Friday, April 26, 2019

This is the first-ever simulation of an entire gene

Largest simulation an entire gene of DNA, LANL image.

Given just how important genes are, it’s somewhat surprising that we have very little direct imagery of them functioning. The problem is that genes are so small and work so quickly that taking any photos or videos of them is nearly impossible. That’s why a group of researchers at Los Alamos National Laboratory turned to a computer simulation as the next best thing.

Using the Trinity supercomputer at Los Alamos, the researchers created a simulation of a single nanosecond of a gene. If one nanosecond sounds short to you—that’s about a billionth of a second—remember that the simulation contains over a billion atoms. For the researchers to simulate this gene, they have to not only simulate those individual atoms but also the electrical and chemical interactions between each pair of them. That’s an enormous amount of calculation. (Full story)

LANL researchers simulate billion-atom biomolecule  HPCwire

Detail of the billion atom DNA model, LANL image.

Researchers from Los Alamos National Laboratory, RIKEN Center for Computational Science in Japan, the New Mexico Consortium, and New York University have successfully created the first billion-atom simulation of an entire gene using a new approach they devised that reduces computational costs for such large simulations.

“It is important to understand DNA at this level of detail because we want to understand precisely how genes turn on and off,” said Karissa Sanbonmatsu, a structural biologist at Los Alamos and author of the paper. “Knowing how this happens could unlock the secrets to how many diseases occur.” It’s worth noting there is enough DNA in the human body to wrap around the earth 2.5 million times, which means it is compacted in a very precise and organized way. (Full story)

See the video

The hidden seismic symphony in earthquake signals

Many of the recent headline-grabbing developments in machine learning hinge on an approach called deep neural networks. Yet a simpler and more transparent form of machine learning called decision trees is unlocking impressive new scientific discoveries. In the case of our earthquake research at Los Alamos National Laboratory, a machine-learning process involving decision trees has revealed previously unsuspected physics principles that a deep neural network would have obscured and humans poring over data sets probably never would have noticed. To our surprise—and delight—this approach has led to a breakthrough in probing the mechanics of earthquakes, which will certainly advance our pursuit of the holy grail of geoscience: earthquake forecasting. (Full story)

Could machine learning be the key to earthquake prediction?

Earthquakes of magnitude 7.0 or higher between
1900 and 2013, USGS image.

Five years ago, Paul Johnson wouldn’t have thought predicting earthquakes would ever be possible. Now, he isn’t so certain. “I can’t say we will, but I’m much more hopeful we’re going to make a lot of progress within decades,” the Los Alamos National Laboratory seismologist says. “I’m more hopeful now than I’ve ever been.”

The main reason for that new hope is a technology Johnson started looking into about four years ago: machine learning. Many of the sounds and small movements along tectonic fault lines where earthquakes occur have long been thought to be meaningless. But machine learning—training computer algorithms to analyze large amounts of data to look for patterns or signals—suggests that some of the small seismic signals might matter after all. (Full story)

Seeing the quantum

Light generated by spontaneous parametric
down-conversion, from Aeon.

I spent a lot of time in the dark in graduate school. Not just because I was learning the field of quantum optics – where we usually deal with one particle of light or photon at a time – but because my research used my own eyes as a measurement tool. I was studying how humans perceive the smallest amounts of light, and I was the first test subject every time. Author Rebecca Holmes is a physicist and staff scientist at Los Alamos National Laboratory. (Full story)

SuperCam developed in Los Alamos to be used on rover in 2020 mission to Mars 
SuperCam undergoing final preperations.

On Monday, a camera developed here in New Mexico makes its first stop on its mission to Mars. Researchers at the Los Alamos National Laboratory say the SuperCam will be a key feature on the 2020 Mars rover. It will be attached to the rover currently at NASA's Jet Propulsion Laboratory in Pasadena, Calif. before heading to space next year.

"SuperCam is like a geological observatory on Mars," said Roger Wiens, principal investigator on the SuperCam at Los Alamos National Laboratory. The future of space exploration is in the works -- and it's happening right here in New Mexico with the development of the SuperCam. (Full story)

In the Lab: Building the next generation of experts

John Kramer, LANL photo.

In a woodsy part of the Los Alamos National Laboratory where elk linger outside his building, John Kramer is guiding the next generations of high explosives experts.

The lab’s esteemed explosives enclave has been Kramer’s turf since he was 19, mopping up water in big bays and growing accustomed to the shaking, rumbling world around him. Now, 37 years later, Kramer is a revered R&D engineer who holds two patents and keeps the lab’s detonator powder production plant humming to meet growing demands. (Full story)

Friday, April 19, 2019

Tiny earthquakes happen every few minutes in Southern California

The 1994 Northridge earthquake in Southern California, photo from NPR.

Detecting very small earthquakes is notoriously difficult. The rumbling of the ocean, a passing car or even the wind can feel a lot like a minor quake to the sensors that blanket seismically active parts of the U.S.

"They have a robust seismic network in Southern California," explains Daniel Trugman, a seismologist at Los Alamos National Laboratory and an author of the study. But while 180,000 might seem like a large number of quakes, there were many, many more hiding undetected in the data.

When Trugman and his collaborators re-analyzed the data using a powerful array of computer processors, they found evidence of 10 times as many earthquakes — 1.81 million temblors in a decade, or roughly one tiny earthquake every 3 minutes or so. (Full Story)

Scientists uncover California’s hidden earthquakes

The new study, published this week in Science, adds nearly two million earthquakes to the catalogue of total seismic events in Southern California over the past decade. Although the newly known quakes were imperceptible to humans, the findings help fill gaps in the earthquake record, shedding light on the geophysical processes that lead to the dreaded “Big Ones.”

Although Daniel Trugman at the Los Alamos National Lab notes that the hints the study gleaned on how foreshocks work are far from definitive, he is confident the new data set will allow scientists to better understand what precisely kicks an earthquake into high gear. And that may one day help scientists forecast earthquakes. “If we could really predict when the next big earthquake will occur, we’re in business—that’s the Holy Grail in seismic hazard analysis,” Trugman says. “I definitely wouldn't say we're there yet, but it's this type of work that's going to hopefully push us forward.” (Full Story)

Also from Scientific American this week:

How Long Do Neutrons Live?

Illustration from SciAm.

Physicist Zhaowen Tang of the Los Alamos lab described how researchers could put a particle detector inside a bottle neutron trap and count neutrons using both methods [beam and bottle]. His team has acquired funding to start building the device.

Another possibility is that the beam and bottle approaches have been measuring the neutron lifetime correctly, but that some unseen factor accounts for the discrepancy between the two. A leading idea is that neutrons might occasionally decay into not just protons but also dark matter, the mysterious unseen material that makes up much of the Universe’s matter. (Full Story)

Stopping an Earth-bound asteroid in its tracks

Kathy Plesko and a Bennu impact computer model, LANL image.

As a research scientist at Los Alamos National Laboratory, I study what happens to the atmosphere and crust of a planet when an asteroid or comet hits and possible ways to stop that from happening. I use the supercomputers at Los Alamos, some of the fastest in the world, to run high-fidelity simulations to accurately model the physics of an impact. These simulations are constantly updated with cutting-edge data from NASA missions and Earth-bound laboratory experiments.

Our first what-if case study focused on asteroid Bennu, the target of the NASA OSIRIS-REx mission. Bennu is about as wide as the Empire State Building is tall, and weighs as much as 800 aircraft carriers. (Full Story)

Unlocking secrets about the origin of the universe

Scientists and engineers from more than 70 organizations have come together to develop the tools to unravel the microscopic secrets hidden within quark-gluon plasma.

Los Alamos researchers are contributing to the project by designing an advanced tracking detector based on a new type of sensor system called MAPS, short for Monolithic Active Pixel Sensor. When the collider produces quark-gluon plasma in the sPHENIX experiment in several years, a new tracking detector will be there to capture the first measurements of the plasma’s internal structure using heavy quarks. (Full Story)

Microbes living in different parts of the human body can still swap genes

Microbes that live in the human gut. From Tech Times.

The research revealed that the most common transfer of genes happened between microbes that are most closely related to each other regardless of whether they are in the same sites or not.

"Some of these could be very old gene transfer events that happened before the microbes colonized the human body," explained Arshan Nasir, a distinguished fellow at the Los Alamos National Laboratory in New Mexico. "It also could be that some bacteria colonize different human body sites at different time points in an individual's lifespan. The others could be the result of the transfer of bacterial DNA from one site to another, perhaps through the blood." (Full Story)

Q&A: Creating ‘smart’ microbial bionsensors

The implications of this smart microbial cell concept are to offer an advanced platform for high throughput screening for enzyme discovery, design, and evolution. The approach, which comes from Los Alamos National Laboratory, can be translated to screening of metagenomic samples, rational enzyme design, or directed evolution of known enzymes. The technology is adaptable to a single enzyme, or a pathway, or global optimization of an industrial strain. To discover more, Digital Journal spoke with researcher Ramesh Jha. (Full Story)

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Friday, April 12, 2019

Predicting space weather could save satellites

A new space weather model under development at Los Alamos National Laboratory could help give a 24-hour warning before a storm of charged particles from the sun bombards crucial satellites, potentially knocking them out of service.

These "killer electrons" move more erratically during solar storms — a type of space weather where particles from the sun smack into Earth's magnetic field — so being able to predict that variability is key for spacecraft operators (Full story).

What's actually going on in that cryptic black hole photo?

Event Horizon Telescope, NSF Image.

From our far-off view of this great black hole, it might look like a bright, flat ring. But that's not exactly the case. We're largely seeing the "face" of the event horizon, like the face of a coin, as opposed to the side or edge, explained Chris Fryer, an astrophysicist at Los Alamos National Laboratory who had no role in the collaboration. 

So when the light (emitted in radio wave form) from the event horizon finally reached us, it had been distorted. Consequently the image, even with correction and sophisticated computer modeling, isn't perfect. But it's pretty darn good.  "I was surprised how good it looked knowing there were all these additional paths it had to travel," said Fryer (Full Story).

New open-source software predicts impacts of extreme events on grids

Carleton Coffrin, LANL photo.

A new, free, open-source software reliably predicts how damage from hurricanes, ice storms, earthquakes and other extreme events will restrict power delivery from utility grids. The Severe Contingency Solver for Electric Power Transmission is the only software available—commercially or open-source—that reliably supports analysis of extreme events that cause widespread damage.

“The software was designed specifically to address extreme events where damage to the power grid and the resulting outages are significant,” said Carleton Coffrin (Full story)

Also from R&D this week:

Scientific computing in the cloud gets down to Earth

In a groundbreaking effort, seismology researchers have conducted a continent-scale survey for seismic signatures of industrial activity in the Amazon Web Services commercial cloud (AWS), then rapidly downloaded the results without storing raw data or needing a local supercomputer.

"Using a traditional workflow, to download-store-calculate on a desktop, this work would've taken more than 40 days to do. Using the cloud service, it took just under 7 hours," said Jonathan MacCarthy of the Earth and Environmental Sciences division at Los Alamos National Laboratory. "To our knowledge, this is the first application of streaming cloud-based research in seismology," (Full story).

Also in PhysOrg

Thom Mason takes the helm at Los Alamos

Thom Mason, LANL photo.

Perhaps it’s no surprise that Thom Mason, who was director at Oak Ridge National Laboratory for 10 years, is now the director at Los Alamos. “I grew up in a science family,” he explains. “My dad worked at a Canadian national lab, so it was sort of the family business, and it never really occurred to me to do anything else.”

He pauses, reconsidering. “I did think about doing an English degree,” he says. “And I decided that if I did physics, I could still read books. But if I took English, I probably couldn’t have physics as a hobby," (full story).