Molecular Science Computing
EMSL's flagship computing resources include:
MSC News
- EMSL introduces a new video about Chinook on EMSL's YouTube channel (script, .pdf, 9kb)
- Chinook - Living Life in the Fastlane [.pdf, 107kb]
Additional Information
- The High-Performance Computing Center, home of the EMSL's parallel supercomputers
- Software, including the Molecular Science Software Suite, MS3 (NWChem, Ecce, ParSoft)
- The Graphics and Visualization Laboratory.
Providing an integrated production computing environment, EMSL links to external facilities within the U.S. Department of Energy (DOE), collaborating universities, and industry. EMSL supports a wide range of computational activities in environmental molecular research, including benchmark calculations on small molecules, reliable calculations on large molecules and solids, simulations of large biomolecules, and reactive chemical transport modeling.
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. Learn about anticipated future challenges in biological and chemical sciences and environmental systems, the role that EMSL supercomputing resources and expert staff will play, and how EMSL's supercomputing upgrades will positively impact the environmental missions of DOE in the Greenbook [.pdf, 2.4mb].
Research
A variety of user projects are supported by EMSL's computing resources. These projects are categorized in three types based on their depth and focus. Brief descriptions of these project types and how to submit a proposal for each follows. In addition, detail is available about current, individual Computing Research Projects.
- Computationally Intensive Research projects (CIR) - formerly known as Computational Grand Challenge projects, these research projects apply to environmental molecular science basic and applied research areas that address environmental problems and research needs facing DOE; CIR projects can be proposed for periods of one to three years, depending on their scope. Potential areas of interest are described by EMSL's Science Themes. EMSL users can submit a proposal for a CIR project in response to an EMSL Science Themes call for proposals, which occur annually.
- EMSL Science Themes projects - specifically applied to one or more of the EMSL Science Themes, these projects frequently support experimental research occurring within EMSL. These projects generally require less computer time depending on the scope of their research. EMSL users can submit a proposal in response to an EMSL Science Themes call for proposals, which occurs annually.
- Pilot projects - smaller and short-term, these projects for general research are typically directed at developing a capability to submit a future CIR project proposal (e.g., a combination of theory/method or code development activities or doing calculations that provide the initial scientific basis of a CIR proposal); some Pilot projects are for computational support of experiments performed in other EMSL facilities. EMSL users and potential EMSL users can submit a proposal for a Pilot project at any time by following EMSL's General Open call Proposal Process.
All Related Publications Related Publications
- Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1.
- A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction.
- Intrinsic Hole Migration Rates in TiO2 from Density Functional Theory.
- Ti 3p electrons: core or valence?
- Long-Range Electron Transfer Across Cytochrome-Hematite (a-Fe2O3) Interfaces.
Related Research Highlights
- Enhanced Understanding of Titania's Catalytic Mechanism Through Computational Modeling (Insights of Titania Proportion)
- Understanding Uranium Complex Formation Through Combined Modeling and Gas-Phase Experiments (Complex Uranium)
- The Synergy Between Molecular Theory and Solid-State NMR Spectroscopy (Model System for NMR)
- Energetics and Dynamics of Electron Transfer and Proton Transfer in Dissociation of MetalIII(salen)-Peptide Complexes in the Gas Phase (Getting a Charge)
Molecular Science Computing Capabilities Available at EMSL
| Instrument | Contact |
|---|---|
| Computing: Altix1 cluster |
Vorpagel, Erich |
| Computing: Chinook (HP 2310-Node Linux Cluster) |
Vorpagel, Erich |
| Computing: Data File Storage (NWfs) |
Cowley, David E Wright, Ryan |
| Computing: NW-ICE | |
| Computing: SGI 16-processor Graphics Server (nwvisus) |
Vorpagel, Erich |
| Computing: Spokane cluster |
Bylaska, Eric Rosso, Kevin M. |
Inquiries
For general questions regarding EMSL computing resources, complete the Computing Scientific Consulting form; email mscf-consulting@emsl.pnl.gov; or call 509-371-6477, Monday – Friday, 8am - 5pm, PST
Computing Capability Steward (MS3): Bert deJong | Wibe.DeJong@pnl.gov, 509-371-6445
Computing Capability Steward (High-Performance Computing Center): Kevin Regimbal | Kevin.Regimbal@.pnl.gov, 509-371-6075

