How bioinformatics tools are bringing genetic analysis to the masses

Illustration from Nature.     

For doctors trying to treat people who have symptoms that have no clear cause, gene-sequencing technologies might help in pointing them to a diagnosis. But the vast amount of data generated can make it hard to get to the answer quickly.

Patrick Chain, who led the development of the software1, at Los Alamos National Laboratory (LANL) in New Mexico, says that EDGE was created to try to square the rapidly growing availability of low-cost DNA sequencers with the relative paucity of know-how required to make sense of the data. (Full story)

Also in Scientific American

What if black holes … weren’t holes after all?

Photo by Elena Giorgi.

The concept of a “black hole” — a celestial body so dense and massive that not even light can escape its gravitational field — dates back to the 18th century, with the theoretical work of Pierre-Simon Laplace and John Michell. But it wasn’t until the early 20th century that these mysterious dark objects were first described mathematically by German physicist Karl Schwarzschild.       

Emil Mottola, a physicist in T-Division at Los Alamos National Laboratory, laughs as he explains this bit of history behind black holes. “Would black holes have captured the popular imagination if they were still known as Schwarzschild’s solution?” The name “black hole” was coined by the American physicist John Wheeler in the 1960s, when these objects became the subject of serious study and first entered the popular vocabulary. (Full story)

Revamped thermonuclear missile warhead passes key milestone

USS Alabama, US Navy image.          

The Department of Energy said Thursday its scientists are taking the final steps to modernize the W88 thermonuclear warhead for Navy Trident II ballistic missiles.

After a four-year effort to alter the warhead with new arming, fuzing and firing components and add a new safety feature, a team from Los Alamos National Laboratory and Sandia National Laboratories has been authorized to begin production engineering, with the first unit scheduled for delivery in late 2019. (Full story)

Science versus the 'Horatio Alger myth'

Horatio Alger was a prolific 19th-century American writer, from Wikipedia.

In a new study published today in the journal PLOS ONE, Los Alamos National Laboratory scientists have taken a condensed matter physics concept usually applied to the way substances such as ice freeze, called "frustration," and applied it to a simple social network model of frustrated components. They show that inequality of wealth can emerge spontaneously and more equality can be gained by pure initiative.

It's a computer-modeling exploration of the 19th-century Horatio Alger theme, whereby a motivated young person overcomes poor beginnings and lives the "rags to riches" life thanks to strength of character. "Most theories of wealth inequality rely on social stratification due to income inequality and inheritance," said Cristiano Nisoli, of the Physics of Condensed Matter and Complex Systems group at Los Alamos and lead author of the study. (Full Story)

Confessions of a dark matter detective

The HAWC Observatory in Mexico. HAWC image.

As a national nuclear security facility, Los Alamos National Laboratory studies dark matter under its global security mission, which includes a focus on particle physics. Increasing our understanding of high-energy astrophysical phenomena helps us develop expertise and capabilities in particle detection, data acquisition  systems, and Big Data analysis. That work brought me to the HAWC team at Los Alamos, where I could pursue the deep mystery of dark matter. (Full Story)

Alien particles wreaking havoc on personal electronic devices

A section of the LANSCE accelerator, LANL image.

To determine the rate of SEUs in 16-nanometer chips, the Vanderbilt researchers took samples of the integrated circuits to the Irradiation of Chips and Electronics (ICE) House at Los Alamos National Laboratory. There they exposed them to a neutron beam and analyzed how many SEUs the chips experienced. Experts measure the failure rate of microelectronic circuits in a unit called a FIT, which stands for failure in time. One FIT is one failure per transistor in one billion hours of operation. (Full Story)

Los Alamos National Laboratory’s Math And Science Academy offers partnership opportunities

Monica Martinez-Archuleta of LANL's Math and Science Academy facilitates a teacher discussion. LANL photo.

The Math and Science Academy of Los Alamos National Laboratory is inviting elementary schools and institutions of higher education in northern New Mexico to partner with them in opportunities to influence educational outcomes, practice and policy.

These opportunities include developing and operating a partnership school and developing and participating in a math teacher leader network. Information sessions are scheduled for the previously announced opportunities to partner with the Laboratory's Math and Science Academy. (Full Story)

Physics greats of the 20th century mixed science and public service

Enrico Fermi, from Science News

When he arrived in the United States in 1939, Fermi almost immediately went to work studying nuclear fission, discovered only weeks earlier in Hitler’s Germany. Eventually Fermi took a major role in the Manhattan Project, leading the team that first demonstrated a controlled nuclear fission chain reaction.

Fermi, a foreigner, assumed a lead role because he was so widely recognized among the world’s physicists as infallible — hence his nickname “the pope.” In The Pope of Physics, Gino Segrè and Bettina Hoerlin chronicle Fermi’s life and science with insight and rich detail. (Full Story)

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Can artificial intelligence predict earthquakes?

Image from SciAm.

So far, no one has found a reliable way to forecast earthquakes, even though many scientists have tried. Some experts consider it a hopeless endeavor. “You’re viewed as a nutcase if you say you think you’re going to make progress on predicting earthquakes,” says Paul Johnson, a geophysicist at Los Alamos National Laboratory. But he is trying anyway, using a powerful tool he thinks could potentially solve this impossible puzzle: artificial intelligence. (Full story)

Also from CBS News

Confessions of a dark matter detective

The HAWC Observatory in Puebla, Mexico. INAOE photo.

As a national nuclear security facility, Los Alamos National Laboratory studies dark matter under its global security mission, which includes a focus on particle physics. Increasing our understanding of high-energy astrophysical phenomena helps us develop expertise and capabilities in particle detection, data acquisition systems, and Big Data analysis. That work brought me to the HAWC team at Los Alamos, where I could pursue the deep mystery of dark matter.

One of our searches uses this unusual telescope to look for gamma rays from relatively near dwarf galaxies. They’re unusually dim given the number of stars in them and are known dark matter hangouts. If we do see gamma rays coming from them, that would be a smoking gun for dark matter interactions. (Full story)

Science on the Hill: Protecting grid from cataclysmic solar storm

Large solar events can disrupt the electrical grid, LANL

illustration.

Mindful of the danger, the nation has developed a plan to support electric utilities in defending against severe geomagnetic storms. As part of that plan, space scientists at Los Alamos National Laboratory are researching the credible scenarios that could lead to large impacts. Los Alamos has been studying space weather for more than 50 years as part of its national security mission to monitor nuclear testing around the globe, and part of that work includes studying how the radiation-saturated environment of near space can affect technology and people. (Full story)

Nuclear reactors to power space exploration

Full-scale system being readied for engineering

demonstration. LANL photo.

Calls for space nuclear power are not new. In fact, numerous reactor concepts have been proposed in the past. Their development is often dampened by the perception that nuclear is too hard, takes too long and costs too much.

Los Alamos National Laboratory, in partnership with NASA Research Centers and other DOE National Labs, is developing and rapidly maturing a suite of very small fission power sources to meet power needs that range from hundreds of Watts-electric (We) to 100 kWe. These designs, commonly referred to as kiloPower reactors, are based on well-established physics that simultaneously simplifies reactor controls necessary to operate the plant and incorporates inherent safety features that guard against consequences of launch accidents and operational transients. (Full story)

Also from R&D this week:

Featured R&D 100 Award winner: Entropy Engine

A portion of the engine’s circuitry,

LANL image.

The Entropy Engine, developed by Los Alamos National Laboratory and Whitewood Encryption Systems, is a computer hardware system that uses quantum mechanics to generate an inexhaustible supply of pure random numbers at speeds of 200 megabits per second. The unpredictability and speed of such entropy provides the highest possible level of defense because the quantum processes used in this technology are irreducibly random. Modern cryptosystems rely on high-quality randomness, consuming surprisingly high quantities of random numbers to generate their keys and perform cryptographic operations. (Full story)

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Los Alamos research on cancer's origins key part of huge grant

Ludmil Alexandrov, LANL photo.

Los Alamos National Laboratory researcher Ludmil Alexandrov has been announced as a member of one of the first four global research teams funded under Cancer Research UK's "Grand Challenge," which seeks to revolutionize the understanding of cancer and its prevention, diagnosis and treatment.

The Grand Challenge aims to help overcome the biggest obstacles to cancer research in a global effort to beat the disease sooner. "This research could dramatically improve our understanding of what causes cancer and lead to better information for people on how to reduce their risk of developing cancer," said Alexandrov, who has used Los Alamos National Laboratory computational tools to aid in cancer research with the Wellcome Trust Sanger Institute partners for several years. (Full Story)

US government agency pops 16 years of solar weather data online

Solar flares influence space weather, from The Register.

National Oceanic and Atmospheric Administration has released 16 years' worth of GPS solar weather data gathered by the Los Alamos National Laboratory for all comers.

Los Alamos explains the release is designed to help researchers create and refine models for understanding and predicting solar weather, to better-protect “satellites, aircraft, communications networks, navigation systems, and [the] electric power grid”.

The sensors measure the energy and intensity of electrons and protons trapped in the Earth's magnetic field to form the Van Allen radiation belts. Each of the 23 sensors in the GPS constellation measures the largest radiation belt every six hours. (Full Story)

Keeping nuclear materials secure in an uncertain world

The Atoms for Peace tour, from the LANL Archives.

Keeping nuclear materials out of the hands of bad actors is critical to keeping the world safe from nuclear attack. To do that requires a team of people who are deployed to countries all over the world to inspect their nuclear-related operations.

These inspectors – from the International Atomic Energy Agency (IAEA) based in Austria – make sure the nuclear materials a country possesses are being used for peaceful purposes (such as for energy or medicine), and not diverted for use in weapons. But how do the inspectors know what to look for? They come to Los Alamos National Laboratory to learn how. (Full Story)

Creating family trees for disease-causing microbes could help control outbreaks

HIV infecting a human cell. NIH image.

A study examining the origins of AIDS recently made headlines for debunking the infamous myth that Gaetan Dugas, the French-Canadian flight attendant dubbed “Patient Zero,” brought the AIDS pandemic to North America.

The international team of researchers sequenced the genomes of HIV viruses that had been recovered from more than 2,000 blood samples taken in the late 1970s — before AIDS had been identified in the United States. By comparing those sequences to other strains of HIV in the Los Alamos National Laboratory HIV database, the scientists were able to build a family tree of the disease, also known as a phylogeny. (Full Story)

Two regional businesses receive Native American VAF awards

Phoebe Suina, owner of High Water Mark, LLC. LANL image.

Two Northern New Mexico Native American-owned and -operated businesses received $30,000 in grants through a Native American Venture Acceleration Fund created by Los Alamos National Security, LLC and the Regional Development Corporation.

“These investments create jobs for pueblo-owned businesses and help strengthen the area’s economy,” LANL Community Partnerships Director Kathy Keith said.

To date, more than $280,000 has been invested in the northern area regional economy through the Native American Venture Acceleration Fund. Funding comes from LANS, which manages Los Alamos National Laboratory. The RDC manages the Native American Venture Acceleration Fund. (Full Story)

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