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Human chromosomes. Courtesy of Jane Ades, NHGRI

Speeding Up Genome Assembly, from Months to Minutes

June 30, 2015 12:23 pm | by Lawrence Berkeley National Laboratory Computing Sciences | News | Comments

By applying some novel algorithms, computational techniques and the innovative programming language Unified Parallel C (UPC) to the cutting-edge de novo genome assembly tool Meraculous, a team of scientists simplified and sped up genome assembly, reducing a months-long process to mere minutes. This was primarily achieved by “parallelizing” the code to harness the processing power of supercomputers.

Pentagon, Lockheed Martin Researchers create Math and Programming Learning Platform

June 30, 2015 8:17 am | by Aaron Dubrow, NSF | News | Comments

The Pentagon's Office of Force Readiness and Training recently teamed with Lockheed Martin and...

Sandia's Z Machine helps solve Saturn's 2-billion-year Age Gap

June 29, 2015 1:50 pm | by Sandia National Labs | News | Comments

Planets tend to cool as they get older, but Saturn is hotter than astrophysicists say it should...

NIST Revises Computer Security Publication on Random Number Generation

June 26, 2015 3:14 pm | by NIST | News | Comments

In response to public concerns about cryptographic security, the National Institute of Standards...

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Are you a Tau-ist? Pi Day is Under Attack

Stories You Shouldn’t Miss — June 19-25

June 26, 2015 12:41 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | News | Comments

As we entered our first week of summer, the week’s biggest hits included a strong bent toward several “lighter” mathematical topics: learning how math drives Formula 1 and launches Angry Birds, inspiring young minds at MoMATH, and Pi Day under attack. You also won’t want to miss molecules exhibiting strange, exotic states, hot lava flows on Venus, and some of the coolest experimental technology showcased at this year’s Paris Air Show.

Tau proponents say that, for many mathematical problems, tau makes more sense and makes calculations easier.

Are you a Tau-ist? Pi Day is Under Attack

June 23, 2015 4:51 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments

As June 28, 2015, approaches, the Internet is once again anticipating controversy as the mathematical constant pi comes under threat from a group of detractors who will be marking "Tau Day." Tau Day’s revelers are campaigning for a constant twice as large as pi (about 6.28) to take its place, hence the June 28 celebration. Tau proponents say that, for many mathematical problems, tau makes more sense and makes calculations easier.

This graphic representation shows how three active sources cloak an incoming circular wave (like ripples from a stone dropped in water), creating a quiet zone for the object to be cloaked. This is just for one frequency. Courtesy of Fernando Guevara Vasqu

Mathematicians Play Key Role in Developing Multi-Frequency Cloaking

June 23, 2015 9:47 am | by NSF | News | Comments

The idea of cloaking and rendering something invisible hit the small screen in 1966 when a Romulan Bird of Prey made an unseen, surprise attack on the Starship Enterprise. Not only did it make for a good storyline, it inspired budding scientists, offering a window of technology's potential. Today, pop culture has embraced the idea of hiding behind force fields, and mathematicians are looking at transforming science fiction into science.

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Researchers used high-resolution microscopy to examine owl feathers in fine detail. They observed that the flight feathers on an owl’s wing have a downy covering, which resembles a forest canopy when viewed from above. In addition to this fluffy canopy, o

How Owls could help make Computer Fans Quieter

June 20, 2015 9:46 am | by University of Cambridge | News | Comments

A newly-designed material, which mimics the wing structure of owls, could help make wind turbines, computer fans and even planes much quieter. Early wind tunnel tests of the coating have shown a substantial reduction in noise without any noticeable effect on aerodynamics.

Tapping at mobile phone games, waking up to sunlight on a pleasant morning or watching a Formula One race — such experiences are at the heart of modern life, and mathematics is working behind the scenes on all of them. Math is also used in many discipline

Free Online Course to teach how Math drives Formula One and launches Angry Birds

June 20, 2015 8:54 am | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments

Tapping at mobile phone games, waking up to sunlight on a pleasant morning or watching a Formula One race — such experiences are at the heart of modern life, and mathematics is working behind the scenes on all of them. Math is also used in many disciplines — from economics to engineering, biology to geography. But many of us struggle with math, and find formulas and theories difficult to grasp. A free online course could help.

Applied Mathematician Theorizes what Happened to Malaysia Airlines Flight 370

Stories You Shouldn’t Miss — June 12-18

June 19, 2015 2:35 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | News | Comments

The top most-visited stories of the past week included an amazing image of Jupiter’s second largest moon, solving billions of equations in just minutes, relief and delight as Philae woke up, Einstein saving the Quantum Cat, a fundamental change in wireless communications, a 40-year-old algorithm problem put to rest, news that a black hole’s surface is no deadly firewall, and an applied mathematician’s theory on MA flight 370.

Harmony of the Spheres: More than 30 exhibits, created exclusively by MoMath, are designed to reveal the wonders of math in an “interactive, hands-on, engaging and fun” way.

MoMATH: Hands-on Mathematics Inspiring Young Minds

June 19, 2015 11:17 am | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments

My first impression upon entering the National Museum of Mathematics could be described as complete mathematical mayhem. Pre-teenagers were swarming dozens of exhibits in what seemed more like a huge play area than a museum dedicated to the study of an abstract science of numbers, quantity and shapes. However, as I waded in and began to understand specific exhibits, it quickly became obvious that this was a special place.

Short inverted repeat sequences of DNA nucleotides are enriched at human cancer breakpoints. Courtesy of Karen Vasquez, UT Austin

Researchers Surprisingly Link DNA Crosses to Cancer using Stampede and Lonestar

June 18, 2015 2:43 pm | by Jorge Salazar, Texas Advanced Computing Center | News | Comments

Supercomputers have helped scientists find a surprising link between cross-shaped (or cruciform) pieces of DNA and human cancer. The study found that small DNA cruciforms are mutagenic, altering DNA in a way that can increase risk of cancer in yeast, monkeys and in humans. Researchers found short inverted repeats of 30 base pairs and under in a reference database of mutations in human cancer that are somatic, meaning not inherited.

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Network scientists have developed a new computational method that can leverage any body of knowledge to aid in the complex human task of fact-checking. In multiple experiments, the automated system consistently matched the assessment of human fact-checker

Computational Algorithm Checks the Facts

June 17, 2015 3:59 pm | by Indiana University | News | Comments

Network scientists have developed a new computational method that can leverage any body of knowledge to aid in the complex human task of fact-checking. In multiple experiments, the automated system consistently matched the assessment of human fact-checkers in terms of their certitude about the accuracy of these statements.

For several years now, researchers have been investigating techniques for amplifying movements captured by video but indiscernible to the human eye. Earlier this month, they presented a new version of the algorithm that can amplify small motions even when

Video-Processing Algorithm Amplifies Small Motions in Large Motions

June 17, 2015 1:49 pm | by Larry Hardesty, MIT | News | Comments

For several years now, researchers have been investigating techniques for amplifying movements captured by video but indiscernible to the human eye. Earlier this month, they presented a new version of the algorithm that can amplify small motions even when they’re contained within objects executing large motions.

Complex models that let you look at the combined action of many different variants have, until now, involved so much computation that it would take a year to run a single complex query.

Complex, Large-scale Genome Analysis made Easier

June 16, 2015 12:45 pm | by European Molecular Biology Laboratory | News | Comments

Researchers have developed a new approach to studying the effect of multiple genetic variations on different traits. The new algorithm makes it possible to perform genetic analysis of up to 500,000 individuals — and many traits at the same time. Complex models that let you look at the combined action of many different variants have, until now, involved so much computation that it would take a year to run a single complex query.

The plight of Malaysia Airlines flight 370 (MH370) is one of the biggest mysteries in aviation history, but an interdisciplinary research team led by a Texas A&M University at Qatar math professor has theorized the ill-fated plane plunged vertically into

Applied Mathematician Theorizes what Happened to Malaysia Airlines Flight 370

June 15, 2015 4:35 pm | by Texas A&M at Qatar | News | Comments

The plight of Malaysia Airlines flight 370 (MH370) is one of the biggest mysteries in aviation history, but an interdisciplinary research team led by a Texas A&M University at Qatar math professor has theorized the ill-fated plane plunged vertically into the southern Indian Ocean in March 2014.

The impact of individual mobility on disease dynamics is investigated by the authors by studying the spread of disease when the population is distributed over two geographically discrete locations, connected by travel. The model uses a three-dimensional s

Modeling Effects of Individual Movement on Infectious Disease Spread

June 12, 2015 5:01 pm | by SIAM | News | Comments

“The impact of human mobility on disease dynamics has been the focus of mathematical epidemiology for many years, especially since the 2002-03 SARS outbreak, which showed that an infectious agent can spread across the globe very rapidly via transportation networks,” says mathematician Gergely Röst. Röst is co-author of a paper that presents a mathematical model to study the effects of individual movement on infectious disease spread.

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Stanford Professor Charbel Farhat and his team accomplished a rare feat in computer engineering through a partnership with the U.S. Army Research Laboratory. Courtesy of Norbert von der Groeben

Now, Billions of Questions can be answered in about 3 Minutes

June 12, 2015 4:16 pm | by James Urton, | News | Comments

Stanford Professor Charbel Farhat and his research team at the Army High Performance Computing Research Center used a new, high-end, massively parallel computer to demonstrate the power of algorithms that instruct processors to work together to solve challenging problems. They directed 22,000 processors to solve billions of mathematical equations in just a few minutes, a rare feat in computer engineering.

The basic algorithm for determining how much two sequences of symbols have in common — the “edit distance” between them — is now more than 40 years old. And for more than 40 years, computer science researchers have been trying to improve upon it, without

Longstanding Problem Put to Rest: 40-year-old Algorithm can’t be solved More Efficiently

June 11, 2015 4:33 pm | by Larry Hardesty, MIT | News | Comments

Comparing the genomes of different species — or different members of the same species — is the basis of a great deal of modern biology. DNA sequences that are conserved across species are likely to be functionally important, while variations between members of the same species can indicate different susceptibilities to disease. The basic algorithm for determining how much two sequences of symbols have in common is more than 40 years old.

A still from a video of MIT's first DARPA Robotics Challenge run, where they scored seven points. Courtesy of the MITDRC team

Competition Generates Cutting-edge Robotics Control Algorithms

June 11, 2015 12:16 pm | by Larry Hardesty, MIT | News | Comments

Last weekend was the final round of DARPA's contest to design control systems for a humanoid robot that could climb a ladder, remove debris, drive a utility vehicle and perform several other tasks related to a hypothetical disaster. When a bipedal robot takes a step, its foot strikes the ground at a number of different points. MIT researchers found a way to generalize the approach to more complex motions in 3-D.

The Wilkinson Prize was established to honor the outstanding contributions of Dr. James Hardy Wilkinson to the field of numerical software. It is awarded every four years to the entry that best addresses all phases of the preparation of numerical software

Partial Differential Equations ‘Dolfin-adjoint’ wins 2015 Wilkinson Prize for Numerical Software

June 11, 2015 11:06 am | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | News | Comments

NAG, Argonne and the National Physical Laboratory have announced awarding of the 2015 Wilkinson Prize for “dolfin-adjoint,” which automatically derives and solves adjoint and tangent linear equations from high-level mathematical specifications of finite element discretizations of partial differential equations. The prize is awarded every four years to the entry that best addresses all phases of the preparation of numerical software.

researchers describe how the learnings from both insects and humans can be applied in a model virtual reality simulation, enabling an artificial intelligence system to 'pursue' an object.

Insect Vision benefits Bio-inspired, Autonomous Robot Eyes

June 11, 2015 8:43 am | by University of Adelaide | News | Comments

The way insects see and track their prey is being applied to a new robot in the hopes of improving robot visual systems. The project — which crosses the boundaries of neuroscience, mechanical engineering and computer science — builds on years of research into insect vision. The learnings from both insects and humans can be applied in a model virtual reality simulation, enabling an artificial intelligence system to 'pursue' an object.

 When he wasn't busy scribbling out the theory of relativity, Albert Einstein seems to have spent a fair amount of time writing letters involving topics such as God, his son's geometry studies, even a little toy steam engine an uncle gave him when he was

27 Einstein Personal Letters on Auction Block

June 11, 2015 8:32 am | by John Rogers, Associated Press | News | Comments

When he wasn't busy scribbling out the theory of relativity, Albert Einstein seems to have spent a fair amount of time writing letters involving topics such as God, his son's geometry studies, even a little toy steam engine an uncle gave him when he was a boy. The Einstein Letters, which include more than two dozen missives, went up for sale at a California-based auction house. Some were in English and others in German.

Axel Tidemann, [self.] and Øyvind Brandtsegg. Courtesy of Ole Morten Melgård, NTNU

Robot learns Everything from Scratch

June 10, 2015 12:10 pm | by Steinar Brandslet, Norwegian University of Science and Technology | News | Comments

Imagine that everything in your mind had been erased, and you had to learn everything all over again. What would that process be like? Two researchers at NTNU have made a robot that learns like a young child. At least, that’s the idea. The machine starts with nothing — it has to learn everything from scratch. The machine is called [self.]. It analyzes sound through a system based on the human ear, and learns to recognize images.

So many choices: Choosing from a universe of possible actions is a daunting task for a robot. Humans do it effortlessly. Researchers have found that video games — particularly Minecraft — can help robots learn how to tell which objects and actions might b

Using Minecraft to Unboggle the Robot Mind

June 9, 2015 9:13 am | by Brown University | News | Comments

A human can make intuitive choices about what actions to take in order to achieve a goal. Robots have a far more difficult time choosing from of a universe of possible actions. Researchers at Brown University are developing a new algorithm that can learn that skill from a video game environment. They are developing the algorithm to help robots better plan their actions in complex environments.

Geoffrey Noer is Senior Director of Product Marketing at Panasas.

RAID: Alive or Dead?

June 8, 2015 8:12 am | by Geoffrey Noer, Panasas | Blogs | Comments

Is RAID dead or alive? Are erasure codes replacing RAID for data protection? We present these questions, because some storage vendors promote RAID, while others promote erasure codes. Looking at how vendors are marketing data protection in their products, it almost appears that there is a battle between RAID and erasure code technology and that everyone will agree on a winner at some point.

Decentralized partially observable Markov decision processes are a way to model autonomous robots’ behavior in circumstances where neither their communication with each other nor their judgments about the outside world are perfect. The problem with Dec-PO

Autonomous Multirobot Collaboration Algorithm makes Complex Models Practical

June 3, 2015 9:58 am | by Larry Hardesty, MIT | News | Comments

Decentralized partially observable Markov decision processes are a way to model autonomous robots’ behavior in circumstances where neither their communication with each other nor their judgments about the outside world are perfect. The problem is that they’re as complicated as their name. They provide the most rigorous mathematical models of multiagent systems — not just robots, but any autonomous networked devices — under uncertainty.

Physicists Andrew Truscott and Roman Khakimov have conducted John Wheeler's delayed-choice thought experiment, which involves a moving object that is given the choice to act like a particle or a wave. Wheeler's experiment then asks — at which point does t

Experiment proves Reality does not exist until it is Measured

June 2, 2015 2:40 pm | by Australian National University | News | Comments

The bizarre nature of reality as laid out by quantum theory has survived another test, with scientists performing a famous experiment and proving that reality does not exist until it is measured. Physicists have conducted John Wheeler's delayed-choice thought experiment, which involves a moving object given the choice to act like a particle or a wave. Wheeler's experiment then asks — at which point does the object decide?

In superdense teleportation of quantum information, Alice (near) selects a particular set of states to send to Bob (far), using the hyperentangled pair of photons they share. The possible states Alice may send are represented as the points on a donut shap

Donuts, Math and Superdense Teleportation of Quantum Information

June 2, 2015 2:34 pm | by Siv K. Schwink, Department of Physics | News | Comments

Putting a hole in the center of a donut allows the pastry to cook evenly, inside and out. As it turns out, the hole in the center of the donut also holds answers for a type of more efficient and reliable quantum information teleportation, a critical goal for quantum information science. Taking advantage of the mathematical properties intrinsic to the torus, researchers have made great strides by realizing superdense teleportation.

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