Damien Anderson receives the Robertson Medal from Professor Dame Anne Glover, Chair of the Carnegie Trust for the Universities of Scotland.

A computer science researcher at the University of Strathclyde has won a prestigious Scotland-wide award from the Carnegie Trust for the Universities of Scotland.

Damien Anderson has been awarded the Robertson Medal, presented annually by the Trust to the most outstanding student on its PhD scholarship programme.

Damien was chosen from the 14 students awarded scholarships from an original list of 58 applicants. His research focuses on artificial intelligence (AI) programming, designed to respond to unpredictable situations.

He is to receive the medal from Professor Dame Anne Glover, former Chief Scientific Adviser to the Scottish Government and the European Commission, at a ceremony at Strathclyde today (Friday 5 February).

Damien, who is from Coatbridge, North Lanarkshire, said: “It’s great to be receiving this award. I’m enjoying everything about my PhD - the people I’m working with are fantastic and it’s a good working environment.

“My research looks into ways to enable computers to figure out something on their own, whatever’s been programmed into them. For example, in computer games, AI could be used for the computer to work out why its performance has gone up or down and apply this to its strategies, so that it can solve a problem without having faced that type of problem before.”

Professor Andy Walker, Chief Executive of the Carnegie Trust, said: “Our PhD Scholarship scheme is highly competitive with only the very best graduates being put forward by the Scottish universities for consideration.  It is to Damien’s great credit that, not only has he been awarded one of our scholarships, but that the selection panel recognised him as this year’s best student.  I am confident that his research project will be very fruitful and wish him well with his studies.”

Damien received a degree in Software Engineering from Strathclyde in 2015 before beginning his PhD. His Robertson Medal win follows his success in the 2015 Young Software Engineer of the Year Awards, in which he was awarded third prize.

During his degree, Damien had a 12-month internship at CERN, the European Organisation for Nuclear Research, in Switzerland. He wrote software protection systems for the particle accelerators at CERN, including the Large Hadron Collider, and the quality of his work led to his internship being extended by two months.

The Robertson Medal was won in 2013 by Strathclyde Engineering students and identical twins Carol and Claire Forsyth. They had previously gained Masters degrees with distinction in Chemical Engineering – achieving the highest and second highest grades in the history of Strathclyde’s department of Chemical and Process Engineering.

The medal was introduced in 2003 to mark the contribution of the retiring Chairman of the Carnegie Trust, Sir Lewis Robertson, who served the Trust for more than 40 years. 

Database searches for DNA sequences that can take biologists and medical researchers days can now be completed in a matter of minutes, thanks to a new search method developed by computer scientists at Carnegie Mellon University.

The method developed by Carl Kingsford, associate professor of computational biology, and Brad Solomon, a Ph.D. student in the Computational Biology Department, is designed for searching so-called “short reads” – DNA and RNA sequences generated by high-throughput sequencing techniques. It relies on a new indexing data structure, called Sequence Bloom Trees, or SBTs, that the researchers describe in a report published online today by the journal Nature Biotechnology.

The National Institutes of Health maintains a humongous database, called the Sequence Read Archive, which contains about three petabases, or sequences totaling three quadrillion base-pairs. The information is useful to a wide swath of researchers, from those asking questions about basic biological processes to those studying potential cancer cures.

“The database contains untold numbers of as-yet undiscovered insights and is heavily used,” Kingsford said. “Its main problem is that it’s very difficult to search.”

Thousands of hard drives would be needed to store these sequences. Searching through the short reads, which are typically 50 to 200 base-pairs each, to see which ones could be assembled to form a target gene of perhaps 10,000 base-pairs, is cumbersome and can take days in some cases, he noted.

Just as an index can speed searches through a book or catalog, the SBT-based index developed by Kingsford and Solomon can greatly speedup searches of this bioinformatics database. They actually represent each short read as a set of fixed-length subsequences, employing data structures called Bloom filters that can efficiently store information in a small space and can test whether an element is part of a set.

At the first level of inquiry, the SBTs can tell whether a target DNA sequence is contained in the database at all. If it is, the search proceeds to the next level, where the SBTs indicate whether the sequence is in one half or the other of the database. At each level, the inquiry branches one way or the other until the desired experiments are identified.

Kingsford and Solomon tested their technique using a database of 2,652 human blood, breast and brain experiments, each of which often contain over a billion base-pairs of RNA sequences. They found that most searches of that database could be completed in an average of 20 minutes. They estimated the comparable search time using existing techniques, known as SRA-BLAST and STAR, would take 2.2 days and 921 days, respectively.

Further speedups are possible because batches of over 200,000 queries can be performed simultaneously, they noted.

The SBT method is available as open source code and can be downloaded.

CAPTION NASA laser expert Mike Krainak and his team plan to replace portions of this fiber-optic receiver with an integrated-photonic circuit, whose size will be similar to the chip he is holding. The team then plans to test the advanced modem on the International Space Station. CREDIT Credits: NASA/W. Hrybyk

A NASA team has been tapped to build a new type of communications modem that will employ an emerging, potentially revolutionary technology that could transform everything from telecommunications, medical imaging, advanced manufacturing to national defense.

The space agency's first-ever integrated-photonics modem will be tested aboard the International Space Station beginning in 2020 as part of NASA's multi-year Laser Communications Relay Demonstration, or LCRD. The cell phone-sized device incorporates optics-based functions, such as lasers, switches, and wires, onto a microchip -- much like an integrated circuit found in all electronics hardware.

Once aboard the space station, the so-called Integrated LCRD LEO (Low-Earth Orbit) User Modem and Amplifier (ILLUMA) will serve as a low-Earth orbit terminal for NASA's LCRD, demonstrating yet another capability for high-speed, laser-based communications.

Data Rates Demand New Technology

Since its inception in 1958, NASA has relied exclusively on radio frequency (RF)-based communications. Today, with missions demanding higher data rates than ever before, the need for LCRD has become more critical, said Don Cornwell, director of NASA's Advanced Communication and Navigation Division within the space Communications and Navigation Program, which is funding the modem's development.

LCRD promises to transform the way NASA sends and receives data, video and other information. It will use lasers to encode and transmit data at rates 10 to 100 times faster than today's communications equipment, requiring significantly less mass and power. Such a leap in technology could deliver video and high-resolution measurements from spacecraft over planets across the solar system -- permitting researchers to make detailed studies of conditions on other worlds, much as scientists today track hurricanes and other climate and environmental changes here on Earth.

The project, which is expected to begin operations in 2019, isn't NASA's first foray into laser communications. A payload aboard the Lunar Atmosphere and Dust Environment Explorer (LADEE) demonstrated record-breaking download and upload speeds to and from lunar orbit at 622 megabits per second (Mbps) and 20 Mbps, respectively, in 2013.

LCRD, however, is designed to be an operational system after an initial two-year demonstration period. It involves a hosted payload and two specially equipped ground stations. The mission will dedicate the first two years to demonstrating a fully operational system, from geosynchronous orbit to ground stations. Once NASA demonstrates that capability, it plans to use ILLUMA to test communications between geosynchronous and low-Earth-orbit spacecraft, Cornwell said.

An Exceptional Terminal

ILLUMA incorporates an emerging technology -- integrated photonics -- that is expected to transform any technology that employs light. This includes everything from Internet communications over fiber optic cable to spectrometers, chemical detectors, and surveillance systems, to name just a few.

"Integrated photonics are like an integrated circuit, except they use light rather than electrons to perform a wide variety of optical functions," Cornwell said. Recent developments in nanostructures, meta-materials, and silicon technologies have expanded the range of applications for these highly integrated optical chips. Furthermore, they could be lithographically printed in mass -- just like electronic circuitry today -- further driving down the costs of photonic devices.

"This technology will enable all types of NASA missions, not just optical communications on LCRD," Cornwell added.

"We've pushed this for a long time," said Mike Krainak, who is leading the modem's development at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "The technology will simplify optical system design. It will reduce the size and power consumption of optical devices, and improve reliability, all while enabling new functions from a lower-cost system. It is clear that our strategy to leverage integrated photonic circuitry will lead to a revolution in Earth and planetary-space communications as well as in science instruments."

In addition to leading ILLUMA's development, Krainak serves as NASA's representative on the country's first consortium to advance integrated photonics. Funded by the U.S. Department of Defense, the non-profit American Institute for Manufacturing Integrated Photonics, with headquarters in Rochester, New York, brings together the nation's leading technological talent to establish global leadership in integrated photonics. Its primary goal is developing low-cost, high-volume, manufacturing methods to merge electronic integrated circuits with integrated photonic devices.

NASA's Space Technology Mission Directorate (STMD) also appointed Krainak as the integrated photonics lead for its Space Technology Research Grants Program, which supports early-stage innovations. The program recently announced a number of research awards under this technology area (see related story).

First Step in Demonstrating Photonics

Under the NASA project, Krainak and his team will reduce the size of the terminal, now about the size of two toaster ovens -- a challenge made easier because all light-related functions will be squeezed onto a microchip. Although the modem is expected to use some optic fiber, ILLUMA is the first step in building and demonstrating an integrated photonics circuit that ultimately will embed these functions onto a chip, he said.

ILLUMA will flight-qualify the technology, as well as demonstrate a key capability for future spacecraft. In addition to communicating to ground stations, future satellites will require the ability to communicate with one another, he said.

"What we want to do is provide a faster exchange of data to the scientific community. Modems have to be inexpensive. They have to be small. We also have to keep their weight down," Krainak said. The goal is to develop and demonstrate the technology and then make it available to industry and other government agencies, creating an economy of scale that will further drive down costs. "This is the pay off," he said.

Although integrated photonics promises to revolutionize space-based science and inter-planetary communications, its impact on terrestrial uses also is equally profound, Krainak added. One such use is with data centers. These costly, very large facilities house servers that are connected by fiber optic cable to store, manage and distribute data.

Integrated photonics promises to dramatically reduce the need for and size of these behemoths -- particularly since the optic hardware needed to operate these facilities will be printed onto a chip, much like electronic circuitry today. In addition to driving down costs, the technology promises faster computing power.

"Google, Facebook, they're all starting to look at this technology," Krainak said. "As integrated photonics progresses to be more cost effective than fiber optics, it will be used," Krainak said. "Everything is headed this way."

For more Goddard technology news, go to http://gsfctechnology.gsfc.nasa.gov/newsletter/Current.pdf

Office of Naval Research-sponsored researchers at the University of California Los Angeles (UCLA) have designed the first detailed supercomputer simulation model of how an injured human leg bleeds.

To make training for combat medics more realistic, researchers at the University of California Los Angeles (UCLA) have designed the first detailed supercomputer simulation model of an injured human leg--complete with spurting blood.

Sponsored by the Office of Naval Research (ONR), the simulator was created at UCLA's Center for Advanced Surgical and Interventional Technology (CASIT). The research team included surgeons, fluid dynamicists, biomedical engineers, mathematicians and psychologists.

"This model truly is a breakthrough in how combat medics can be taught to control hemorrhaging," said Dr. Ray Perez, a program officer in ONR's Warfighter Performance Department. "Leg injuries are particularly difficult to treat since different points of entry cause different levels of blood loss. This new simulator model can better prepare medics with various ways to staunch bleeding."

The goal of the simulator is to provide future medics with a virtual patient that reacts in realistic fashion to leg wounds. Although previous work has measured blood fluid dynamics and the impact of gunshot and shrapnel wounds to different parts of the body, this is the first such modeling for legs.

Legs, which are rich in blood vessels, are particularly vulnerable places to be injured. Bullets or shrapnel can slice through veins and arteries, resulting in lost limbs or even death. Another threat is damage caused by improvised explosive devices, roadside bombs or mines.

To create the simulator model, researchers combined detailed knowledge of anatomy with real-life CAT scans and MRIs to map out layers of a human leg--the bone, the soft tissue containing muscle and blood vessels and the skin surrounding everything. Then the design team applied physics and mathematical equations, fluid dynamics, and pre-determined rates of blood flow from specific veins and arteries to simulate blood loss for wounds of varying sizes and severity.

"This simulator is unique because it uses mathematics and fluid physics to replicate blood flow," said Dr. Erik Dutson, a general surgeon and CASIT's executive medical director, who oversaw the simulator's design. "Other simulators provide a less detailed, more cartoonish picture of blood flow. We worked with experts in fluid dynamics to create an accurate, realistic vision of the speed and distribution of blood loss."

Dutson envisions the simulator being used in real-time training exercises by combat medics. It would enable them to test different methods of staunching blood flow to perform more effectively in actual battlefield situations. Even better, Dutson said, medics could change the size and shape of virtual wounds--as well as the speed and amount of blood flow--and complete exercises multiple times to improve proficiency.

The CASIT team also designed the simulator to reflect the latest breakthroughs in the science of learning--targeting how the human brain best processes information, adapting to an individual's learning proficiencies, and accelerating learning time and retention during training.

While Dutson is pleased with the simulator's design, his team already is planning improvements--chiefly, enhancing the liquid model representing blood.

"As it stands, the liquid model is similar to water in its composition," he said. "We eventually want to have it mirror more closely the physiological characteristics of blood, which is a living tissue. These include red and white blood cells, plasma, and platelets and clotting properties. We feel we'll get to that level of accuracy soon."

Perez said talks are underway with the Navy and Marine Corps to test the simulator on a trial basis among combat medic recruits.

"Dr. Dutson and his team have created an ambitious suite of technologies serving a major need for the military," said Perez. "We look forward to helping him get this in the hands of combat medics."

CAPTION (Illustration) This comparison shows the relative complexity of the solar magnetic field between January 2011 (left) and July 2014. In January 2011, three years after solar minimum, the field is still relatively simple, with open field lines concentrated near the poles. At solar maximum, in July 2014, the structure is much more complex, with closed and open field lines poking out all over - ideal conditions for solar explosions.

The surface of the sun writhes and dances. Far from the still, whitish-yellow disk it appears to be from the ground, the sun sports twisting, towering loops and swirling cyclones that reach into the solar upper atmosphere, the million-degree corona - but these cannot be seen in visible light. Then, in the 1950s, we got our first glimpse of this balletic solar material, which emits light only in wavelengths invisible to our eyes.

Once this dynamic system was spotted, the next step was to understand what caused it. For this, scientists have turned to a combination of real time observations and supercomputer simulations to best analyze how material courses through the corona. We know that the answers lie in the fact that the sun is a giant magnetic star, made of material that moves in concert with the laws of electromagnetism. 

"We're not sure exactly where in the sun the magnetic field is created," said Dean Pesnell, a space scientist at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "It could be close to the solar surface or deep inside the sun - or over a wide range of depths."

Getting a handle on what drives that magnetic system is crucial for understanding the nature of space throughout the solar system: The sun's magnetic field is responsible for everything from the solar explosions that cause space weather on Earth - such as auroras - to the interplanetary magnetic field and radiation through which our spacecraft journeying around the solar system must travel.

So how do we even see these invisible fields? First, we observe the material on the sun. The sun is made of plasma, a gas-like state of matter in which electrons and ions have separated, creating a super-hot mix of charged particles. When charged particles move, they naturally create magnetic fields, which in turn have an additional effect on how the particles move. The plasma in the sun, therefore, sets up a complicated system of cause and effect in which plasma flows inside the sun - churned up by the enormous heat produced by nuclear fusion at the center of the sun - create the sun's magnetic fields. This system is known as the solar dynamo.

We can observe the shape of the magnetic fields above the sun's surface because they guide the motion of that plasma - the loops and towers of material in the corona glow brightly in EUV images. Additionally, the footpoints on the sun's surface, or photosphere, of these magnetic loops can be more precisely measured using an instrument called a magnetograph, which measures the strength and direction of magnetic fields.

Next, scientists turn to models. They combine their observations - measurements of the magnetic field strength and direction on the solar surface - with an understanding of how solar material moves and magnetism to fill in the gaps. Simulations such as the Potential Field Source Surface, or PFSS, model - shown in the accompanying video - can help illustrate exactly how magnetic fields undulate around the sun. Models like PFSS can give us a good idea of what the solar magnetic field looks like in the sun's corona and even on the sun's far side.

A complete understanding of the sun's magnetic field - including knowing exactly how it's generated and its structure deep inside the sun - is not yet mapped out, but scientists do know quite a bit. For one thing, the solar magnetic system is known to drive the approximately-11-year activity cycle on the sun. With every eruption, the sun's magnetic field smooths out slightly until it reaches its simplest state. At that point the sun experiences what's known as solar minimum, when solar explosions are least frequent. From that point, the sun's magnetic field grows more complicated over time until it peaks at solar maximum, some 11 years after the previous solar maximum.

"At solar maximum, the magnetic field has a very complicated shape with lots of small structures throughout - these are the active regions we see," said Pesnell. "At solar minimum, the field is weaker and concentrated at the poles. It's a very smooth structure that doesn't form sunspots."

Take a look at the side-by-side comparison to see how the magnetic fields change, grew and subsided from January 2011 to July 2014. You can see that the magnetic field is much more concentrated near the poles in 2011, three years after solar minimum. By 2014, the magnetic field has become more tangled and disorderly, making conditions ripe for solar events like flares and coronal mass ejections.

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