Molecular Science Computing
Environmental molecular research is accelerated when combined with leading-edge hardware, efficient parallel software, accurate and predictive theories and visualization capabilities. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools that make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.
The Molecular Science Computing (MSC) capability supports EMSL's flagship computing resources including:
- Cascade, a supercomputer with theoretical peak performance of 3.4 petaflops, that came online in December 2013. See announcements about the current status of Cascade
- NWChem, a molecular modeling software developed to take full advantage of the advanced computing systems installed. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wavefunction or density.
- GA Tools (Global Arrays Programming Models)
- Ecce, a domain encompassing problem-solving environment for molecular modeling, analysis, and simulations, and
- Aurora, a 15.8 Petabyte HPSS data storage system
EMSL employs a forward-looking strategy to maintain leading-edge supercomputing capabilities and encourages users to combine computational and state-of-the-art experimental tools, providing a cross-disciplinary environment to further research.
Additional Information
Science Theme:
Environmental molecular research is accelerated when combined with leading-edge hardware, efficient parallel software, accurate and predictive theories and visualization capabilities. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools that make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.
The Molecular Science Computing (MSC) capability supports EMSL's flagship computing resources including:
- Cascade, a supercomputer with theoretical peak performance of 3.4 petaflops, that came online in December 2013. See announcements about the current status of Cascade
- NWChem, a molecular modeling software developed to take full advantage of the advanced computing systems installed. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wavefunction or density.
- GA Tools (Global Arrays Programming Models)
- Ecce, a domain encompassing problem-solving environment for molecular modeling, analysis, and simulations, and
- Aurora, a 15.8 Petabyte HPSS data storage system
EMSL employs a forward-looking strategy to maintain leading-edge supercomputing capabilities and encourages users to combine computational and state-of-the-art experimental tools, providing a cross-disciplinary environment to further research.
Additional Information
Cream of the Crop: Top-Tier Publications from 2016
Photochemical Dynamics of Methylamine and Bromoacetyl Chloride: Model Systems for Method Testing and Development
Design of Cathode Materials for Li-ion Batteries with High Capacity
Does Forest-to-Pasture conversion decrease functional turnover across space? Measuring the effects of deforestation on the
The lower atmosphere's mixing messages
Compute Allocation in support of EMSL User Proposal 47483
In silico Chemical Library Engine (ISICLE) for Expo/Metabo-lomics and Modeling
First Complete Genome of a Bacterial Strain from Soil
Microbial CH4 and CO2 Fluxes and C Stabilization Mechanisms in Soils -- supplement to Proposal 47865
Pages
Description
Resources and Techniques
Molecular Science Computing – Sophisticated and integrated computational capabilities, including scientific consultants, software, Cascade supercomputer and a data archive, enable the following:
• Simulations that accurately mimic real molecules, solids, nanoparticles and biological systems
• Reactive chemical transport modeling for subsurface and atmospheric study
• State-of-the-art integration between theory and experiment
• Parallel and efficient computer architectures
• Computational models built on open-source framework.
Molecular Science Software Suite – Complex chemical systems at the atomic level are investigated using comprehensive, integrated tools coupled with advanced computational chemistry techniques and high-performance, massive parallel computing systems.
Graphics and Visualization Laboratory – Complex experimental and computational data sets are analyzed using high-performance graphics systems for illustration and image editing, data modeling and image analysis, scene rendering and model creation, and audio-video composition and editing.
Instruments
The 3.4 petaflop system's 23,000 Intel processors have 184,000 gigabytes of memory available, about four times as much memory per processor as other...
Custodian(s): Doug Baxter
Aurora, EMSL's scientific data archive, is a dedicated computer system specifically designed for long-term storage of data collected by EMSL...
Custodian(s): Ryan Wright, Dave Cowley
Publications
Pt-based core−shell (M@Pt where M stands for core element) nanoparticles (NPs) have recently been under increasing scrutiny in the fields...
Chemical reactivity descriptors are a powerful means for understanding reactivity in a wide variety of chemical compounds. These descriptors, rooted...
Mechanistic assessments based on kinetic and isotopic methods combined with density functional theory are used to probe the diverse pathways by which...
The initial structures for the search for the global minimum of TiO2 nanoclusters were generated by combining a tree growth (TG) algorithm with a...
Most binary materials formed by early group 13 and 15 elements are semiconductors identical in their structures and properties. We show that in the...
Science Highlights
Posted: October 10, 2016
A team of researchers at Pacific Northwest National Laboratory, NASA Langley Research Center, Colorado University Boulder and Brookhaven National...
Posted: September 22, 2016
The Science
Soil metagenomics have been termed a grand challenge due to the complexity and diversity of microbial communities in soil ecosystems. A...
Posted: September 15, 2016
Scientists from the University of Minnesota and Pacific Northwest National Laboratory used capabilities at EMSL and other facilities to make...
Posted: July 12, 2016
The Science
The degradation of soil organic matter by microbes plays an important role in atmospheric carbon levels. A recent study examined how...
Posted: July 05, 2016
A team of scientists from Pacific Northwest National Laboratory and Technische Universität München studied how water slows a solid acid catalyst's...
Instruments
Criegee intermediates (CI) are key intermediates in the reaction of ozone with alkenes. The stabilized Criegee intermediates (sCI) can react with...
Microbial activities on which humanity and ecosystems depend, and which influence climate and support biofuel production, are determined both by...
Advancing predictive models of complex environmental systems, such as the Earth's subsurface and terrestrial ecosystems, requires that high-...
A major PNNL's research effort funded through DOE's Atmospheric System Research (ASR) Program focuses on current knowledge gaps in aerosol...
We propose to use EMSL supercomputing resources to gain a molecular level understanding of how substrate binding, electron, and proton delivery are...
Leads
509/371-6955
Dr. McCue is the capability lead for EMSL’s molecular science computing scientific consulting. She collaborates with EMSL users to ensure integration between experimental and computational resources for improved scientific discovery.