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

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...
High-quality static electric dipole polarizabilities have been determined for the ground states of the hard-sphere cations of U, Np, and Pu in the...

Science Highlights

Posted: January 15, 2016
Green fluorescent protein, or GFP, is a substance from a jellyfish found off the western coast of North America that has transformed modern cellular...
Posted: January 13, 2016
The Science Technetium-99 (99Tc) is a long-lived radionuclide byproduct of the nuclear fuel cycle, making it a major radiological concern at nuclear...
Posted: January 08, 2016
Pacific Northwest National Laboratory, or PNNL, and University of Washington researchers used measurements from a western North America survey of...
Posted: November 23, 2015
Scientists at Pacific Northwest National Laboratory, or PNNL, mapped the reaction that turns wind-generated electricity into fuel and the amount of...
Posted: November 16, 2015
Scientists at Pacific Northwest National Laboratory, or PNNL, discovered that carbon sequestering minerals can form without water-using carbonic...

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 would like to use the Cascade supercomputer to compute the structures, spectroscopic properties, and reactive capabilities of Zr6 based Metal-...

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

Site-Specific Scaling Relations for Hydrocarbon Adsorption on Hexagonal Transition Metal Surfaces.

Abstract: 

Screening a large number of surfaces for their catalytic performance remains a challenge, leading to the need for simple models to predict adsorption properties. To
facilitate rapid prediction of hydrocarbon adsorption energies, scaling relations that allow for calculation of the adsorption energy of any intermediate attached to any symmetric site on any hexagonal metal surface through a carbon atom were
developed. For input, these relations require only simple electronic properties of the surface and of the gas-phase reactant molecules. Determining adsorption energies consists of up to four steps: (i) calculating the adsorption energy of methyl in the top site using density functional theory or by simple relations based on the electronic structure of the surface; (ii) using modified versions of classical scaling relations to scale between methyl in the top site and C1 species with more metal−surface bonds (i.e., C, CH, CH2) in sites that complete adsorbate tetravalency; (iii) using gas-phase bond energies to predict adsorption energies of longer hydrocarbons (i.e., CR, CR2, CR3); and (iv) expressing energetic changes upon translation of hydrocarbons to various sites in terms of the number of agostic interactions and the change in the number of carbon−metal bonds. Combining all of these relations allows accurate scaling over a wide range of adsorbates and surfaces, resulting in efficient screening of catalytic surfaces and a clear elucidation of adsorption trends. The relations are used to explain trends in methane reforming, hydrocarbon chain growth, and propane dehydrogenation.

Citation: 
Montemore MM, and JW Medlin.2013."Site-Specific Scaling Relations for Hydrocarbon Adsorption on Hexagonal Transition Metal Surfaces."Journal of Physical Chemistry C 117(39):20078–20088. doi:10.1021/jp4076405
Authors: 
MM Montemore
JW Medlin
Volume: 
Issue: 
Pages: 
Publication year: 
2013

DFT Study of Uranyl Peroxo Complexes with H2O, F−, OH−, CO3 2, and NO3−.

Abstract: 

The structural and electronic properties of monomeric uranyl peroxo complexes with aquo, hydroxo, fluoro, carbonate, and nitrate ligands have been studied using DFT calculations with relativistic pseudopotentials. The calculated affinity of the peroxo group for the actinyl moiety far exceeds that of the other ligands tested in this work.

Citation: 
Odoh SO, and G Schreckenbach.2013."DFT Study of Uranyl Peroxo Complexes with H2O, F?, OH?, CO3 2?, and NO3?."Inorganic Chemistry 52(9):5590-5602. doi:10.1021/ic400652b
Authors: 
SO Odoh
G Schreckenbach
Volume: 
52
Issue: 
9
Pages: 
5590-5602
Publication year: 
2013

Static Electric Dipole Polarizabilities of Tri- and Tetravalent U, Np, and Pu Ions.

Abstract: 

High-quality static electric dipole polarizabilities have been determined for the ground
states of the hard-sphere cations of U, Np, and Pu in the III and IV oxidation states. The polarizabilities have been calculated using the numerical finite field technique in a four-component relativistic framework. Methods including Fock-space coupled cluster (FSCC) and Kramers-restricted configuration interaction (KRCI) have been performed in order to account for electron correlation effects. Comparisons between polarizabilities calculated using Dirac−Hartree−Fock (DHF), FSCC, and KRCI methods have been made using both triple- and quadruple-ζ basis sets for U4+. In addition to the ground state, this study also reports the polarizability data for the first two excited states of U3+/4+, Np3+/4+, and Pu3+/4+ ions at different levels of theory. The values reported in this work are the most accurate to date calculations for the dipole polarizabilities of the hard-sphere tri- and tetravalent actinide ions and may serve as reference values, aiding in the calculation of various electronic and
response properties (for example, intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications.

Citation: 
Parmar P, KA Peterson, and AE Clark.2013."Static Electric Dipole Polarizabilities of Tri- and Tetravalent U, Np, and Pu Ions."Journal of Physical Chemistry A 117(46):11874–11880. doi:10.1021/jp403078j
Authors: 
P Parmar
KA Peterson
AE Clark
Volume: 
Issue: 
Pages: 
Publication year: 
2013

Pages

Leads

509/371-6955

McCue is the capability lead for EMSL’s Molecular Science Computing Scientific Consulting. She will collaborate with users to help ensure the integration between experimental and computational resources for improved scientific discovery.