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.

Additonal 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

Nanostructured silicon is a promising anode material for high performance lithium-ion batteries, yet scalable synthesis of such materials, and...
Transition Al2O3 derived from thermal decomposition of AlOOH Boehmite have complex structures and to a large extent remain poorly understood. Here we...
A hydrogen-evolving homogeneous Ni(P2N2)2 electrocatalyst with peripheral ester groups has been covalently attached to a 1,2,3-triazolyllithium-...
The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and...
We have studied the reactions of 1,2-propylene glycol (1,2-PG), DOCH(CH3)CH2OD, on partially reduced, hydroxylated and oxidized TiO2(110) surfaces...

Science Highlights

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...
Posted: November 20, 2014
The Science All eukaryotes have three essential DNA-dependent RNA polymerase enzymes. These enzymes control gene activity by constructing chains of...

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.

Additonal Information

A Hydrogen-Evolving Ni(P2N2)2 Electrocatalyst Covalently Attached to a Glassy Carbon Electrode: Preparation, Characterization,

Abstract: 

A hydrogen-evolving homogeneous Ni(P2N2)2 electrocatalyst with peripheral ester groups has been covalently attached to a 1,2,3-triazolyllithium-terminated glassy carbon electrode. The surface-confined complex is an electroctalyst for hydrogen evolution, showing onset of catalytic current at the same potential as the soluble parent complex. X-ray photoemission spectra show excellent agreement between the coupled and homogeneous species. Coverage approaches a dense monolayer. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy. The XPS measurements were performed at 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: 
Das AK, MH Engelhard, RM Bullock, and JA Roberts.2014."A Hydrogen-Evolving Ni(P2N2)2 Electrocatalyst Covalently Attached to a Glassy Carbon Electrode: Preparation, Characterization, and Catalysis. Comparisons With the Homogeneous Analog."Inorganic Chemistry 53(13):6875-6885. doi:10.1021/ic500701a
Authors: 
AK Das
MH Engelhard
RM Bullock
JA Roberts
Facility: 
Volume: 
53
Issue: 
13
Pages: 
6875-6885
Publication year: 
2014

Structure of δ-Alumina: Toward The Atomic Level Understanding Of Transition Alumina Phases.

Abstract: 

Transition Al2O3 derived from thermal decomposition of AlOOH Boehmite have complex structures and to a large extent remain poorly understood. Here we report a detailed atomic level analysis of ΔAl2O3 for the first time using a combination of Scanning Transmission Electron Microscopy imaging, XRD refinement, and DFT calculations. We show that the structure of ΔAl2O3 represents a complex structural intergrowth from several crystallographic variants. The two main crystallographic variants, which are identified as Δ1-Al2O3 and Δ2−Al2O3, are fully structurally described. In addition, we also derive the energy of formation for Δ1 and Δ2-Al2O3 and the other relevant transition Al2O3 phases, and show how energetic degeneracy leads to structural disorder and complex intergrowths among several transition Al2O3. The results of the work have important implications for understanding thermodynamic stability and transformation processes in transition alumina.

Citation: 
Kovarik L, ME Bowden, A Genc, J Szanyi, CHF Peden, and JH Kwak.2014."Structure of ?-Alumina: Toward The Atomic Level Understanding Of Transition Alumina Phases."Journal of Physical Chemistry C 118:18051-18058. doi:10.1021/jp500051j
Authors: 
L Kovarik
ME Bowden
A Genc
J Szanyi
CHF Peden
JH Kwak
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Mesoporous Silicon Sponge as an Anti-Pulverization Structure for High-Performance Lithium-ion Battery Anodes.

Abstract: 

Nanostructured silicon is a promising anode material for high performance lithium-ion batteries, yet scalable synthesis of such materials, and retaining good cycling stability in high loading electrode remain significant challenges. Here, we combine in-situ transmission electron microscopy and continuum media mechanical calculations to demonstrate that large (>20 micron) mesoporous silicon sponge (MSS) prepared by the scalable anodization method can eliminate the pulverization of the conventional bulk silicon and limit particle volume expansion at full lithiation to ~30% instead of ~300% as observed in bulk silicon particles. The MSS can deliver a capacity of ~750 mAh/g based on the total electrode weight with >80% capacity retention over 1000 cycles. The first-cycle irreversible capacity loss of pre-lithiated MSS based anode is only <5%. The insight obtained from MSS also provides guidance for the design of other materials that may experience large volume variation during operations.

Citation: 
Li X, M Gu, SY Hu, R Kennard, P Yan, X Chen, CM Wang, MJ Sailor, J Zhang, and J Liu.2014."Mesoporous Silicon Sponge as an Anti-Pulverization Structure for High-Performance Lithium-ion Battery Anodes."Nature Communications 5:Article No. 4105. doi:10.1038/ncomms5105
Authors: 
Li X
M Gu
SY Hu
R Kennard
P Yan
X Chen
CM Wang
MJ Sailor
J Zhang
J Liu
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Conversion of 1,2-Propylene Glycol on Rutile TiO2(110).

Abstract: 

We have studied the reactions of 1,2-propylene glycol (1,2-PG), DOCH(CH3)CH2OD, on partially reduced, hydroxylated and oxidized TiO2(110) surfaces using temperature programmed desorption. On reduced TiO2(110), propylene, propanal, and acetone are identified as primary carbon-containing products. While the propylene formation channel dominates at low 1,2-PG coverages, all of the above-mentioned products are observed at high coverages. The carbon-containing products are accompanied by the formation of D2O and D2. The observation of only deuterated products shows that the source of hydrogen (D) is from the 1,2-PG hydroxyls. The role of bridging oxygen vacancy (VO) sites was further investigated by titrating them via hydroxylation and oxidation. The results show that hydroxylation does not change the reactivity because the VO sites are regenerated at 500 K, which is a temperature lower than the 1,2-PG product formation temperature. In contrast, surface oxidation causes significant changes in the product distribution, with increased acetone and propanal formation and decreased propylene formation. Additionally D2 is completely eliminated as an observed product at the expense of D2O formation.

Citation: 
Chen L, Z Li, RS Smith, BD Kay, and Z Dohnalek.2014."Conversion of 1,2-Propylene Glycol on Rutile TiO2(110)."Journal of Physical Chemistry C 118(28):15339-15347. doi:10.1021/jp504770f
Authors: 
L Chen
Z Li
RS Smith
BD Kay
Z Dohnalek
Facility: 
Volume: 
118
Issue: 
28
Pages: 
15339-15347
Publication year: 
2014

Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations.

Abstract: 

The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and chemically, sandwiched between two distinct boundaries - pristine glass surface at the inner most interface and aqueous solution at the outer most. The physico-chemical processes that control the development of this region have a significant impact on the long-term glass-water reaction. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include Geochemical Reaction Path simulations, Glass Reactivity in Allowance for Alteration Layer simulations, Monte Carlo simulations, and Molecular Dynamics methods. Discussed in this manuscript are the advances and limitations of each modeling approach placed in the context of the glass water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers; thus providing the fundamental data needed to develop pore-scale equations that enable more accurate predictions of nuclear waste glass corrosion in a geologic repository.

Citation: 
Pierce EM, P Frugier, LJ Criscenti, KD Kwon, and SN Kerisit.2014."Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations."International Journal of Applied Glass Science 5(4):421-435. doi:10.1111/ijag.12077
Authors: 
EM Pierce
P Frugier
LJ Criscenti
KD Kwon
SN Kerisit
Volume: 
5
Issue: 
4
Pages: 
421-435
Publication year: 
2014

Reflection High-Energy Electron Diffraction Beam-Induced Structural and Property Changes on WO3 Thin Films.

Abstract: 

Reduction of transition metal oxides can greatly change their physical and chemical properties. Using deposition of WO3 as a case study, we demonstrate that reflection high-energy electron diffraction (RHEED), a surface-sensitive tool widely used to monitor thin-film deposition processes, can significantly affect the cation valence and physical properties of the films through electron-beam induced sample reduction. The RHEED beam is found to increase film smoothness during epitaxial growth of WO3, as well as change the electronic properties of the film through preferential removal of surface oxygen.

Citation: 
Du Y, H Zhang, T Varga, and SA Chambers.2014."Reflection High-Energy Electron Diffraction Beam-Induced Structural and Property Changes on WO3 Thin Films."Applied Physics Letters 105(5):051606. doi:10.1063/1.4892810
Authors: 
Du Y
H Zhang
T Varga
SA Chambers
Volume: 
Issue: 
Pages: 
Publication year: 
2014

A Preorganized Hydrogen Bond Network and Its Effect on Anion Stability.

Abstract: 

Rigid tricyclic locked in all axial 1,3,5-cyclohexanetriol derivatives with 0–3 trifluoromethyl groups were synthesized and photoelectron spectra of their conjugate bases and chloride anion clusters are reported along with density functional computations. The resulting vertical and adiabatic detachment energies provide measures of the anion stabilization due to the hydrogen bond network and inductive effects. The latter mechanism is found to be transmitted through space via hydrogen bonds

Citation: 
Samet M, XB Wang, and SR Kass.2014."A Preorganized Hydrogen Bond Network and Its Effect on Anion Stability."Journal of Physical Chemistry A 118(31):5989-5993. doi:10.1021/jp505308v
Authors: 
M Samet
XB Wang
SR Kass
Volume: 
118
Issue: 
31
Pages: 
5989-5993
Publication year: 
2014

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

Abstract: 

Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified marine waters. Currently OMZs are expanding due to global climate change. This expansion alters marine ecosystem function and the productivity of fisheries due to habitat compression and changes in biogeochemical cycling leading to fixed nitrogen loss and greenhouse gas production. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally anoxic fjord, Saanich Inlet to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification and inorganic carbon fixation predominantly co-varied with abundance and distribution patterns of Thaumarchaeota, Nitrospira, Planctomycetes and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Within these groups, pathways mediating inorganic carbon fixation and nitrogen and sulfur transformations were differentially expressed across the redoxcline. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters and denitrification, sulfur-oxidation and inorganic carbon fixation pathways affiliated with SUP05 dominated suboxic and anoxic waters. Nitrite-oxidation and anammox pathways affiliated with Nitrospina and Planctomycetes respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The differential expression of these pathways under changing water column redox conditions has quantitative implications for coupled biogeochemical cycling linking different modes of inorganic carbon fixation with distributed nitrogen and sulfur-based energy metabolism extensible to coastal and open ocean OMZs.

Citation: 
Hawley AK, HM Brewer, AD Norbeck, L Pasa-Tolic, and SJ Hallam.2014."Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes."Proceedings of the National Academy of Sciences of the United States of America 111(31):11395-11400. doi:10.1073/pnas.1322132111
Authors: 
AK Hawley
HM Brewer
AD Norbeck
L Pasa-Tolic
SJ Hallam
Volume: 
111
Issue: 
31
Pages: 
11395-11400
Publication year: 
2014

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