Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

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Molecular Science Computing

Environmental molecular research is enhanced when combined with advance data analytics and visualization, computational modeling and simulation, and efficient parallel software. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools to make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.

Resources and Techniques

*NEW* EMSL's new supercomputer, Tahoma, is planned to be available for research starting October 1. This system will support computational research requiring significant memory as well as processing speed to enable data mining, image processing, and multiscale modeling.

  • Tahoma provides 160 CPU nodes and 24 GPU nodes, with an estimated peak performance of 0.57 PetaFLOPs.
  • The 160 CPU nodes each have 36 3.1 GHz Intel Xeon processor cores, 384 GB of memory and 2 TB of flash storage.
  • The 24 GPU nodes each have 36 processor cores and 2 NVIDIA v100 GPGPUs, 1536 GB of memory and 7 TB of flash storage.
  • Tahoma’s 10 PB global file system is capable of 100 Gigabyte/sec bandwidth.

Additional flagship computing resources also offered include:

  • Cascade, a 1440-node supercomputer with theoretical peak performance of 3.4 petaflops; Cascade came online in December 2013.
  • Aurora, a 17 Petabyte HPSS data storage system
  • NWChem, a molecular modeling software. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wave-function or density.
  • Data Analysis & Visualization, a web-based front end for visualizations of data generated in EMSL.

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

Molecular Science Computing Experts

Description

Molecular Science Computing – EMSL offers sophisticated and integrated computational capabilities, including scientific consultants, software, Cascade supercomputer and the Aurora data archive, to enable the following:

  • Quantum chemistry and molecular dynamics simulations of molecules, surface interfaces, nanoparticles and biological systems
  • Subsurface flow and reactive transport modeling
  • Simulations of aerosols and atmospheric particles
  • Agent-based modeling framework for simulation of biological systems
  • Data analysis and visualization tools to enable exploration of complex data sets from experimental platforms.

Instruments

No instruments are available at this time.

Publications

Formic Acid Decomposition on Au catalysts: DFT, Microkinetic Modeling, and Reaction Kinetics Experiments.
A combined theoretical and experimental approach is presented that uses a comprehensive mean-field microkinetic model, reaction kinetics experiments...
Steam Reforming of Ethylene Glycol over MgAl2O4 Supported Rh, Ni, and Co Catalysts.
Steam reforming of ethylene glycol (EG) over MgAl2O4 supported metal (15 wt.% Ni, 5 wt.% Rh, and 15 wt.% Co) catalysts were investigated using...
Bio-inspired Design of Electrocatalysts for Oxalate Oxidation: a Combined Experimental and Computational Study of Mn–N–C
We report a novel non-platinum group metal (non-PGM) catalyst derived from Mn and amino- antipyrine (MnAAPyr) that shows electrochemical activity...
Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality.
Conspectus Boron is an interesting element with unusual polymorphism. While three-dimensional (3D) structural motifs are prevalent in bulk boron,...
Promotional Effect of Surface Hydroxyls on Electrochemical Reduction of CO2 over SnOx/Sn electrode.
Tin oxide (SnOx) formation on tin-based electrode surfaces during CO2 electrochemical reduction can have a significant impact on the activity and...
View all Molecular Science Computing Publications

Science Highlights

Setting the stage for fuel-efficient fertilizer
Posted: August 02, 2019
Pacific Northwest National Laboratory web feature Ammonia, the primary ingredient in nitrogen-based fertilizers, has helped feed the world since...
Scientists Discover Approach to Activate Inert Gases
Posted: July 25, 2019
The Science Inert gases like argon typically do not form chemical bonds except under extreme conditions, such as the icy cold of outer space. As...
Aluminum complexes identified via vibrational fingerprints
Posted: January 23, 2019
From Pacific Northwest National Laboratory's Physical Sciences Division Dissolved aluminum formed during industrial processing has perplexed chemists...
Illuminating how nitrogenase makes ammonia
Posted: January 04, 2019
From Pacific Northwest National Laboratory's Physical Sciences Division A team of researchers led by PNNL computational scientist Simone Raugei have...
Fitting a Square Peg in a Round Hole: The Surprising Structure of Uranium Bound in Hematite
Posted: August 13, 2018
The Science One promising approach to stabilize uranium contamination in soils is to envelop the radioactive uranium into iron-bearing minerals like...
View all Molecular Science Computing Science Highlights

Instruments

There are no related projects at this time.

Science Theme: 
Atmospheric Aerosol Systems
Biosystem Dynamics & Design
Molecular Transformations
Terrestrial & Subsurface Ecosystems

Environmental molecular research is enhanced when combined with advance data analytics and visualization, computational modeling and simulation, and efficient parallel software. Users are encouraged to combine computation with EMSL's state-of-the-art experimental tools to make an integrated platform for scientific discovery. See a complete list of Molecular Science Computing instruments.

Resources and Techniques

*NEW* EMSL's new supercomputer, Tahoma, is planned to be available for research starting October 1. This system will support computational research requiring significant memory as well as processing speed to enable data mining, image processing, and multiscale modeling.

  • Tahoma provides 160 CPU nodes and 24 GPU nodes, with an estimated peak performance of 0.57 PetaFLOPs.
  • The 160 CPU nodes each have 36 3.1 GHz Intel Xeon processor cores, 384 GB of memory and 2 TB of flash storage.
  • The 24 GPU nodes each have 36 processor cores and 2 NVIDIA v100 GPGPUs, 1536 GB of memory and 7 TB of flash storage.
  • Tahoma’s 10 PB global file system is capable of 100 Gigabyte/sec bandwidth.

Additional flagship computing resources also offered include:

  • Cascade, a 1440-node supercomputer with theoretical peak performance of 3.4 petaflops; Cascade came online in December 2013.
  • Aurora, a 17 Petabyte HPSS data storage system
  • NWChem, a molecular modeling software. NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum-mechanical descriptions of the electronic wave-function or density.
  • Data Analysis & Visualization, a web-based front end for visualizations of data generated in EMSL.

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

Pages

Leads

Lee Ann McCue
Dr. McCue develops and implements computational strategy for data analysis, storage and retrieval as well as develops, acquires, and provides software and hardware to enable EMSL Sciences Areas. Responsible for infrastructure health, development,...