Cartography of the Cosmos

Silvio Rizzi and Joe Insley, Argonne Leadership Computing Facility, Argonne National Laboratory This shows the HACC cosmology simulation, which combines high spatial and temporal resolution in a large cosmological volume. The high temporal resolution tracks the evolution of structures in great detail and correlates formation histories to the environments in which the structures form.

There are hundreds of billions of stars in our own Milky Way galaxy. Estimates indicate a similar number of galaxies in the observable universe, each with its own large assemblage of stars, many with their own planetary systems. Beyond and between these stars and galaxies are all manner of matter in various phases, such as gas and dust. Another form of matter, dark matter, exists in a very different and mysterious form, announcing its presence indirectly only through its gravitational effects.

This is the universe Salman Habib is trying to reconstruct, structure by structure, using precise observations from telescope surveys combined with next-generation data analysis and simulation techniques currently being primed for exascale computing.

"We're simulating all the processes in the structure and formation of the universe. It's like solving a very large physics puzzle," said Habib, a senior physicist and computational scientist with the High Energy Physics and Mathematics and Computer Science divisions of the U.S. Department of Energy's (DOE) Argonne National Laboratory.

Habib leads the "Computing the Sky at Extreme Scales" project or "ExaSky," one of the first projects funded by the recently established Exascale Computing Project (ECP), a collaborative effort between DOE's Office of Science and its National Nuclear Security Administration.

From determining the initial cause of primordial fluctuations to measuring the sum of all neutrino masses, this project's science objectives represent a laundry list of the biggest questions, mysteries and challenges currently confounding cosmologists.

There is the question of dark energy, the potential cause of the accelerated expansion of the universe, called inflation. Another question is the nature and distribution of dark matter in the universe.

These are immense questions that demand equally expansive computational power to answer. The ECP is readying science codes for exascale systems, the new workhorses of computational and big data science.

Initiated to drive the development of an "exascale ecosystem" of cutting-edge, high-performance architectures, codes and frameworks, the ECP will allow researchers to tackle data and computationally intensive challenges such as the ExaSky simulations of the known universe.

In addition to the magnitude of their computational demands, ECP projects are selected based on whether they meet specific strategic areas, ranging from energy and economic security to scientific discovery and healthcare.

"Salman's research certainly looks at important and fundamental scientific questions, but it has societal benefits, too," said Paul Messina, Argonne Distinguished Fellow. "Human beings tend to wonder where they came from, and that curiosity is very deep."

HACC'ing the night sky

For Habib, the ECP presents a two-fold challenge -- how do you conduct cutting-edge science on cutting-edge machines?

The cross-divisional Argonne team has been working on the science through a multi-year effort at the Argonne Leadership Computing Facility (ALCF), a DOE Office of Science User Facility. The team is running cosmological simulations for large-scale sky surveys on the facility's 10-petaflop high-performance computer, Mira. The simulations are designed to work with observational data collected from specialized survey telescopes, like the forthcoming Dark Energy Spectroscopic Instrument (DESI) and the Large Synoptic Survey Telescope (LSST).

Survey telescopes look at much larger areas of the sky -- up to half the sky, at any point -- than does the Hubble Space Telescope, for instance, which focuses more on individual objects. One night concentrating on one patch, the next night another, survey instruments systematically examine the sky to develop a cartographic record of the cosmos, as Habib describes it.

Working in partnership with Los Alamos and Lawrence Berkeley National Laboratories, the Argonne team is readying itself to chart the rest of the course.

Their primary code, which Habib helped develop, is already among the fastest science production codes in use. Called HACC (Hardware/Hybrid Accelerated Cosmology Code), this particle-based cosmology framework supports a variety of programming models and algorithms.

Unique among codes used in other exascale computing projects, it can run on all current and prototype architectures, from the basic X86 chip used in most home PCs, to graphics processing units, to the newest Knights Landing chip found in Theta, the ALCF's latest supercomputing system.

As robust as the code is already, the HACC team continues to develop it further, adding significant new capabilities, such as hydrodynamics and associated subgrid models.

"When you run very large simulations of the universe, you can't possibly do everything, because it's just too detailed," Habib explained. "For example, if we're running a simulation where we literally have tens to hundreds of billions of galaxies, we cannot follow each galaxy in full detail. So we come up with approximate approaches, referred to as subgrid models."

Even with these improvements and its successes, the HACC code still will need to increase its performance and memory to be able to work in an exascale framework. In addition to HACC, the ExaSky project employs the adaptive mesh refinement code Nyx, developed at Lawrence Berkeley. HACC and Nyx complement each other with different areas of specialization. The synergy between the two is an important element of the ExaSky team's approach.

A cosmological simulation approach that melds multiple approaches allows the verification of difficult-to-resolve cosmological processes involving gravitational evolution, gas dynamics and astrophysical effects at very high dynamic ranges. New computational methods like machine learning will help scientists to quickly and systematically recognize features in both the observational and simulation data that represent unique events.

A trillion particles of light

The work produced under the ECP will serve several purposes, benefitting both the future of cosmological modeling and the development of successful exascale platforms.

On the modeling end, the computer can generate many universes with different parameters, allowing researchers to compare their models with observations to determine which models fit the data most accurately. Alternatively, the models can make predictions for observations yet to be made.

Models also can produce extremely realistic pictures of the sky, which is essential when planning large observational campaigns, such as those by DESI and LSST.

"Before you spend the money to build a telescope, it's important to also produce extremely good simulated data so that people can optimize observational campaigns to meet their data challenges," said Habib.

But the cost of realism is expensive. Simulations can range in the trillion-particle realm and produce several petabytes -- quadrillions of bytes -- of data in a single run. As exascale becomes prevalent, these simulations will produce 10 to 100 times as much data.

The work that the ExaSky team is doing, along with that of the other ECP research teams, will help address these challenges and those faced by computer manufacturers and software developers as they create coherent, functional exascale platforms to meet the needs of large-scale science. By working with their own codes on pre-exascale machines, the ECP research team can help guide vendors in chip design, I/O bandwidth and memory requirements and other features.

Read more at Science Daily

Amount of water in stem cells can determine its fate as fat or bone

Top images (A): Illustrates the development of stem cells on hydrogel, a soft substrate, to pre-bone cells after the removal of water. Bottom images (B): Depicts the development of stem cells on glass, a hard substrate, to pre-fat cells after the addition of water.

Adding or removing water from a stem cell can change the destiny of the cell, researchers have discovered in a new study published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS).

The research found that altering the volume of a cell changed its internal dynamics, including the rigidness of the matrix lining the outer surface. In stem cells, removing water condenses the cell, influencing the stem cells to become stiff pre-bone cells, while adding water causes the cells to swell, forming soft pre-fat cells.

Researchers have long understood that stem cells are influenced by the cells around them, picking up cues on what their function should be based on the stiffness of the matrices of neighboring cells.

The results, however, confirm that nature plays as much of a role as nurture in stem cell behavior and development.

"The findings from this study add a fascinating new tool to our understanding and utilization of stem cell biology for regenerative medicine," says Praveen Arany, DDS, PhD, co-author and assistant professor in the Department of Oral Biology in the University at Buffalo School of Dental Medicine.

The study was led by Ming Guo, PhD, d'Arbeloff Assistant Professor in the Department of Mechanical Engineering at the Massachusetts Institute of Technology; and David Weitz, PhD, Mallinckrodt Professor of Physics and of Applied Physics in the John A. Paulson School of Engineering and Applied Sciences at Harvard University.

"For the first time, we're beginning to understand the importance of cell volume and cellular water content in the mechanical properties and physiological functions of cells," says Guo, who began the research as a graduate student in Weitz's lab at Harvard.

The Line Between Bone and Fat

The research originally sought to understand the effects of volume on a cell's characteristics and functions. Cell volume is highly regulated and changes frequently over the course of a cell's life, increasing as the cell grows and decreasing when it divides.

These changes in volume are a result of variations in the amount of protein, DNA and other materials within the cell, though they mostly remain constant. But cells can also experience rapid and extreme changes in size and density through the absorption or release of water, spreading or shrinking in as little as 20 minutes.

By increasing or decreasing the volume of cells by 20 percent, the investigators found that the cells experienced several internal changes, including in gene expression and stiffness.

Knowing the role cell stiffness plays in the development of stem cells, the researchers began to wonder if cell volume could affect their fate as well.

To test the premise, investigators placed stem cells at their normal volume in a hardened hydrogel substrate to simulate the rigidness of bone cells. After one week, a large portion of the stem cells developed into pre-bone cells.

The experiment was repeated with a softened hydrogel substrate. In the softer environment, there was a significant decrease in the number of stem cells that became pre-bone cells. However, when water was removed from the cells to decrease their volume by 20 percent, the number of stem cells that became pre-bone cells increased, despite being in the softer substrate.

A similar experiment was conducted using glass. Researchers placed stem cells on glass to simulate a stiffer environment and found that few of the cells developed into pre-fat cells. It was not until the volume of the stem cells was increased by 20 percent that a spike in the formation of fat cells was found.

The investigators discovered that changing the volume of the cells caused them to behave similarly to as if they were under environmental pressures.

"The surprising thing about these experiments is the observation that volume seems to be related to so much about the cell. It seems to dictate the cell stiffness as well as the cell fate," says Weitz, also a core faculty member of the Wyss Institute for Biologically Inspired Engineering and director of the Materials Research Science and Engineering Center at Harvard.

"These observations may also have implications in external means of monitoring cell fate, which may be important for future biotech applications."

Future studies are needed to examine the effects of varied changes in volume, as well as if cell volume or external cues are the dominating factor in the fate of stem cells.

The Future of Regenerative Medicine

Stem cells sit at the forefront of regenerative medicine, providing researchers and clinicians with the potential to repair or replace damaged tissue and organs.

With the ability to develop into any type of specialized cell -- from a muscle cell to a red blood or brain cell -- stem cells hold the potential to treat various diseases and conditions, from heart disease to tooth loss. Bone marrow transplantation, one form of stem cell therapy, is already in widespread use.

Stem cells may also aid in drug development and the understanding of how cancer and birth defects occur.

Learning what causes differentiation among these cells will help researchers generate methods that influence their behavior and, ultimately, develop new therapies.

Read more at Science Daily

Pigeons better at multitasking than humans

Sara Letzner had humans compete against pigeons in a behavioural experiment.

Pigeons are capable of switching between two tasks as quickly as humans -- and even more quickly in certain situations. These are the findings of biopsychologists who had performed the same behavioural experiments to test birds and humans. The authors hypothesize that the cause of the slight multitasking advantage in birds is their higher neuronal density.

Dr Sara Letzner and Prof Dr Dr h. c. Onur Güntürkün from Ruhr-Universität Bochum published the results in the journal "Current Biology" in collaboration with Prof Dr Christian Beste from the University Hospital Carl Gustav Carus at Technische Universität Dresden.

"For a long time, scientists used to believe the mammalian cerebral cortex to be the anatomical cause of cognitive ability; it is made up of six cortical layers," says Sara Letzner. In birds, however, such a structure does not exist. "That means the structure of the mammalian cortex cannot be decisive for complex cognitive functions such as multitasking," continues Letzner.

Six times as densely packed

The pallium of birds does not have any layers comparable to those in the human cortex; but its neurons are more densely packed than in the cerebral cortex in humans: pigeons, for example, have six times as many nerve cells as humans per cubic millimetre of brain. Consequently, the average distance between two neurons in pigeons is fifty per cent shorter than in humans. As the speed at which nerve cell signals are transmitted is the same in both birds and mammals, researchers had assumed that information is processed more quickly in avian brains than in mammalian brains.

They tested this hypothesis using a multitasking exercise that was performed by 15 humans and 12 pigeons. In the experiment, both the human and the avian participants had to stop a task in progress and switch over to an alternative task as quickly as possible. The switchover to the alternative task was performed either at the same time the first task was stopped, or it was delayed by 300 milliseconds.

What makes pigeons faster

In the first case, real multitasking takes place, which means that two processes are running simultaneously in the brain, those being the stopping of the first task and switching over to the alternative task. Pigeons and humans both slow down by the same amount under double stress.

In the second case -- switching over to the alternative task after a short delay -- the processes in the brain undergo a change: the two processes, namely stopping the first task and switching over to the second task, alternate like in a ping-pong game. For this purpose, the groups of nerve cells that control both processes have to continuously send signals back and forth. The researchers had assumed that pigeons must have an advantage over humans because of their greater nerve cell density. They were, in fact, 250 milliseconds faster than humans.

Read more at Science Daily

Minimal Consciousness Restored in Man Who Was in a Vegetative State for 15 Years

Persistent vegetative states lasting longer than 12 months has long been considered irreversible. But a 35-year-old man severely injured in a car accident was partially revived by vagus nerve stimulation after lying in a vegetative state for 15 years.

The technique has been in use for many years for treating people with epilepsy or depression. But this is the first time that doctors attempted to treat a vegetative patient with the technique.

The vagus nerve connects the human brain stem to the heart, lungs, and digestive tract. It's the longest nerve in the body's autonomous nervous system, which mostly regulates unconscious functions like heart rate, digestion, and breathing.

Angela Sirigu, who led the research at the Institute of Cognitive Sciences – Marc Jeannerod in Lyon, France, said the technique could trigger a radical change in neurological treatments worldwide.

“Brain plasticity and brain repair are still possible even when hope seems to have vanished,” Sirigu said in a statement accompanying publication of research describing the procedure.

The research team began the experiment by looking for a particularly difficult case, to reduce the possibility that any improvements weren't simply a matter of chance and good timing. The patient chosen for the experiment had shown no signs of improvement in 15 years.

Doctors then implanted a vagus nerve simulator in the man's chest designed to send small pulses of electricity up the vagus nerve and into the brain.

After a month of constant stimulation, the patient's movements and brain activity improved significantly. He responded to simple commands, such as following an object with his eyes and turning his head upon request.

Computer monitoring of the patient’s brain activity confirmed major changes took place. Imaging scans showed increased metabolic activity in areas of the brain associated with movement, awareness, and sensation. A series of electroencephalogram tests suggested that the patient had improved from a “vegetative state” to a “minimally conscious state.”

By stimulating the vagus nerve, “it is possible to improve a patient's presence in the world,” Sirigu said.

The research was published in the journal Current Biology.

An estimated 25,000 people in the US lie in a vegetative state at any given time.

While the new study marks a positive development, researchers caution that the study is, by design, extremely limited in scope.

“We need to be a little cautious about this, because it's just one patient,” said neurologist Hae Won Shin, an associate professor at the University of North Carolina School of Medicine who was not involved in the research. “I'm really glad to hear that the patient responded positively to vagus nerve stimulation treatment after 15 years in a vegetative state, but it's only one case.”

The researchers are currently planning a larger collaborative study to confirm the therapeutic potential of VNS for patients in a vegetative state. The initial study was supported by France's National Center for Scientific Research, the French National Research Agency, and by a grant from the University of Lyon

Hae, who specializes in epileptic disorders, said vagus nerve stimulation has a track record of proven efficacy in treating certain disorders — but there's a caveat: No one is quite sure how it works.

Read more at Seeker

Genes are controlled by 'Nano footballs,' scientists discover

Rendering of DNA.

Research at the University of York has revealed that genes are controlled by 'nano footballs' -- structures that look like footballs but 10 million times smaller than the average ball.

By placing tiny glowing probes on transcription factors -- special chemicals inside cells which control whether a gene is switched 'on' or 'off' -- researchers gained a remarkable new insight into the way in which genes are controlled.

Crucially, they discovered that transcription factors operate not as single molecules as was previously thought, but as a spherical football-like cluster of around seven to ten molecules of roughly 30 nanometres in diameter.

The discovery of these nano footballs will not only help researchers understand more about the basic ways in which genes operate, but may also provide important insights into human health problems associated with a range of different genetic disorders, including cancer.

The research, supported by the Biotechnology and Biological Sciences Research Council (BBSRC) and published in eLife was carried out by scientists from the University of York, and the University of Gothenburg and Chalmers University of Technology, Sweden.

The researchers employed advanced super-resolution microscopy to look at the nano footballs in real time, using the same type of yeast cells utilised in baking and brewing beer.

Professor Mark Leake, Chair of Biological Physics at the University of York who led the work, said: "Our ability to see inside living cells, one molecule at a time, is simply breathtaking.

"We had no idea that we would discover that transcription factors operated in this clustered way. The textbooks all suggested that single molecules were used to switch genes on and off, not these crazy nano footballs that we observed."

The team believe the clustering process is due to an ingenious strategy of the cell to allow transcription factors to reach their target genes as quickly as possible.

Professor Leake said: "We found out that the size of these nano footballs is a remarkably close match to the gaps between DNA when it is scrunched up inside a cell. As the DNA inside a nucleus is really squeezed in, you get little gaps between separate strands of DNA which are like the mesh in a fishing net. The size of this mesh is really close to the size of the nano footballs we see.

"This means that nano footballs can roll along segments of DNA but then hop to another nearby segment. This allows the nano football to find the specific gene it controls much more quickly than if no nano hopping was possible. In other words, cells can respond as quickly as possible to signals from the outside, which is an enormous advantage in the fight for survival."

Genes are made from DNA, the so-called molecule of life. Since the discovery that DNA has a double helix shape, made in the 1950s by pioneering biophysics researchers, much has been learned about transcription factors which can control whether a gene is switched on or off.

If a gene is switched on, specialised molecular machinery in the cell reads off its genetic code and converts it into a single protein molecule.Thousands of different types of protein molecules can then be made, and when they interact that can drive the building of all of the remarkable structures found inside living cells.

The process of controlling which genes are switched on or off at any particular point in time is fundamental to all life. When it goes wrong, this can lead to serious health problems. In particular, dysfunctional switching of genes can result in cells which grow and divide uncontrollably, which can ultimately lead to cancer.

Read more at Science Daily

Ancient Egyptians Provided a Proper Burial to a Statue of a Revered Deity

Osiris statuette

After years of being washed, perfumed and fed in ancient Egypt, the statue of a revered Egyptian deity was given a proper burial with other "dead" statues more than 2,000 years ago, a new study finds.

Ancient Egyptians buried the statue of the deity Ptah — the god of craftsmen and sculptors — with other revered statues, including those of a sphinx, baboon, cat, Osiris, and Mut, in a pit next to Ptah's temple.

The statue of Ptah had likely sat in the temple for years, but it and the other sacred objects were respectfully buried after they accumulated damage and were declared useless by the ancient Egyptians, the researchers said.

"We can consider that when a new statue was erected in the temple, this one [of Ptah] was set aside in a pit," said study co-researcher Christophe Thiers, director of the French-Egyptian Center for the Study of the Temples of Karnak. "The other artifacts were also previously damaged during their ‘lifetime’ in the temple, and then they were buried with the Ptah statue."

Archaeologists discovered the pit in December 2014 at Karnak, an Egyptian temple precinct, and spent about a month excavating its rich assemblage. The pit held 38 objects, including:

Fourteen statuettes and figurines of Osiris.
Eleven fragments of inlay from statues.
The inlay included that of an iris, a cornea, a false beard, a cap, a strand of hair and an inlay plaque.
Three baboon statuettes (representing the god Thoth).
Two statuettes of the goddess Mut (one with hieroglyphic inscriptions).
Two unidentified statuette bases.
One head and one fragmentary statuette of a cat (Bastet).
One small fragmentary faience stele (a stone slab) recording the name of the god Ptah.
One head of a statuette of a man in gilded limestone.
One lower part of a statue of the seated god Ptah, sawn and repaired.
One sphinx.
One unidentified metal piece.

The favissa contained 38 objects, including (clockwise from top left) a male head made of gilded limestone, the lower part of the limestone statue of the god Ptah, a statuette of Osiris, and a limestone sphinx.

It appeared that the artifacts were buried in a certain order. After digging the pit, also known as a favissa (a cache of sacred objects that are no longer in use), the ancient Egyptians would have put down the lower part of Ptah's limestone statue. The statue was large, and it probably took two to three people to carry it, the researchers said.

Next to the statue, the Egyptians would have placed a wooden effigy of the god Osiris that had metal appliqué, including a beard and two feathers in its crown. Then, the other artifacts would have been distributed around these two artifacts, which were then covered with about 8 inches (20 centimeters) of backfill. This is where the ancient Egyptians placed a statue of a small limestone sphinx.

The pit was then covered with more backfill. At the top, the Egyptians placed a small male head made of gilded limestone, likely for protection, the researchers said.

The objects were made at different times, the researchers found. The statue of Ptah dates to the New Kingdom; the style of the sphinx supports a late Ptolemaic date; and the gilded head dates to the early Ptolemaic period, the researchers said. However, by studying the site's rock layers, the researchers found that the artifacts were buried by the temple's priests during the second half of the Ptolemaic period, between the second century B. and the middle of the first century BC, the researchers wrote in the study.

Read more at Seeker

This Airship Might Provide a Better View of the Big Bang’s Relic Radiation

Airlander 10’s first flight on 2016 August 17

Despite the universe being billions of years old, today we can still see the early stages of the its expansion through a phenomenon called cosmic microwave background radiation. NASA describes the CMB as "literally the remnant heat left over from the Big Bang."

The energy is visible in microwave wavelengths, which means it can't be seen unless you're above the atmosphere somewhere. But observations taken for spacecraft caught something extraordinary: a remarkably uniform background about 2.275 degrees Celsius (36 degrees Fahrenheit) above absolute zero, or the coldest possible temperature allowed by physics. Mapping and understanding the tiny variations of temperature at the part per million level that require ongoing observations and modeling.

Scientists have observed the CMB before with spacecraft, and even a specially adapted 747 called SOFIA (Stratospheric Observatory for Infrared Astronomy). A proposal published in the Monthly Notices of the Royal Astronomical Society suggests using an airship called Airlander 10, which is cheaper than a spacecraft, but allows for lengthy observations of up to weeks at a time.

"The main advantage is flight duration," Stephen Feeney, lead author and a postdoctoral researcher at the Flatiron Institute's Center for Computational Astrophysics in New York City, told Seeker in an email.

"Using remote piloting, Airlander 10 should fly for up to three weeks at a time,” he said. “We could therefore observe the sky roughly 20 times longer on an Airlander 10 flight than using, for example, a 747 like SOFIA. Airlander 10 is also able to operate without an airport, and should have a significantly smaller environmental impact, as it generates 60 percent of its lift through buoyancy."

An image of the cosmic microwave background radiation, including the foreground signal from the Milky Way galaxy (in red). This picture is based on observations from NASA's Wilkinson Microwave Anisotropy Probe, which operated from 2001 to 2010.

Airlander 10 is a hybrid airship — meaning that part of its lift, or ability to fly, comes from being filled with lighter-than-air gas, and the other part of its lift comes from aerodynamics. Originally designed and built for the US Army, the military sold the airship back to the manufacturer in 2016 for civilian use. It is now in test flights, having survived an accident, which damaged the airship, but left the crew unharmed. This means that Feeney's proposal is still in a very early stage.

"We are currently working with Hybrid Air Vehicles, Airlander 10's designers, to ascertain whether the vibrations from Airlander 10's engines are low enough to allow a CMB telescope to gather useful data,” Feeney said. “If this critical criterion is satisfied, we will look to develop the concept further.”

Feeney's research, in part, concerns how to operate CMB detectors at higher altitudes, which requires knowledge of how they perform at sea level, then extrapolating their performance at higher and higher altitudes. The research also seeks to ways to avoid confusing radiation from galaxies, which are closer to us than the CMB. Both galaxies and CMB can emit radiation at the same wavelengths.

"These foregrounds can be cleaned from the CMB by observing the sky at many different wavelengths, as the amplitudes of the foregrounds and CMB change differently with wavelength," Feeney said.

Read more at Seeker

Cosmic Rays Originate Far Beyond the Milky Way

Something out in space has been bombarding Earth with incredibly high energy particles called cosmic rays. The origin of cosmic rays has been a mystery since their discovery over a century ago.

But twelve years of data from an unusual observatory in South America has now confirmed that cosmic rays with the highest energies come from sources outside the Milky Way. In particular, the majority of the high-energy particles originate from an area of the sky that lies almost opposite from the center of our own galaxy, in a region of space with a high concentration of other galaxies. 

“The distribution of arrival directions of the highest energy cosmic ray particles has an enhancement in a broad patch of the sky which is roughly 120 degrees away from a line pointing from Earth to the center of our Milky Way galaxy, meaning cosmic rays coming to the Earth from that patch must be coming from other galaxies,” Gregory Snow, a physics professor from the University of Nebraska-Lincoln, said in an email to Seeker. He is also the education and outreach coordinator for the Pierre Auger Observatory, which is located in western Argentina and was the source of the data.

Snow and a group of more than 400 scientists from 18 countries published last week their analysis of cosmic rays in the journal Science.

He explained the direction of the enhanced patch is consistent with a region of galaxies that is more dense than other regions of the sky.

“This makes sense since we might expect more cosmic ray particles coming from places in the universe where there is a lot of ‘stuff,’” he said.

Scientists collected a dozen years of data on cosmic rays at the Pierre Auger Observatory in Argentina.

Cosmic rays are electrically charged particles, such as protons, that travel near the speed of light. They strike Earth from all directions, and have energies up to one hundred million times higher than those created in man-made accelerators like the Large Hadron Collider. These high-energy cosmic rays — ones with energies reaching quintillions of electron volts — are different from the ones emitted by our sun during flares and coronal mass ejections.

"The sun emits low-energy cosmic ray particles that are detected here on Earth, but they are nowhere near as high energy as the particles detected at the Auger Observatory," Snow explained in a press release.

When the high energy cosmic rays travel across space, the particles can be deflected by magnetic fields, which scramble their paths and sometimes mask their origins.

Detecting cosmic rays is even more challenging because the highest energy particles — the ones that are most mysterious and rare — reach Earth at a rate of only one particle per square kilometer each year.

That’s where the Pierre Auger Observatory comes in. The observatory uses 1,660 tanks filled with ultra-pure water, spread over a 1,800-square-mile (3,000-square-kilometer) grid in Argentina. Each 3,000-gallon (12,000 liter) tank is separated from the other tanks by about a mile (1.5 km) and are enclosed to make them completely dark inside. When cosmic ray particles pass through the water, their electromagnetic shock waves produce radiation called Cherenkov light that can be measured by special instruments mounted in the tanks.

There are also separate, independent detectors called air fluorescence telescopes that track the development of what is called “air showers.” Cosmic rays interacting with Earth’s atmosphere produce a cascade effect, creating extensive showers that contain billions of secondary particles. The air fluorescence telescopes observe ultraviolet light emitted high in Earth's atmosphere from the showers.  These air showers can also cause nearly simultaneous bursts of light in more than five tanks.

Using the two detectors, scientists can determine the energy of the primary cosmic ray particles based on the amount of light they detect from a sample of secondary particles. Additionally, slight differences in the detection times at different tank positions help scientists determine the trajectory of the incoming cosmic rays.

In over a dozen years of operation, the Auger Observatory has collected some of the highest quality information about the types of particles in primary cosmic rays. Comparing results from the different types of detectors also helps scientists reconcile the two sets of data and produce the most accurate results about the energy of primary cosmic rays.

University of Nebraska-Lincoln physics professor Gregory Snow stands near one of the cosmic ray particle detectors used by the Pierre Auger Observatory in Argentina.

But why study these high-energy cosmic rays?

For one thing, scientists like a good mystery and the origins of cosmic rays is one of the biggest unknowns in physics.

But understanding them better could lead to improved insights on fundamental physics, such as how our universe was created, and why objects have mass. Snow told Seeker high-energy cosmic rays are clues to the very structure of the universe.

“High-energy cosmic ray particles are one of several messengers from outer space that we use to learn about the structure of the universe, for example, the distribution of where the billions of other galaxies apart from the Milky Way are located,” he said. “We now know that galaxies are not uniformly distributed in outer space. Rather they group themselves in clusters and super-clusters.”

Also, scientists don’t know the exact source of high-energy cosmic rays. There have been theories, but the intense conditions needed to generate such energetic particles can be mind-boggling.

“We know that shock waves coming from stars dying in the form of a supernova could accelerate cosmic ray particles up to energies reaching about 10 to the 15th electron volts,” Snow explained. “But our paper is about cosmic ray particles of much higher energies, greater than 8 times 10 to the 18th electron volts. We can only speculate what the sources of these particles may be.”

Snow said physicists can learn the most about specific sources by studying the arrival directions of the very highest energy particles, since their measured arrival directions essentially point straight back to their sources.

Read more at Seeker

World's first 'molecular robot' capable of building molecules

Molecular robotics represents the ultimate in the miniaturization of machinery, researchers say.

Scientists at The University of Manchester have created the world's first 'molecular robot' that is capable of performing basic tasks including building other molecules.

The tiny robots, which are a millionth of a millimetre in size, can be programmed to move and build molecular cargo, using a tiny robotic arm.

Each individual robot is capable of manipulating a single molecule and is made up of just 150 carbon, hydrogen, oxygen and nitrogen atoms. To put that size into context, a billion billion of these robots piled on top of each other would still only be the same size as a single grain of salt.

The robots operate by carrying out chemical reactions in special solutions which can then be controlled and programmed by scientists to perform the basic tasks.

In the future such robots could be used for medical purposes, advanced manufacturing processes and even building molecular factories and assembly lines. The research will be published in Nature on Thursday 21st September.

Professor David Leigh, who led the research at University's School of Chemistry, explains: 'All matter is made up of atoms and these are the basic building blocks that form molecules. Our robot is literally a molecular robot constructed of atoms just like you can build a very simple robot out of Lego bricks. The robot then responds to a series of simple commands that are programmed with chemical inputs by a scientist.

'It is similar to the way robots are used on a car assembly line. Those robots pick up a panel and position it so that it can be riveted in the correct way to build the bodywork of a car. So, just like the robot in the factory, our molecular version can be programmed to position and rivet components in different ways to build different products, just on a much smaller scale at a molecular level.'

The benefit of having machinery that is so small is it massively reduces demand for materials, can accelerate and improve drug discovery, dramatically reduce power requirements and rapidly increase the miniaturisation of other products. Therefore, the potential applications for molecular robots are extremely varied and exciting.

Prof Leigh says: 'Molecular robotics represents the ultimate in the miniaturisation of machinery. Our aim is to design and make the smallest machines possible. This is just the start but we anticipate that within 10 to 20 years molecular robots will begin to be used to build molecules and materials on assembly lines in molecular factories.'

Whilst building and operating such tiny machine is extremely complex, the techniques used by the team are based on simple chemical processes.

Prof Leigh added: 'The robots are assembled and operated using chemistry. This is the science of how atoms and molecules react with each other and how larger molecules are constructed from smaller ones.

Read more at Science Daily

Scientists sequence asexual tiny worm whose lineage stretches back 18 million years

Pictured is Diploscapter pachys (D. pachys), a newly sequenced roundworm that is approximately one-third of a millimeter long and one of a very few known animals that have only a single chromosome.

A team of scientists has sequenced, for the first time, a tiny worm that belongs to a group of exclusively asexual species that originated approximately 18 million years ago -- making it one of the oldest living lineages of asexual animals known. The work reveals how it has escaped the evolutionary dead end usually met by organisms that do not engage in sex.

"Scientists have been trying to understand how some animals can survive for millions of years without sex because such strict, long-term abstinence is very rare in the animal world," explains New York University Biology Professor David Fitch, one of the co-authors of the research. "This phenomenon is a significant one in understanding evolutionary genetics because it runs counter to the widely accepted view that sexual reproduction is required to eliminate deleterious mutations and for adaptation to a changing environment."

"For example, in the short term, inheriting copies of both parents' genes usually provides good insurance against mutations that might kill the function of one of those gene copies -- a process called complementation," Fitch continues. "In the long term, producing offspring via intercourse allows for adaptation to changing conditions over time because it produces variation through genetic shuffling, or recombination. However, because such shuffling does not occur within asexual species, they tend to go extinct rapidly. So, it has been a longstanding mystery in biology how some asexual animals have survived for so many generations."

The research, conducted by researchers in NYU's Center for Genomics and Systems Biology and Duke University's Center for Genomic and Computational Biology, appears in the journal Current Biology.

The newly sequenced worm, Diploscapter pachys, is a tiny, transparent, free-living roundworm and closely related to Caenorhabditis elegans, an organism commonly used for biomedical research.

Unlike C. elegans, however, D. pachys is asexual.

In making this determination, the scientists used DNA to derive a genealogy that revealed D. pachys belongs to a group of exclusively asexual species that originated approximately 18 million years ago.

In a closer examination of how D. pachys reproduces, the research team found that, like many other asexual organisms, the process of making germ cells -- sperm or ova -- had been modified to prevent recombination, or the reshuffling that results from sexual reproduction.

"Basically, the animals were cloning themselves," explains Fitch. In addition, when the researchers studied its chromosomes, they found something even more surprising: there was only one pair of chromosomes.

Close relatives, such as C. elegans, have 5-7 chromosomes, but a single-chromosome pair, the scientists say, is so rare in higher organisms that only two other animal species are known with this condition: an ant and a parasitic roundworm.

The researchers decided to sequence the genome of D. pachys to test how the single chromosome was structured, whether by loss or by fusion of multiple ancestral chromosomes.

Their results showed that D. pachys fuses the six chromosomes of its ancestor into a single chromosome and skips the first division of meiosis, where genes are recombined, so that its offspring keeps the high genetic diversity of the parents.

Read more at Science Daily