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
  • 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

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-...
Melanoma is a malignant tumor of melanocytes. Although extensive investigations have been done to study metabolic changes in primary melanoma in...
Characterization of an α-(Fe0.75,Cr0.25)2O3(0001) mixed oxide single crystal surface was conducted using x-ray photoelectron spectroscopy (...
Dendrimer-encapsulated ruthenium nanoparticles (DEN-Ru) have been used as catalysts in lithium-O2 batteries for the first time. Results obtained from...
Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time,...

Science Highlights

Posted: March 09, 2015
The dynamic process to turn poisonous carbon monoxide into more benign carbon dioxide requires a single atom. Scientists at Pacific Northwest...
Posted: February 27, 2015
Small design decisions when developing a catalyst can impact complex reaction paths. For example, inserting a potentially useful bit of molecular...
Posted: February 23, 2015
To reduce emissions from coal-fired power plants, scientists want to transform the carbon dioxide into minerals that last for thousands of years....
Posted: January 07, 2015
The Science Modeling hydrological processes in ecosystems containing both surface water and groundwater is crucial for understanding fluid flow, the...
Posted: November 20, 2014
Aluminum oxide, or alumina, has numerous industrial uses, including as a catalyst and a catalytic support. Characterizing alumina has been difficult...

Instruments

There are no related projects at this time.

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
  • 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

1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen.

Abstract: 

Melanoma is a malignant tumor of melanocytes. Although extensive investigations have been done to study metabolic changes in primary melanoma in vivo and in vitro, little effort has been devoted to metabolic profiling of metastatic tumors in organs other than lymph nodes. In this work, NMR-based metabolomics combined with multivariate data analysis is used to study metastatic B16-F10 melanoma in C57BL/6J mouse spleen. Principal Component Analysis (PCA), an unsupervised multivariate data analysis method, is used to detect possible outliers, while Orthogonal Projection to Latent Structure (OPLS), a supervised multivariate data analysis method, is employed to find important metabolites responsible for discriminating the control and the melanoma groups. Two different strategies, i.e., spectral binning and spectral deconvolution, are used to reduce the original spectral data before statistical analysis. Spectral deconvolution is found to be superior for identifying a set of discriminatory metabolites between the control and the melanoma groups, especially when the sample size is small. OPLS results show that the melanoma group can be well separated from its control group. It is found that taurine, glutamate, aspartate, O-Phosphoethanolamine, niacinamide ,ATP, lipids and glycerol derivatives are decreased statistically and significantly while alanine, malate, xanthine, histamine, dCTP, GTP, thymidine, 2'-Deoxyguanosine are statistically and significantly elevated. These significantly changed metabolites are associated with multiple biological pathways and may be potential biomarkers for metastatic melanoma in spleen.

Citation: 
Wang X, MY Hu, J Feng, M Liu, and JZ Hu.2014."1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen."Metabolomics 10(6):1129-1144. doi:10.1007/s11306-014-0652-z
Authors: 
X Wang
MY Hu
J Feng
M Liu
JZ Hu
Volume: 
10
Issue: 
6
Pages: 
1129-1144
Publication year: 
2014

ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?

Abstract: 

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi-conductive samples, whereas non-interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non-interlaced mode for insulator depth profiling. Two representative cases are presented: (1) depth profiling of a leached glass sample, and (2) depth profiling of a single crystal MgO sample. In brief, the interlaced mode should be attempted first, because (1) it may provide reasonable-quality data, and (2) it is time-saving for most cases, and (3) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non-interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non-interlaced mode may introduce strong H/C/O background but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating, but at the edge (outside) of the coating.

Citation: 
Wang Z, K Jin, Y Zhang, F Wang, and Z Zhu.2014."ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?"Surface and Interface Analysis 46(S1):257-260. doi:10.1002/sia.5419
Authors: 
Z Wang
K Jin
Y Zhang
F Wang
Z Zhu
Volume: 
46
Issue: 
0
Pages: 
257-260
Publication year: 
2014

In Situ Study of CO2 and H2O Partitioning Between Na-Montmorillonite and Variably Wet Supercritical Carbon Dioxide.

Abstract: 

Shale formations play fundamental roles in large-scale geologic carbon sequestration (GCS) aimed primarily to mitigate climate change, and in smaller-scale GCS targeted mainly for CO2-enhanced gas recovery operations. In both technologies, CO2 is injected underground as a supercritical fluid (scCO2), where interactions with shale minerals could influence successful GCS implementation. Reactive components of shales include expandable clays, such as montmorillonites and mixed-layer illite/smectite clays. In this work, we used in situ X-ray diffraction (XRD) and in situ infrared (IR) spectroscopy to investigate the swelling/shrinkage and water/CO2 sorption of a pure montmorillonite, Na-SWy-2, when the clay is exposed to variably hydrated scCO2 at 50 °C and 90 bar. Measured interlayer spacings and sorbed water concentrations at varying levels of scCO2 hydration are similar to previously reported values measured in air at ambient pressure over a range of relative humidities. IR spectra show evidence of both water and CO2 intercalation, and variations in peak shapes and positions suggest multiple sorbed types with distinct chemical environments. Based on the intensity of the asymmetric CO stretching band of the CO2 associated with the Na-SWy-2, we observed a significant increase in sorbed CO2 as the clay expands from a 0W to a 1W state, suggesting that water props open the interlayer so that CO2 can enter. However, as the clay transitions from a 1W to a 2W state, CO2 desorbs sharply. These observations were placed in the context of two conceptual models concerning hydration mechanisms for expandable clays and were also discussed in light of recent theoretical studies on CO2-H2O-clay interactions. The swelling/shrinkage of expandable clays could affect solid volume, porosity, and permeability of shales. Consequently, the results from this work could aid predictions of shale caprock integrity in large-scale GCS, as well as methane transmissivity in enhanced gas recovery operations.

Citation: 
Loring JS, ES Ilton, J Chen, CJ Thompson, PF Martin, P Benezeth, KM Rosso, AR Felmy, and HT Schaef.2014."In Situ Study of CO2 and H2O Partitioning Between Na-Montmorillonite and Variably Wet Supercritical Carbon Dioxide."Langmuir 30(21):6120-6128. doi:10.1021/la500682t
Authors: 
JS Loring
ES Ilton
J Chen
CJ Thompson
PF Martin
P Benezeth
KM Rosso
AR Felmy
HT Schaef
Volume: 
30
Issue: 
21
Pages: 
6120-6128
Publication year: 
2014

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater.

Abstract: 

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a major benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.

Citation: 
Wang YC, DK Schreiber, JJ Neeway, S Thevuthasan, JE Evans, JV Ryan, Z Zhu, and W Wei.2014."NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater."Surface and Interface Analysis 46(S1):233-237. doi:10.1002/sia.5585
Authors: 
YC Wang
DK Schreiber
JJ Neeway
S Thevuthasan
JE Evans
JV Ryan
Z Zhu
W Wei
Volume: 
46
Issue: 
Pages: 
233-237
Publication year: 
2014

Dendrimer-Encapsulated Ruthenium Nanoparticles as Catalysts for Lithium-O2 Batteries.

Abstract: 

Dendrimer-encapsulated ruthenium nanoparticles (DEN-Ru) have been used as catalysts in lithium-O2 batteries for the first time. Results obtained from UV-vis spectroscopy, electron microscopy and X-ray photoelectron spectroscopy show that the nanoparticles synthesized by the dendrimer template method are ruthenium oxide instead of metallic ruthenium reported earlier by other groups. The DEN-Ru significantly improve the cycling stability of lithium (Li)-O2 batteries with carbon black electrodes and decrease the charging potential even at low catalyst loading. The monodispersity, porosity and large number of surface functionalities of the dendrimer template prevent the aggregation of the ruthenium nanoparticles making their entire surface area available for catalysis. The potential of using DEN-Ru as stand-alone cathode materials for Li-O2 batteries is also explored.

Citation: 
Bhattacharya P, EN Nasybulin, MH Engelhard, L Kovarik, ME Bowden, S Li, DJ Gaspar, W Xu, and J Zhang.2014."Dendrimer-Encapsulated Ruthenium Nanoparticles as Catalysts for Lithium-O2 Batteries."Advanced Functional Materials 24(47):7510-7519. doi:10.1002/adfm.201402701
Authors: 
P Bhattacharya
EN Nasybulin
MH Engelhard
L Kovarik
ME Bowden
S Li
DJ Gaspar
W Xu
J Zhang
Facility: 
Volume: 
24
Issue: 
47
Pages: 
7510-7519
Publication year: 
2014

Impact of a Mixed Oxide’s Surface Composition and Structure on Its Adsorptive Properties: Case of the (Fe,Cr)3O4(111)

Abstract: 

Characterization of an α-(Fe0.75,Cr0.25)2O3(0001) mixed oxide single crystal surface was conducted using x-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), low energy electron diffraction (LEED) and temperature programmed desorption (TPD). After sputter/anneal cleaning in ultra-high vacuum (UHV), the mixed oxide surface became terminated with a magnetite-(111) structure based on the presence of (2x2) spots in LEED and Fe2+ in XPS. The composition of the surface was close to that of M3O4 based on XPS, with the metal (M) content of Fe2+/3+ and Cr3+ being close to 1.4:1, despite the fact that the film’s bulk was 3:1 with respect to the metal cations. The enrichment of the surface with Cr was not altered by high temperature oxidation in UHV, but could be returned to that of the bulk film composition by exposure to the ambient. Adsorption of various probe molecules (NO, O2, CO2 and H2O) was used to identify the active cation sites present in the (Fe,Cr)3O4(111) terminated surface. Although XPS and SIMS both indicated that the near-surface region was enriched in Cr3+, no adsorption states typically associated with Cr3+ sites on -Cr2O3 single crystal surfaces were detected. Instead, the TPD behaviors of O2 and CO2 pointed toward the main active sites being Fe2+ and Fe3+, with O2 preferentially adsorbing at the former and CO2 at the latter. NO was observed to bind at both Fe2+ and Fe3+ sites, and H2O TPD looked nearly identical to that for H2O on the Fe3O4(111) surface. Competition for adsorption sites between coadsorbed combinations of CO2, O2, H2O and NO corroborated these assignments. These results indicate that the surface composition of a mixed oxide can vary significantly from its bulk composition depending on the treatment conditions. Even then, the surface composition does not necessarily provide direct insight into the active adsorption sites. In the case of the (Fe,Cr)3O4(111) termination of the α-(Fe0.75,Cr0.25)2O3(0001) surface, Cr3+ cations in the near-surface region appear to be fully coordinated and unavailable for adsorbing molecules. The authors thank Drs. Sara Chamberlin and Scott Chambers for supplying the film used in this work. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Citation: 
Henderson MA, and MH Engelhard.2014."Impact of a Mixed Oxide’s Surface Composition and Structure on Its Adsorptive Properties: Case of the (Fe,Cr)3O4(111) Termination of the ?-(Fe,Cr)2O3(0001) Surface."Journal of Physical Chemistry C 118(50):29058-29067. doi:10.1021/jp5038975
Authors: 
MA Henderson
MH Engelhard
Facility: 
Volume: 
118
Issue: 
50
Pages: 
29058-29067
Publication year: 
2014

Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy.

Abstract: 

A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate efficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localization patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells.

Citation: 
Gunsolus IL, D Hu, C Mihai, SE Lohse, CS Lee, M Torelli, RJ Hamers, C Murphy, G Orr, and CL Haynes.2014."Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy."Analyst 139(12):3174-3178. doi:10.1039/c4an00574k
Authors: 
IL Gunsolus
D Hu
C Mihai
SE Lohse
CS Lee
M Torelli
RJ Hamers
C Murphy
G Orr
CL Haynes
Facility: 
Volume: 
139
Issue: 
12
Pages: 
3174-3178
Publication year: 
2014

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Leads

(509) 371-6471

Cowley is the capability lead for EMSL’s Molecular Science Computing capability. Primarily, he provides terascale supercomputing and petascale data storage services for EMSL users. His operations team performs engineering, as well as...