Friday, February 21, 2014

The Human Brain Project

Thinking it through: Scientists seek to unlock mysteries of the brain  
by Staff Writers Chicago IL (SPX) Feb 20, 2014

This is a group of neurons. Image courtesy EPFL/Human Brain Project.

Understanding the human brain is one of the greatest challenges facing 21st century science. If we can rise to this challenge, we will gain profound insights into what makes us human, develop new treatments for brain diseases, and build revolutionary new computing technologies that will have far reaching effects, not only in neuroscience.

Scientists at the European Human Brain Project-set to announce more than a dozen new research partnerships worth Eur 8.3 million in funding later this month-the Allen Institute for Brain Science, and the US BRAIN Initiative are developing new paradigms for understanding how the human brain works in health and disease.

Today, their international and collaborative projects are defined, explored, and compared during "Inventing New Ways to Understand the Human Brain," at the 2014 AAAS Annual Meeting in Chicago.

Brain Simulation, Big Data, and a New Computing Paradigm

Henry Markram from the Ecole Polytechnique Federale de Lausanne (EPFL), in Switzerland, where the Human Brain Project is based, describes how the project will leverage available experimental data and basic principles of brain organization to reconstruct the detailed structure of the brain in computer models. The models will allow the HBP to run super-computer based simulations of the inner working of the brain.

"Brain simulation allows measurements and manipulations impossible in the lab, opening the road to a new kind of in silico experimentation," Markram says.

The data deluge in neuroscience is resulting in a revolutionary amount of brain data with new initiatives planning to acquire even more. But searching, accessing, and analyzing this data remains a key challenge.
Sean Hill, also of EPFL and a speaker at AAAS, leads The Neuroinformatics Platform of the Human Brain Project (HBP). In this scientific panel, he explains how the platform will provide tools to manage, navigate, and annotate spatially referenced brain atlases, which will form the basis for the HBP's modeling effort-turning Big Data into deep knowledge.

The Neuroinformatics Platform will bring together many different kinds of data. University of Edinburgh's Seth Grant, a key member of the HBP, describes how he is deriving new methods to decode the molecular principles underlying the brain's organization, such as how individual proteins assemble into larger complexes.
As Grant explains in Chicago, this has important practical applications as many mutations in schizophrenia and autism converge on these so-called supercomplexes in the brain.

As we understand more and more about the way the brain computes we can apply this knowledge to technology. Karlheinz Meier, of Heidelberg University in Germany and a speaker at AAAS, outlines how he is working to create entirely new computing systems as part of the HBP. These Neuromorphic Computing Systems will merge realistic brain models with new hardware for a completely new paradigm of computing-one that more closely resembles how the brain itself processes information.

"The brain has the ability to efficiently perform computations that are impossible even for the most powerful computers while consuming only 30 Watts of power," Meier says.

Brain: Get Ready For Your Close-up

At AAAS, Christof Koch lays out another ambitious, 10-year plan from the Allen Institute for Brain Science: to understand the structure and function of the brain by mapping cell types from mice and humans with computer simulations and figuring out how the cells connect, and how they encode, relay, and process information. The project, Koch says, promises massive, multimodal, and open-access datasets and methodology that will be reproducible and scalable.

At Harvard University, George Church is participating in the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, which aims to map every neuron in the brain with rapidly advancing technologies. At AAAS, he describes progress on new tools for measurements of brain cell development, connectivity, and functional state dynamics in rodent and human clinical samples.

What do all of these projects have in common? They seek to help find some of the most elusive answers known to man: what makes us human, how does the brain function, what causes neurological and mental illness, and, most importantly, how can we treat or cure these afflictions?

Human Brain Project

The goal of the HBP is to build a completely new Information and Communications Technology infrastructure for neuroscience and for brain-related research in medicine and computing, catalyzing a global collaborative effort to understand the human brain and its diseases and ultimately to emulate its computational capabilities.
The 10-year, 1 billion Euro project funded by the EU's FET Flagship Program was launched on October 1, 2013, and involves 80 leading universities and research institutions from 22 European countries as well as the US, Canada, Japan, and China.

Later this month (February 2014), the HBP and the EU will announce more than a dozen new research partnerships worth up to Eur 8.3 million based on the results of competitive calls for proposals opened in October, 2013, and currently in the final stages of selection. Research proposals cover topics from cognitive architectures to virtual robotic environments to the theory of multiscale circuits. The winners become full members of the global Human Brain Project Consortium.

A key aspect of the HBP is the use of supercomputer-based modeling. As supercomputers move towards the exascale and the quality of our models improves, HBP models will make it possible to conduct in silico experiments impossible in the lab.

The project has a strong focus on applications in computing and in medicine. In computing, the project will transfer simplified versions of its brain models into novel "neuromorphic computing systems" with capabilities completely lacking in current computing technology.

In medicine, the project will create tools making it possible to mine large volumes of anonymized patient data, to identify the "biological signatures" of neurological and psychiatric disease, and ultimately to build computer models of specific conditions. Such models will facilitate the screening of new treatments, speeding up drug development, and encouraging urgently needed investment in Central Nervous System research.

Monday, February 17, 2014

IBEX Helps Paint Picture of the Magnetic System Beyond the Solar Wind

by Karen C. Fox for Goddard Space Flight Center Greenbelt MD (SPX) Feb 16, 2014

A model of the interstellar magnetic fields - which would otherwise be straight -- warping around the outside of our heliosphere, based on data from NASA's Interstellar Boundary Explorer. The red arrow shows the direction in which the solar system moves through the galaxy. Image courtesy NASA/IBEX/UNH.

Understanding the region of interstellar space through which the solar system travels is no easy task. Interstellar space begins beyond the heliosphere, the bubble of charged particles surrounding the sun that reaches far beyond the outer planets. Voyager 1 has crossed into this space, but it's difficult to gain a complete global picture from measurements in only one direction.

Spacecraft data in the past five years from near Earth and cosmic ray observations have painted a better picture of the magnetic system that surrounds us, while at the same time raising new questions. Scientists are challenging our current understanding in a new study that combines observations of massively energetic cosmic ray particles streaming in from elsewhere in the Milky Way along with observations from NASA's Interstellar Boundary Explorer, or IBEX.

The data sets show a magnetic field that is nearly perpendicular to the motion of our solar system through the galaxy. In addition to shedding light on our cosmic neighborhood, the results offer an explanation for a decades-old mystery on why we measure more incoming high-energy cosmic rays on one side of the sun than on the other. The research appears in the Feb. 13, 2014, issue of Science Express.
"It's a fascinating time," said Nathan Schwadron, of the University of New Hampshire in Durham and first author on the paper. "Fifty years ago, we were making the first measurements of the solar wind and understanding the nature of what was just beyond near-Earth space. Now, a whole new realm of science is opening up as we try to understand the physics all the way outside the heliosphere."

The heliosphere is formed as the constant stream of particles from the sun's solar wind flows outward in all directions until it slows down to balance the pressure from the interstellar wind. The only information gathered directly from the heart of this complex boundary region is from NASA's Voyager mission. Voyager 1 entered the boundary region in 2004, passing beyond the termination shock where the solar wind abruptly slows down. Voyager 1 crossed into interstellar space in 2012.

IBEX, which orbits Earth, studies these regions from afar. The spacecraft detects energetic neutral atoms that form from interactions at the heliosphere's boundaries - an area that holds fascinating clues to what lies beyond.

These interactions are dominated by electromagnetic forces. The incoming particles from the galaxy are made up of negatively-charged electrons, positively-charged atoms called ions, neutral particles and dust. Charged particles are forced to travel along the magnetic field lines that snake throughout space.

Sometimes, a charged particle collides with a neutral atom at the outskirts of the heliosphere and captures an electron from the neutral atom. After stealing the electron, the charged particle becomes electrically neutral and speeds off in a straight line.

Some of these fast neutral particles stream into the inner solar system and reach IBEX's detectors. Depending on the speed and direction of those neutral particles, scientists can determine information about the atoms and magnetic field lines involved in the original collision.

In 2009, IBEX scientists presented research showing an uneven distribution of neutral atoms. There was a ribbon along the heliospheric boundaries sending a preponderance of neutral atoms toward IBEX.

Researchers wondered if this shape might also relate to an unevenness seen in cosmic rays. On Earth, we measure more cosmic rays - particles that stream in from the rest of the galaxy at 99% the speed of light - coming in from near the tail side of the heliosphere than from the other side. Teasing out the source and paths of incoming cosmic rays isn't easy as the rays gyrate around magnetic field lines both inside and outside our heliosphere before colliding with other particles in Earth's atmosphere, giving a shower of secondary particles that, in turn, are what we detect. To complicate things further, the heliosphere is moving through the galaxy.

"At some level, it's like trying to determine the wind direction when you're riding a bike very quickly and the wind isn't particularly strong," said Eric Christian, the IBEX project scientist at NASA's Goddard Space Flight Center in Greenbelt, Md., and a co-author on the paper. "There's some effect from the wind, but it's small and hard to measure."

To see if the IBEX data related to the cosmic ray observations, Schwadron used IBEX data to build a computer model of what the interplanetary magnetic field would look like around the heliosphere. Without the heliosphere, the field lines would be straight and parallel.

"But the heliosphere is kind of like an egg sitting in the middle of all these magnetic field lines," said Schwadron. "The field lines have to distort themselves around that."

With this model in hand, he simulated how the heliosphere would affect the cosmic rays. He assumed that the rays came in to the heliosphere evenly from everywhere in space, but allowed them to be warped based on the local magnetic geometry. The simulations showed a non-uniform distribution of cosmic ray particles that jibed well with the unevenness seen in observations.

"The analysis of this important paper strongly correlates with the theoretical view of the heliosphere from the numerical model developed by our team, which uses IBEX observations to derive the interstellar magnetic field direction," said Nick Pogorelov, a space scientist at the University of Alabama in Huntsville, who works with IBEX data.

"It shows that the heliopause that separates solar and interstellar plasmas is very long, maybe 2 trillion miles in the downwind direction, and therefore may affect the transport of high-energy cosmic rays toward the solar system."

Unfortunately, this doesn't prove that the heliosphere and the interstellar magnetic field are exclusively responsible for the cosmic ray mystery. However, this research shows that the magnetic configuration of our neighborhood does offer a potential answer.

Moreover, the agreement between what's seen in the cosmic ray data and by IBEX provides outside confirmation of IBEX's results of what the magnetic fields outside our heliosphere look like. That's an interesting piece of the puzzle, when compared with Voyager 1's measurements, because the Voyager 1 data provide a different direction for the magnetic fields just outside our heliosphere.

This doesn't mean that one set of data is wrong and one is right, says Schwadron. Voyager 1 is taking measurements directly, gathering data at a specific time and place; IBEX gathers information averaged over great distances, so, there is room for discrepancy.

Indeed, that discrepancy can be used as a clue. Understand why there's a difference between the two measurements and we gain additional information. More IBEX observations and more Voyager observations will keep coming in. As with all research, more data will help unravel the picture and soon we will learn even more about how we fit into the rest of the universe.

Monday, February 10, 2014

Solving a physics mystery: Those 'solitons' are really vortex rings

by Staff Writers Seattle WA (SPX) Feb 07, 2014

An example of a vortex ring, also called a toroidal bubble, which dolphins create under water. The concept of vortex rings lies at the heart of new University of Washington physics research. 
 Image by Paul Nylander ("
The same physics that gives tornadoes their ferocious stability lies at the heart of new University of Washington research, and could lead to a better understanding of nuclear dynamics in studying fission, superconductors and the workings of neutron stars.

The work seeks to clarify what Massachusetts Institute of Technology researchers witnessed when in 2013 they named a mysterious phenomenon - an unusual long-lived wave traveling much more slowly than expected through a gas of cold atoms. They called this wave a "heavy soliton" and claimed it defied theoretical description.

But in one of the largest supercomputing calculations ever performed, UW physicists Aurel Bulgac and Michael Forbes and co-authors have found this to be a case of mistaken identity: The heavy solitons observed in the earlier experiment are likely vortex rings - a sort of quantum equivalent of smoke rings.

"The experiment interpretation did not conform with theory expectations," said Bulgac. "We had to figure out what was really happening there. It was not obvious it was one thing or another - thus it took a bit of police work."

A vortex ring is a doughnut-shaped phenomenon where fluids or gases knot and spin in a closed, usually circular loop. The physics of vortex rings is the same as that which gives stability to tornadoes, volcanic eruptions and mushroom clouds. (Dolphins actually create their own vortex rings in water for entertainment.)
"Using state-of-the-art computing techniques, we demonstrated with our simulation that virtually all aspects of the MIT results can be explained by vortex rings" said Forbes, an UW affiliate professor who in January became an assistant professor of physics at Washington State University.

He said the simulations they used "could revolutionize how we solve certain physics problems in the future," such as studying nuclear reactions without having to perform nuclear tests. As for neutron stars, he said the work also could lead to a better understanding of "glitches," or rapid increases in such a star's pulsation frequency, as this may be due to vortex interactions inside the star.

"We are now at a cusp where our computational capabilities are becoming sufficient to shed light on this longstanding problem. This is one of our current directions of research - directly applying what we have learned from the vortex rings," Forbes said.

The computing work for the research - one of the largest direct numerical simulations ever - was performed on the supercomputer Titan, at the Oak Ridge Leadership Computing Facility in Tennessee, the nation's most powerful computer for open science. Work was also performed on the UW's Hyak high-performance computer cluster.