Molecular Modeling
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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.

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...

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...

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...

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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

The New Frontier of Biologics ELN

September 1, 2013 5:36 pm | by Michael H. Elliott | Articles | Comments

The rapid increase of investment in biotherapeutics is changing the profile of the biopharmaceutical industry and, along with it, data management in the laboratory. With attention on longer patent life, high barriers to generic equivalents and personalized medicine, an increasing portion of R&D spending is being allocated to large molecule therapies

Schrödinger and DeltaSoft Announce Strategic Partnership

July 25, 2013 8:27 am | by Schrödinger | News | Comments

Schrödinger and DeltaSoft jointly announced that they have entered into a strategic partnership that will allow Schrödinger to enhance its current Enterprise Informatics offerings with DeltaSoft's flagship product ChemCart and associated tool base.

Pistoia Releases HELM Biomolecular Representation Tools

June 29, 2013 12:44 pm | by The Pistoia Alliance | News | Comments

The Pistoia Alliance has released the HELM biomolecular representation standard software toolkit and editor under the permissive open source MIT license. HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide range of biomolecules whose size and complexity render existing small-molecule and sequence-based informatics methodologies impractical or unusable.

Computer Models Predict More Effective Therapies

June 27, 2013 8:14 am | by AlphaGalileo | News | Comments

Scientist at Charité – Universitätsmedizin Berlin have used a computer simulation for predicting the effectiveness of various combination therapies for colon tumors. In most tumors, the communication between the individual cells is disturbed and the cells permanently receive growth and survival signals. For this reason, drugs are increasingly used in modern tumor therapy that targets those molecules to shut down these faulty signals.


Core Informatics and OpenEye Scientific Software Forge Partnership

April 10, 2013 12:25 pm | News | Comments

Core Informatics, a provider of data management solutions to the life sciences, molecular diagnostics and energy industries, and OpenEye Scientific Software, a developer of innovative molecular modeling and cheminformatics solutions for molecular discovery, have announced a new partnership and the integration of OpenEye cheminformatics software into Core Informatics’ web-based Core LIMS and Core ELN.

At Nearly 10 Petaflops, Stampede Provides Advanced Computing for US Scientists

March 27, 2013 2:39 pm | News | Comments

A National Science Foundation (NSF)-supported world-class supercomputer named Stampede, which has already enabled research teams to predict where and when earthquakes may strike, how much sea levels could rise, and how fast brain tumors grow- was officially dedicated on March 27, 2013.

New Mechanism for Long-term Memory Formation Discovered

March 25, 2013 3:29 pm | News | Comments

Irvine, Calif., March 25, 2013 — UC Irvine neurobiologists have found a novel molecular mechanism that helps trigger the formation of long-term memory. The researchers believe the discovery of this mechanism adds another piece to the puzzle in the ongoing effort to uncover the mysteries of memory and, potentially, certain intellectual disabilities.

Flip of Single Molecular Switch Makes Old Brain Young

March 6, 2013 1:56 pm | News | Comments

The flip of a single molecular switch helps create the mature neuronal connections that allow the brain to bridge the gap between adolescent impressionability and adult stability. Now Yale School of Medicine researchers have reversed the process, recreating a youthful brain that facilitated both learning and healing in the adult mouse.

New Glimpse of DNA’s Processing Hub

January 23, 2013 11:32 am | News | Comments

Vanderbilt University researchers have combined small-angle X-ray and neutron scattering with dynamic molecular modeling to determine how the structure of RPA responds as it engages DNA

Cycle Computing provisioned an over 50,000-core utility supercomputer in the Amazon Web Services (AWS) cloud for Schrödinger and Nimbus Discovery to accelerate lead identification via virtual screening.

Cycle Computing Caps Record 2012 with IDC HPC Innovation Excellence Award

January 16, 2013 3:06 pm | by Cycle Computing | News | Comments

Cycle Computing announced it has ended its record-breaking 2012 by winning the IDC HPC Innovation Excellence Award. IDC recognized Cycle’s 50,000-core utility supercomputer run in the Amazon Web Services (AWS) cloud for pharmaceutical companies Schrödinger and Nimbus Discovery. The unprecedented cluster completed 12.5 processor years in less than three hours with a cost of less than $4,900 per hour to facilitate computational drug discovery

Scientists Discover Bilayer Structure in Efficient Solar Material

April 24, 2012 2:10 pm | News | Comments

Detailed studies of one of the best-performing organic photovoltaic materials reveal an unusual bilayer lamellar structure that may help explain the material’s superior performance at converting sunlight to electricity and guide the synthesis of new materials with even better properties.

TACC Offers New, Broader Computational Biology Software Stack to Open Science Community

November 29, 2011 5:42 am | News | Comments

One of the fastest growing areas in science is comparative genomics, which is driven by advances in next-generation sequencing technology. To meet the needs of scientists in this rapidly expanding field, the Texas Advanced Computing Center (TACC) has announced a significantly improved software set of more than 30 new and updated applications for life science researchers across the country.

NVIDIA, Gaussian and PGI Announce Collaboration

September 13, 2011 6:02 am | News | Comments

NVIDIA has announced plans with Gaussian, Inc. and The Portland Group (PGI) to develop a future GPU-accelerated release of the Gaussian software application for quantum chemistry.

P7 Protein Resistance Mutations Identified-Represent Drug Targets for Hepatitis C Virus

June 28, 2011 10:14 pm | News | Comments

Combination Therapies Inhibiting P7 Could Prevent Spread of HCV in the Body British researchers have identified specific resistance mutations for two classes of p7 inhibitor, which may explain their lack of effectiveness in clinical trials combined with current standard of care. Study...

Mutations in Single Gene May Have Shaped Human Cerebral Cortex

May 16, 2011 6:27 am | News | Comments

The size and shape of the human cerebral cortex, an evolutionary marvel responsible for everything from Shakespeare's poetry to the atomic bomb, are largely influenced by mutations in a single gene, according to a team of researchers

Altruistic decision making focus of NIDA's Addiction Science Award

May 13, 2011 2:14 pm | News | Comments

A study of what influences decision making on issues whose consequences will only be felt by future generations won first prize in the annual Addiction Science Awards at this year's Intel International Science and Engineering Fair (ISEF) -- the world's largest science competition for high...

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