researchers and collaborators from Columbia University; Cornell University; University of California, Merced; and University of Wisconsin-Madison.


In 6 videos, the SyNAPSE team explains the hardware, software and science that forms the foundation of their cognitive computing project.

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Some quite interesting facts about flying animals

Some quite interesting facts about flying animals | Amazing Science |

Flying insects: 

Insects do not fly by “flapping” their wings - they do it by making their exoskeletons quiver. By contracting their muscles, insects force their whole body to vibrate. The wings are affected in the same way and vibrate like a tuning fork.

Flying birds: 

The longest non-stop bird migration was 7,145 miles (11,500km) by a godwit from Alaska to New Zealand.


Satellite tracking reveals that some albatrosses fly around the entire planet in less than two months and can soar for six days without flapping their wings. They sleep on the wing, each half of the brain taking it in turns to turn off and rest.


The way a hummingbird flies is as different from other birds as a helicopter is from an aircraft. While hovering, hummingbirds’ wing tips move horizontally, tracing a figure-of-eight pattern. This means they can generate lift on both strokes, enabling flight forwards, backwards, and even upside down.

Geese can lose altitude by “whiffling” – a spiralling nosedive, sometimes flying upside down with their heads still pointed straight ahead.

Big fliers:
The mute swan is the heaviest bird in the world that can fly – it can weigh up to 22.5kg (about 3.5 stone). It isn’t mute: it hisses, snorts and grunts.

The Pterosaur, a flying reptile that lived 100 million years ago is the largest known animal to have taken to the air. It had a wingspan the length of two buses.

Flying lemurs:
Flying lemurs aren’t lemurs and they can’t fly. There are two species: the Sunda flying lemur found over south-east Asia and the Philippine flying lemur, found only in the Philippines. They are the only species in the order Dermoptera (“skin wings”). Their wings stretch from shoulder to forepaw and even their fingers are webbed like bats. Despite this they can only glide: they can’t gain altitude, nor maintain it for more than a few seconds.


Flying snakes:
Chrysopelea or the flying snake is another south-east Asian glider – they flatten their ribs to get themselves aerodynamically ready to glide, then as they fall they undulate their bodies in an exaggerated S-shaped pattern to give stability in the air.

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Bioengineered marine algae expands environments where biofuels can be produced

Bioengineered marine algae expands environments where biofuels can be produced | Amazing Science |

Biologists at UC San Diego have demonstrated for the first time that marine algae can be just as capable as fresh water algae in producing biofuels. Salt ponds in the SF Bay area where the marine algae Dunaliella salina display a bright red color in response to the stress of high salt concentrations.


The scientists genetically engineered marine algae to produce five different kinds of industrially important enzymes and say the same process they used could be employed to enhance the yield of petroleum-like compounds from these salt water algae. Their achievement is detailed in a paper published online in the current issue of the scientific journal Algal Research.


The ability to genetically transform marine algae into a biofuel crop is important because it expands the kinds of environments in which algae can be conceivably grown for biofuels. Corn, for example, which is used to produce ethanol biofuel, requires prime farmland and lots of fresh water. But the UC San Diego study suggests that algal biofuels can be produced in the ocean or in the brackish water of tidelands or even on agricultural land on which crops can no longer be grown because of high salt content in the soil.


"What our research shows is that we can achieve in marine species exactly what we've already done in fresh water species," said Stephen Mayfield, a professor of biology at UC San Diego, who headed the research project. "There are about 10 million acres of land across the United States where crops can no longer be grown that could be used to produce algae for biofuels. Marine species of algae tend to tolerate a range of salt environments, but many fresh water species don't do the reverse. They don't tolerate any salt in the environment."


"The algal community has worked on fresh water species of algae for 40 years," added Mayfield, who also directs the San Diego Center for Algae Biotechnology, or SD-CAB, a consortium of research institutions in the region working to make algal biofuels a viable transportation fuel in the future. "We know how to grow them, manipulate them genetically, express recombinant proteins—all of the things required to make biofuels viable. It was always assumed that we could do the same thing in marine species, but there was always some debate in the community as to whether that could really be done."


Scaling up the production of biofuels made from algae to meet at least 5 percent – about 10 billion gallons – of U.S. transportation fuel needs would place unsustainable demands on energy, water and nutrients, says a new report from the National Research Council, or NRC. However, these concerns are not a definitive barrier for future production, and innovations that would require research and development could help realize algal biofuels' full potential.

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Snail shells are already dissolving in Southern Ocean due to ocean acification

Snail shells are already dissolving in Southern Ocean due to ocean acification | Amazing Science |

In a small patch of the Southern Ocean, the shells of sea snails are dissolving. The finding is the first evidence that marine life is already suffering as a result of man-made ocean acidification.


"This is actually happening now," says Geraint Tarling of the British Antarctic Survey in Cambridge, UK. He and colleagues captured free-swimming sea snails called pteropods from the Southern Ocean in early 2008 and found under an electron microscope that the outer layers of their hard shells bore signs of unusual corrosion.


As well as warming the planet, the carbon dioxide we emit is changing the chemistry of the ocean. CO2 dissolves in water to form carbonic acid, making the water less alkaline. The pH is currently dropping at about 0.1 per century, faster than any time in the last 300 million years.


Lab experiments have shown that organisms with hard shells, such as corals and molluscs, will suffer as a result. To build their shells, corals and molluscs need to take up calcium carbonate from the water, but more carbonic acid means more hydrogen ions in the water. These react with carbonate ions, making them unavailable to form calcium carbonate.


The most vulnerable animals are those, like pteropods, that build their shells entirely from aragonite, a form of calcium carbonate that is very sensitive to extra acidity. By 2050, there will be a severe shortage of aragonite in much of the ocean. Aragonite is still relatively plentiful in most of the ocean, but Tarling suspected that some regions might already be affected by shortages.

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Intelligent Future-Singularity Wall Chart (updated continuously)

Intelligent Future-Singularity Wall Chart (updated continuously) | Amazing Science |

Stay up-to-date with future / singularity news every minute, every day.

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The rise of Megacities - an interactive slide show experience

The rise of Megacities - an interactive slide show experience | Amazing Science |

Sixty-two years ago New York and Tokyo were the world's only megacities – 'urban agglomerations' with over 10 million residents. Now in 2012, there are 23, and by 2025 the UN predicts nine new megacities in Asia will bring the total to 37. All but eight will be in the developing world – and the quality of life for millions will be determined by the quality of their cities. This interactive map shows the 100 most populous cities as of 2012 according to the UN.

Via Brice Terdjman, association concert urbain, olsen jay nelson
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"Preventing the Next Easter Island" --Scientists Pioneer a Technique to Predict Ecosystem Collapse

"Preventing the Next Easter Island" --Scientists Pioneer a Technique to Predict Ecosystem Collapse | Amazing Science |
A team at the University of Southampton are pioneering a technique to predict when an ecosystem is likely to collapse, which may also have potential for foretelling crises in agriculture, fisheries or even social systems preventing another "Easter Island" collapse from occuring. The scientists applied a mathematical model to a real world situation, the environmental collapse of a lake in China, to help prove a theory which suggests an ecosystem 'flickers', or fluctuates dramatically between healthy and unhealthy states, shortly before its eventual collapse.


"We wanted to prove that this 'flickering' occurs just ahead of a dramatic change in a system – be it a social, ecological or climatic one – and that this method could potentially be used to predict future critical changes in other impacted systems in the world around us," said John Dearing, head of geography at Southampton.


Eminent Australian scientist Professor Frank Fenner, emeritus professor of microbiology at the Australian National University (ANU), who helped to wipe out smallpox, predicts humans will probably be extinct within 100 years, because of overpopulation, environmental destruction and climate change. Tools, such as that being pioneered at Southampton, may prevent this dire prediction from becoming a reality. If past is prolgue, 70,000 years ago the human population was reduced to small isolated groups in Africa, apparently because of drought, according to a 2010 analysis by researchers at Stanford University. The estimated the number of early humans may have shrunk as low as 2,000 before numbers began to expand again in the early Stone Age.


Tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA." Wells is director of the Genographic Project, launched in 2005 to study anthropology using genetics. The report was published in the American Journal of Human Genetics.


Fenner says homo sapiens will not be able to survive the population explosion and “unbridled consumption,” and will become extinct, perhaps within a century, along with many other species. United Nations official figures from last year estimate the human population is seven billion, and is predicted to pass seven billion next year.

Ali and bradyn's curator insight, October 3, 2013 11:52 AM

geography article on Australia about how there ecosystem might collapse and become the new Easter island

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Scientists describe the elusive replication machinery of flu viruses

Scientists describe the elusive replication machinery of flu viruses | Amazing Science |

Scientists at The Scripps Research Institute (TSRI) have made a major advance in understanding how flu viruses replicate within infected cells. The researchers used cutting-edge molecular biology and electron-microscopy techniques to "see" one of influenza's essential protein complexes in unprecedented detail. The images generated in the study show flu virus proteins in the act of self-replication, highlighting the virus's vulnerabilities that are sure to be of interest to drug developers.


Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies of the viral nucleoprotein. In vitro cell expression of all RNP protein components with four of the eight influenza virus gene segments enabled structural determination of native influenza virus RNPs by cryo-EM. The cryo-EM structure reveals the architecture and organization of the native RNP, thereby defining the attributes of its largely helical structure and how polymerase interacts with NP and the viral genome. Observations of branched-RNP structures in negative stain EM and their putative identification as replication intermediates suggest a mechanism for viral replication by a second polymerase on the RNP template.

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Techonomy 2012: Where's My Robot?

The future for robots seems boundless. Is there a limit to the invasion? Rodney Brooks of Rethink Robotics, MIT's Andrew McAfee, and John Markoff of The New York Times take a closer look at the present and future of robotics at the Techonomy 2012 conference in Tucson, Ariz.


For full transcript, go to

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Canadian scientists create first functioning, virtual brain

Canadian scientists create first functioning, virtual brain | Amazing Science |

Chris Eliasmith has spent years contemplating how to build a brain. Eliasmith's team built Spaun, which was billed Thursday as "the world's largest simulation of a functioning brain."


Spaun can recognize numbers, remember lists and write them down. It even passes some basic aspects of an IQ test, the team reports. Spaun, which stands for Semantic Pointer Architecture Unified Network, has 2.5 million simulated neurons organized into subsystems to resemble the prefrontal cortex, basil ganglia, thalamus and other cognitive machinery in the brain. It also has a simulated eye that can see, and an arm that draws.


The simplified model of the brain, which took a year to build, captures many aspects of neuroanatomy, neurophysiology and psychological behaviour, says Eliasmith, director of Waterloo's Centre for Theoretical Neuroscience. Spaun's cognition and behavior is very basic, but it can learn patterns it has never seen before and use that knowledge to figure out the best answer to a question. "So it does learn," says Eliasmith.


But it is not - at least not yet - a match for the real thing. "Spaun is not as adaptive as a real brain, as the model is unable to learn completely new tasks," the team reports in Science. "In addition, both attention and eye position of the model is fixed, making Spaun unable to control its own input."


Eliasmith is now working with groups in the US and Britain to try speed up Spaun and expand its tasks and behaviors. He says such brain simulations might one day be used to better understand and model neurological disorders and diseases and to improve "machine intelligence."


Eliasmith notes that humans have about 100 billion neurons in their brains, far more than other animals and artificial brains taking in shape in the lab. Today's "smart" machines can play chess, backgammon and act as personal assistants, like Siri on Apple's iPhone, but Eliasmith says the processes they use have little in common with the brain. He says it hard to predict the future, but he expects to see an explosion in artificial intelligence and more "human-like" machines." A robot that is able to navigate through a city and deliver a package from one place to another," he says. "I think that kind of thing will be within reach in the next 10 years."

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New tunable material hides from infrared cameras

New tunable material hides from infrared cameras | Amazing Science |

Now you see it, now you don’t.

A new device invented at the Harvard School of Engineering and Applied Sciences (SEAS) can absorb 99.75 percent of infrared light that shines on it. When activated, it appears black to infrared cameras.

Composed of just a 180-nanometer-thick layer of vanadium dioxide (VO2) on top of a sheet of sapphire, the device reacts to temperature changes by reflecting dramatically more or less infrared light. This perfect absorber is ultrathin, tunable, and exceptionally well suited for use in a range of infrared optical devices.


Perfect absorbers have been created many times before, but not with such versatile properties. In a Fabry-Pérot cavity, for instance, two mirrors sandwich an absorbing material, and light simply reflects light back and forth until it’s mostly all gone. Other devices incorporate surfaces with nanoscale metallic patterns that trap and eventually absorb the light.

“Our structure uses a highly unusual approach, with better results,” says principal investigator Federico Capasso, Robert L. Wallace Professor of Applied Physics and Vinton Hayes Senior Research Fellow in Electrical Engineering at SEAS. “We exploit a kind of naturally disordered metamaterial, along with thin-film interference effects, to achieve one of the highest absorption rates we’ve ever seen. Yet our perfect absorber is structurally simpler than anything tried before, which is important for many device applications.”

With collaborators at Harvard and at the University of California, San Diego, Capasso’s research group took advantage of surprising properties in both of the materials they used.


Vanadium dioxide is normally an insulating material, meaning that it does not conduct electricity well. Take it from room temperature up to about 68 degrees Celsius, however, and it undergoes a dramatic transition. The crystal quickly rearranges itself as the temperature approaches a critical value. Metallic islands appear as specks, scattered throughout the material, with more and more appearing until it has become uniformly metallic.

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Lake life survives in total isolation for 3000 years - good news for extraterrestrial life

Lake life survives in total isolation for 3000 years - good news for extraterrestrial life | Amazing Science |

It is seven times as salty as the sea, pitch dark and 13 degrees below freezing. Lake Vida in East Antarctica has been buried for 2800 years under 20 metres of ice, but teems with life.


The discovery of strange, abundant bacteria in a completely sealed, icebound lake strengthens the possibility that extraterrestrial life might exist on planets such as Mars and moons such as Jupiter's Europa.


"Lake Vida is a model of what happens when you try to freeze a lake solid, and this is the same fate that any lakes on Mars would have gone through as the planet turned colder from a watery past," says Peter Doran of the University of Illinois, Chicago. He is co-leader of a team working in the Dry Valleys of Antarctica where Vida is situated. "Any Martian water bodies that did form would have gone through this Vida stage before freezing solid, entombing the evidence of the past ecosystem."


The Vida bacteria, brought to the surface in cores drilled 27 metres down, belong to previously unknown species. They probably survive by metabolising the abundant quantities of hydrogen and oxides of nitrogen that Vida's salty, oxygen-free water has been found to contain.


Co-research leader Alison Murray of the Desert Research Institute in Reno, Nevada, is now investigating this further by growing some of the extracted cells in the lab. Murray and her colleagues were surprised to find so much hydrogen, nitrous oxide and carbon in the water. They speculate that these substances might originate from reactions between salt and nitrogen-containing minerals in the surrounding rock. Over the centuries, bacteria denied sunlight may have evolved to be completely reliant on these substances for energy. "I think the unusual conditions found in the lake have likely played a significant role in shaping the diversity and capabilities of life we found," she says.


But the existence of life in Lake Vida does not necessarily increase the likelihood that life exists in much older, deeper lakes under investigation in Antarctica, most notably Vostok and Ellsworth, which are 3 kilometres down and have been isolated for millions rather than thousands of years. "It doesn't give us clues about whether there's life in Vostok or Ellsworth, but it says that under these super-salty conditions, life does OK," says Martin Siegert of the University of Bristol, UK, and leader of an expedition to Ellsworth which set off on 25 November. "We'll be drilling down 3 kilometres into the lake," he says.

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‘Neural fingerprints’ of memory associations allow ‘mind reading’

‘Neural fingerprints’ of memory associations allow ‘mind reading’ | Amazing Science |

Researchers have begun to show that it is possible to use brain recordings to reconstruct aspects of an image or movie clip someone is viewing, a sound someone is hearing or even the text someone is reading. A new study by University of Pennsylvania and Thomas Jefferson University scientists brings this work one step closer to actual mind reading by using brain recordings to infer the way people organize associations between words in their memories.


Epilepsy patients who volunteered for the study while awaiting brain surgery had tiny electrodes implanted in their brains, which allowed researchers to precisely observe electrical signals that would not have been possible to measure outside the skull. While recording these electrical signals, the researchers asked the participants to study lists of 15 randomly chosen words and, a minute later, to repeat the words back in whichever order they came to mind.


The researchers examined the brain recordings as the participants studied each word to home in on signals in the participant’ brains that reflected the meanings of the words. About a second before the participants recalled each word, these same “meaning signals” that were identified during the study phase were spontaneously reactivated in the participants’ brains.


Because the participants were not seeing, hearing or speaking any words at the times these patterns were reactivated, the researchers could be sure they were observing the neural signatures of the participants’ self-generated, internal thoughts.


Critically, differences across participants in the way these meaning signals were reactivated predicted the order in which the participants would recall the words. In particular, the degree to which the meaning signals were reactivated before recalling each word reflected each participant’s tendency to group similar words (like “duck” and “goose”) together in their recall sequence.


Since the participants were instructed to say the words in the order they came to mind, the specific sequence of recalls a participant makes provides insights into how the words were organized in that participant’s memory.

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Nanomagnetic remote control of animal behavior

Nanomagnetic remote control of animal behavior | Amazing Science |

Magnetic nanoparticles targeted to nerve cell membranes can be used to remotely control cellular activity and even the simple reflex behaviors of C. elegans nematode worms, according to research by a team of biophysicists at the University of Buffalo. The new method could be very useful for investigating how cells interact in neuronal networks, and may eventually lead to new therapies for cancer and diabetes.


Heng Huang and her colleagues synthesized manganese-iron nanoparticles, each just 6 millionths of a millimeter in diameter, and coated with the bacterial protein straptavidin attached to a fluorescent molecule called DyLight549. Strepdavidin binds another molecule, much like a key fits into a lock, enabling specified cells to be targeted, while DyLight549 acts like a molecular thermometer, whose fluoresence intensity changes with temperature. The researchers first tested whether the nanoparticles could be used to activate specified cells maintained in culture dishes. They inserted the gene encoding TRPV1, one member of a family of temperature-sensitive membrane proteins, into human embryonic kidney cells and neurons isolated from the rat hippocampus. The cells were also made to express a genetically engineered membrane protein ‘marker’, consisting of cyan fluorescent protein and two peptides, one that anchors it to the membrane, and another that binds the streptavidin molecules coating the nanoparticles.


A solution of nanoparticles was added to the culture dishes, and the cells examined under the microscope. Cyan fluorescence was found to be localized exclusively to the membranes, showing that the nanoparticles had targeted only those cells expressing the marker protein. The researchers then applied a small magnetic field to the culture dishes, to heat the nanoparticles, and monitored the intensity of the fluorescence emitted by DyLight549. This revealed a highly localized increase in temperature: as soon as the magnetic field was applied, the fluorescence intensity in the immediate vicinity of the cell surface decreased, indicating a temperature increase of more than 15°C within 15 seconds. The heat generated by the nanoparticles was sufficient to trigger activation of the TRPV1 proteins expressed by the cultured cells. This was established using a genetically encoded calcium sensor, whose fluoresence signal changes in response to the tiny increases in calcium ion concentration that are characteristic of neuronal activity. The increases in calcium ion concentration were found to be due to influxes of calcium through the activated TRPV1 – they were observed in cells expressing both the membrane marker and TRPV1, but not in control cells expressing the membrane marker alone. Significantly, the calcium influxes were found to elicit nervous impulses in the TRPV1-expressing cells.


Huang and her colleagues then showed that this approach can be adapted to remotely control a simple behavioural response in the nematode worm Caenhorhabditis elegans. When this tiny organism encounters noxious heat, it acts reflexively by moving in the opposite direction, and this heat avoidance response is initiated by TRPV1. The sensory neurons expressing TRPV1 have not been identified, however, so the researchers could not target them directly. Instead, they used nanoparticles coated with polyethylene glycol, a fatty molecule that causes the particles to accumulate in the mucus layer near the mouth.


Although questions have been raised regarding the safety of using nanoparticles in humans, the method could eventually have various clinical applications, because, as this study demonstrates, it can heat cells without causing them any damage. One possible application is hyperthermic cancer therapy, in which heat is used to kill off rapidly dividing tumour cells. Another is to stimulate pancreatic cells to secrete insulin in diabetics. The first step towards developing any such an application will be to demonstrate that the method works effectively in the brains of rats or mice. In the immediate future though, studies will probably focus on targeting the nanoparticles to specified cells in the nematode worm.

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Milky Way's Age Narrowed Down - It Was Original Member Of The Early Universe!

Milky Way's Age Narrowed Down - It Was Original Member Of The Early Universe! | Amazing Science |

A new estimate of the age of our Milky Way Galaxy suggests it was an original member of the universe, having been born just about as early on as was possible. The overall universe is about 13.7 billion years old. That figure, after decades of wildly varying estimates, was pinned down last year to within 200 million years of accuracy. Scientists used space-based observations of a microwave background radiation that had been unleashed as a dense fog cleared, shortly after the universe's formation.


The background radiation also suggested that the first stars formed about 200 million years after the Big Bang, theorists say, just as the fog lifted on the initial dark ages. Astronomers have known that the Milky Way is among the oldest of galaxies. The new observations suggest it was indeed one of the first to get under construction. The study puts its age at 13.6 billion years, give or take 800 million years. Further studies will be needed to reduce that margin of error.


A key to generating the new number was knowledge that the earliest stars formed almost entirely from hydrogen. They lived short lives and exploded violently, spewing new and heavier elements into their surroundings. The new age estimate is based on measurements of the element beryllium in two stars within a globular cluster of stars called NGC 6397. The amount of Beryllium, one of the lightest elements, increased with time and serves as a sort of "cosmic clock," according to the team, led by Luca Pasquini of the European Southern Observatory. The stars were found to be roughly 13.4 billion years old. The researchers added to that an interval of about 200 million years they say it took for previous generations of stars in the Milky Way to form, explode, and seed the fledgling galaxy with the goods necessary to forge the types of stars found in NGC 6397.

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Time's quantum arrow has a preferred direction: BaBar experiment confirms time asymmetry

Time's quantum arrow has a preferred direction: BaBar experiment confirms time asymmetry | Amazing Science |
Time marches relentlessly forward for you and me; watch a movie in reverse, and you'll quickly see something is amiss. But from the point of view of a single, isolated particle, the passage of time looks the same in either direction. For instance, a movie of two particles scattering off of each other would look just as sensible in reverse – a concept known as time reversal symmetry.


Now the BaBar experiment at the Department of Energy's (DOE) SLAC National Accelerator Laboratory has made the first direct observation of a long-theorized exception to this rule. Digging through nearly 10 years of data from billions of particle collisions, researchers found that certain particle types change into one another much more often in one way than they do in the other, a violation of time reversal symmetry and confirmation that some subatomic processes have a preferred direction of time. The results are impressively robust, with a 1 in 10 tredecillion (10E43) or 14-sigma level of certainty – far more than needed to declare a discovery.


"It was exciting to design an experimental analysis that enabled us to observe, directly and unambiguously, the asymmetrical nature of time," said BaBar collaborator Fernando Martínez-Vidal, associate professor at the University of Valencia and member of the Instituto de Fisica Corpuscular (IFIC), who led the investigation. "This is a sophisticated analysis, the kind of experimental work that can only be done when an experiment is mature."


BaBar, which collected data at SLAC from 1999 to 2008, was designed to tease out subtle differences in the behavior of matter and antimatter that might help account for the preponderance of matter in the universe. It produced almost 500 million pairs of particles called B mesons and their antimatter counterparts B-bar mesons for study. BaBar scientists found that B mesons and B-bar mesons do, indeed, behave differently in ways that violate so-called CP symmetry, which incorporates the symmetries of charge (positive versus negative) and parity (which can be thought of as left-handedness versus right-handedness). This discovery of CP violation contributed to the 2008 Nobel Prize in Physics.

Patricio Díaz's curator insight, October 20, 2013 6:02 PM

La Teoría Cuántica confirma la asimetría del tiempo

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Astronauts bring back new life (from a training session in a cave)

Astronauts bring back new life (from a training session in a cave) | Amazing Science |

It is not every day that astronauts can claim to return to Earth with a new species of life. But when the astronauts on ESA's CAVES underground training course returned to the surface they were carrying a special type of woodlouse.


The ancestors of the terrestrial isopods seem to have evolved from aquatic life to live on land. Surprisingly, the astronauts found a species that has returned to living in water, completing an evolutionary full circle. "This find is important because the few aquatic woodlice we know of were thought to be primitive forms from which terrestrial woodlice had evolved. Now it is clear that these animals have evolved to live in water again," explains isopod specialist Stefano Taiti. "It is changing our point of view on evolutionary processes in regards to terrestrial isopods living in an aquatic environment. "The find also confirms the theory that evolution is not a one-way process but that species can evolve to live in previously forgotten habitats." "This shows that CAVES offers a truly interesting scientific programme while keeping to its main goal: to train spaceflight teams in an operational space analogue on Earth," affirms Loredana.

Via The QI Elves
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Transhumanism (WIRED) - The Big Question... What Is The Future of Human Physical Enhancement?

Transhumanism (WIRED) - The Big Question... What Is The Future of Human Physical Enhancement? | Amazing Science |

News and features about transhumanism, Humanity Plus, H+, Humanity 2.0 and the ethical, medical and social issues associated with them. How can we enhance the human body and mind through a series of improvements already in the workings? Are cryonics, avatars and futuristic medicine providing a dilemma for transhumanists? Do military modifications give rise to an army of supersoldiers? Already existing: Cyborg cockroaches that can be remotely controlled. A bodyhacker's wish list: Sleep replacement and 3D-printed shapeshifting. Smart drugs lead to 'moral enhancement' - a chemical approach to transhumanism.

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Moore's Law: The rule that really matters in tech

Moore's Law: The rule that really matters in tech | Amazing Science |

Year in, year out, Intel executive Mike Mayberry hears the same doomsday prediction: Moore's Law is going to run out of steam. Sometimes he even hears it from his own co-workers.

But Moore's Law, named after Intel co-founder Gordon Moore, who 47 years ago predicted a steady, two-year cadence of chip improvements, keeps defying the pessimists because a brigade of materials scientists like Mayberry continue to find ways of stretching today's silicon transistor technology even as they dig into alternatives.

Via Szabolcs Kósa, olsen jay nelson
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