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Like a Chinese Finger Puzzle Trap, the bond between scaffolding proteins in the cellulosome strengthens when force is exerted on it and becomes one of the strongest found in living systems.

Solving Puzzle-Like Bond for Biofuels: First Look at One of Nature's Strongest Biomolecular Interactions

March 17, 2015 3:02 pm | by Texas Advanced Computing Center | News | Comments

One of life's strongest bonds has been discovered by a science team researching biofuels with the help of supercomputers. Their find could boost efforts to develop catalysts for biofuel production from non-food waste plants. Renowned computational biologist Klaus Schulten of the University of Illinois at Urbana-Champaign led the analysis and modeling of the bond, which behaves like a Chinese Finger Trap puzzle.

Life 'Not as We Know It' Possible on Saturn's Moon Titan

March 2, 2015 11:31 am | by Anne Ju, Cornell University | News | Comments

Liquid water is a requirement for life on Earth. But in other, much colder worlds, life might...

Exotic States Materialize with Supercomputers

February 13, 2015 11:26 am | by Jorge Salazar, Texas Advanced Computing Center | News | Comments

Scientists used supercomputers to find a new class of materials that possess an exotic state of...

Mathematics to Reveal Secrets of the Brain

February 5, 2015 4:33 pm | by Yngve Vogt, University of Oslo | News | Comments

Top researchers are using mathematical modelling and heavy computations to understand how the...

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A code hidden in the arrangement of the genetic information of single-stranded RNA viruses tells the virus how to pack itself within its outer shell of proteins.

Molecular Warfare: Researchers Discover Viral "Enigma Machine"

February 4, 2015 2:21 pm | by University of Leeds | News | Comments

Researchers have cracked a code that governs infections by a major group of viruses, including the common cold and polio. The unnoticed code had been hidden in plain sight in the sequence of the ribonucleic acid (RNA) that makes up this type of viral genome. But researchers have unlocked its meaning and demonstrated that jamming the code can disrupt virus assembly. Stopping a virus assembling can stop it functioning.

“In nanomedicine we need to understand physical phenomena on a nano scale, forming as correct a picture as possible of molecular phenomena. In this context, quantum chemical calculations are important,” says Michele Cascella. Courtesy of Hanne Utigard

Quantum Chemistry Closing in on Quantum Mechanics of Living Cells

January 30, 2015 11:19 am | by Yngve Vogt, University of Oslo | News | Comments

Quantum chemical calculations have been used to solve big mysteries in space. Soon the same calculations may be used to produce tomorrow’s cancer drugs. Quantum chemical calculations are needed to explain what happens to the electrons’ trajectories within a molecule, and the results of a quantum chemical calculation are often more accurate than what is achievable experimentally.

Map of diffuse interstellar bands Courtesy of T.W. Lan, G. Zasowski, B. Ménard, SDSS and 2MASS/UMass/IPAC-Caltech/NASA/NSF

Astronomers Map Mysterious Molecules in our Galaxy

January 12, 2015 10:20 am | by Phil Sneiderman, Johns Hopkins University | News | Comments

By analyzing the light of hundreds of thousands of celestial objects, astronomers have created a unique map of enigmatic molecules in our galaxy that are responsible for puzzling features in the light from stars, called diffuse interstellar bands. DIBs have been a mystery ever since they were discovered in 1922 — exactly which of the many thousands of possible molecules are responsible for these features?

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Watson's Nobel prize for the discovery of the structure of DNA sold at Christie's in a New York auction for $4.7 million, a world auction record for any Nobel.

Tycoon buys Watson's Nobel Prize, Gives it Back

December 10, 2014 2:25 pm | by AP | News | Comments

Russia's richest man says he has bought James D. Watson's Nobel Prize medal at Christie's in order to return it to the scientist. The 1962 Nobel Prize in Physiology or Medicine was awarded jointly to Francis Harry Compton Crick, James Dewey Watson and Maurice Hugh Frederick Wilkins "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material."

Biological engineers have created a new computer model that allows them to design the most complex three-dimensional DNA shapes ever produced, including rings, bowls, and geometric structures such as icosahedrons that resemble viral particles.

Computer Model Enables Design of Complex DNA Shapes

December 3, 2014 3:45 pm | by Anne Trafton, MIT | News | Comments

Biological engineers have created a new computer model that allows them to design the most complex three-dimensional DNA shapes ever produced, including rings, bowls, and geometric structures such as icosahedrons that resemble viral particles. 

The Gecko has good sticking power thanks to the van der Waals force.

Van der Waals Force Re-measured, may Help Improve Fundamental Simulation Methods

November 26, 2014 10:16 am | by Forschungszentrum Jülich | News | Comments

Van der Waals forces act like a sort of quantum glue on all types of matter. Using a new measuring technique, scientists from Forschungszentrum Jülich experimentally determined for the first time all of the key details of how strongly the single molecules bind to a surface. With an atomic force microscope, they demonstrated that the forces do not just increase with molecular size, but that they even grow disproportionately fast.

HPC Innovation Excellence Award: Ohio State University Cancer Comprehensive Care Center

November 17, 2014 5:36 pm | Award Winners

Researchers at Ohio State University Cancer Comprehensive Care Center developed and implemented bioinformatics and molecular methods to understand what happens to human papillomavirus (HPV) DNA in the "end game" of HPV-positive human cancers.

Indiana University received one of the largest individual awards from the NSF’s $31 million Data Infrastructure Building Blocks program this year. Researchers will use the $5 million in funding to help boost the nation’s big data efforts. Courtesy of NSF

NSF Awards $5M to Empower Researchers with New Data Analysis Tools

October 29, 2014 10:15 am | by Indiana University Bloomington | News | Comments

A team of computer scientists working to improve how researchers across the sciences empower big data to solve problems have been awarded $5 million by the National Science Foundation. The team will address one of the leading challenges in tackling some of the world’s most pressing issues in science: the ability to analyze and compute large amounts of data.

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A carbapenem molecule, a last resort antibiotic, enters the carbapenemase enzyme (blue arrow), where the crucial beta-lactam structure gets broken down. The ineffective molecule then leaves (orange arrow)

Nobel Prize-winning Technique Helps Design Antibiotics of Future

October 17, 2014 11:52 am | by Bristol University | News | Comments

Scientists have used computer simulations to show how bacteria are able to destroy antibiotics — a breakthrough that will help develop drugs which can effectively tackle infections in the future. Researchers at the University of Bristol focused on the role of enzymes in the bacteria, which split the structure of the antibiotic and stop it from working, making the bacteria resistant.

Fusion research simulated with supercomputers. Courtesy of KTH PDC

Computationally Intensive Research to get Boost, Break Petaflop Barrier

September 26, 2014 10:21 am | by KTH Royal Institute of Technology | News | Comments

Computationally intensive research in Sweden will soon get a boost from the fastest academic supercomputer in the Nordic countries, to be installed in October 2014 at KTH Royal Institute of Technology. KTH is due to begin using the fastest academic supercomputer of any university in Scandinavia. A Cray XC30 with 1,676 nodes and a memory of 104.7 terabytes will be installed at KTH’s PDC Center for High Performance Computing.

Caris Life Sciences is accelerating precision medicine for cancer treatment using IBM technical computing and software defined storage solutions.  Courtesy of Caris Life Science

Accelerating Use of Molecular Profiling in Cancer Treatment Selection

September 25, 2014 4:43 pm | by IBM | News | Comments

IBM announced that Caris Life Sciences is using IBM technical computing and storage technology to accelerate the company’s molecular profiling services for cancer patients. The Caris tumor profiling database is one of the largest datasets in the application of advanced molecular profiling technologies to support clinicians in delivering personalized treatment recommendations — or precision oncology.

This protein model represents an NMDA receptor, which juts halfway out of the surface of cells of the nervous system that include the brain and spinal cord. It relays signals between nerve cells. Researchers found that a mechanical coupling was needed bet

Stampede used to Perform Modeling to Advance Potential Drug Targets for Alzheimer's, Parkinson's, Schizophrenia

September 23, 2014 3:59 pm | by Jorge Salazar, TACC | News | Comments

It all begins in the brain as a flood, tens of millions of neurotransmitters handed off from one neuron to another in just a fraction of a second. Memories, dreams and learning share a common thread in this exchange of electrical and chemical signals by the nearly 100 billion spindly neurons of the brain, each cell networked to 10,000 others.

Initial research focused on optimization of the PMEMD classical molecular dynamics code, part of the widely used AMBER Molecular Dynamics software, on multi-core Intel Xeon processors and “manycore” Intel Xeon Phi processors.

SDSC Joins Intel Parallel Computing Centers Program with Focus on Molecular Dynamics, Neuroscience and Life Sciences

September 12, 2014 2:44 pm | by San Diego Supercomputer Center | News | Comments

The San Diego Supercomputer Center (SDSC) at the University of California, San Diego, is working with semiconductor chipmaker Intel to further optimize research software to improve the parallelism, efficiency, and scalability of widely used molecular and neurological simulation technologies.

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Grammatikopoulos simulated two palladium nanoparticles colliding at different temperatures. The hotter the temperature, the more homogenous the resulting product, and the further the atoms in the particle crystallize.

Simulating the Invisible

July 29, 2014 2:07 pm | by Poncie Rutsch, Okinawa Institute of Science and Technology Graduate University (OIST) | News | Comments

Every trillionth of a second, Panagiotis Grammatikopoulos calculates the location of each individual atom in a particle based on where it is and which forces apply. He uses a computer program to make the calculations, and then animates the motion of the atoms using visualization software. The resulting animation illuminates what happens, atom-by-atom, when two nanoparticles collide.

Jeffrey Potoff is a professor of Chemical Engineering and Materials Science, and Loren Schwiebert is an associate professor of Computer Science at Wayne State University.

Using Powerful GPU-Based Monte Carlo Simulation Engine to Model Larger Systems, Reduce Data Errors, Improve System Prototyping

July 22, 2014 8:33 am | by Jeffrey Potoff and Loren Schwiebert | Blogs | Comments

Recently, our research work got a shot in the arm because Wayne State University was the recipient of a complete high-performance compute cluster donated by Silicon Mechanics as part of its 3rd Annual Research Cluster Grant competition. The new HPC cluster gives us some state-of-the-art hardware, which will enhance the development of what we’ve been working on — a novel GPU-Optimized Monte Carlo simulation engine for molecular systems.

Liquid Water Exists in Extreme Cold

July 2, 2014 10:59 am | by SLAC National Accelerator Laboratory | News | Comments

Scientists at the Department of Energy’s SLAC National Accelerator Laboratory have made the first structural observations of liquid water at temperatures down to minus 51 degrees Fahrenheit, within an elusive “no man’s land” where water’s strange properties are super-amplified.

Jack Collins, Director of the Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research

Jack Collins

April 23, 2014 3:12 pm | Biographies

Dr. Collins is the director of the Advanced Biomedical Computing Center at the Frederick National Laboratory for Cancer Research. Dr. Collins’ research focuses on biomedical computing applications pertaining to cancer. His research group develops and applies high-performance algorithms to solve data-intensive computational biology problems in the areas of genomic analysis, pattern recognition in proteomics and imaging, molecular modeling, and systems biology.

Accelrys Insight

April 10, 2014 2:37 pm | Accelrys | Product Releases | Comments

Accelrys Insight and Accelrys Insight for Excel are designed to enhance scientific data analysis with capabilities that include the ability to run database searches directly from the Excel spreadsheet environment. The Web-based life science, discovery and innovation support environment speeds decisions by simplifying access to complex hierarchical data and implementing data-rich tooltips for scatterplots...

Klaus Schulten Talks about the Evolution of Computational Biophysics

March 14, 2014 10:26 am | by ISC | Articles | Comments

At this year's International Supercomputing Conference, Professor Klaus Schulten will deliver the opening keynote address on computing in biomedicine and bioengineering. Schulten, a physicist by training, now devotes his time to computation biophysics. He has contributed to several key discoveries in this area, has garnered numerous awards and honors for his work, and is considered one of preeminent leaders in field.

Dimer Molecules Help Gauge Exoplanet Pressure, Aid Hunt for Life

March 4, 2014 8:34 pm | by Peter Kelley, University of Washington | News | Comments

Astronomers at the University of Washington have developed a new method of gauging the atmospheric pressure of exoplanets, or worlds beyond the solar system, by looking for a certain type of molecule. And if there is life out in space, scientists may one day use this same technique to detect its biosignature — the telltale chemical signs of its presence — in the atmosphere of an alien world.

Fossil Pigments reveal Colors of Ancient Sea Monsters

February 4, 2014 11:35 am | by University of Southampton | News | Comments

An international team of scientists has, for the first time, revealed the color scheme of an extinct marine animal using fossilized skin pigment from three multi-million-year old marine reptiles. Previously, scientists could only guess what colors huge reptiles, such as mosasaurs and ichthyosaurs had

NERSC Flips Switch on New Flagship Supercomputer, Edison

January 31, 2014 2:21 pm | by Margie Wylie, Berkeley Lab | News | Comments

The National Energy Research Scientific Computing (NERSC) Center recently accepted “Edison,” a new flagship supercomputer designed for scientific productivity. Named in honor of American inventor Thomas Alva Edison, the Cray XC30 will be dedicated in a ceremony held at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) on February 5, 2014, and scientists are already reporting results.

Dassault Systèmes Acquires Accelrys

January 30, 2014 8:54 am | by Accelrys | News | Comments

Dassault Systèmes, a 3-D design software, 3-D Digital Mock Up and Product Lifecycle Management (PLM) solutions provider, and Accelrys, a provider of scientific innovation lifecycle management software for chemistry, biology and materials, have announced the signing of a definitive merger agreement for Dassault Systèmes to acquire San Diego-based Accelrys, Inc.

eQUEUE Job Submission Tool

December 19, 2013 9:21 am | by Advanced Clustering Technologies | Product Releases | Comments

eQUEUE is designed to be an intuitive Web-based front-end job submission tool and management portal that increases cluster utilization by making it easier to run jobs from any Web browser. It has the added value of virtually eliminating errors through pre-defined job submission scripts.

Three Win Nobel Chemistry Prize for Cyber Experiments

October 9, 2013 9:55 am | by Karl Ritter and Malin Rising, Associated Press | News | Comments

Three U.S.-based scientists won this year's Nobel Prize in chemistry on October 9, 1013, for developing powerful computer models that any researcher can use to understand complex chemical interactions and create new drugs. Research in the 1970s by Martin Karplus, Michael Levitt and Arieh Warshel has led to programs that unveil chemical processes such as how exhaust fumes are purified or how photosynthesis takes place in green leaves

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