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.

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...
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

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere...
Long-range electron transfer (ET) plays a key role in many biological energy conversion and synthesis processes. We show that nonlinear spectroscopy...
Results from enriched 57Fe isotope tracer experiments have shown that atom exchange can occur between structural Fe in Fe(III) oxides and aqueous Fe(...
Using a traditional aqueous solution ion-exchange method under a protecting atmosphere of N2, an Fe/SSZ-13 catalyst active in NH3-SCR was synthesized...
Atom flux sensors based on atomic absorption (AA) spectroscopy are of significant interest in thin film growth as they can provide unobtrusive,...

Science Highlights

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...
Posted: November 04, 2014
The Science Projecting variations in the carbon cycle is important for predicting long-term climate changes. However, climate models used to...
Posted: September 02, 2014
The impacts of soil moisture on the carbon cycle are well known from previous research. However, interactions among soil moisture, groundwater and...

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.

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

Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity .

Abstract: 

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the
catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni–Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.

Citation: 
Smith DMA, S Raugei, and TC Squier.2014."Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity ."Physical Chemistry Chemical Physics. PCCP 16(43):24026-24033. doi:10.1039/c4cp03518f
Authors: 
DMA Smith
S Raugei
TC Squier
Facility: 
Volume: 
16
Issue: 
43
Pages: 
24026-24033
Publication year: 
2014

Fe/SSZ-13 as an NH3-SCR Catalyst: A Reaction Kinetics and FTIR/Mössbauer Spectroscopic Study.

Abstract: 

Using a traditional aqueous solution ion-exchange method under a protecting atmosphere of N2, an Fe/SSZ-13 catalyst active in NH3-SCR was synthesized. Mössbauer and FTIR spectroscopies were used to probe the nature of the Fe sites. In the fresh sample, the majority of Fe species are extra-framework cations. The likely monomeric and dimeric ferric ions in hydrated form are [Fe(OH)2]+ and [HO-Fe-O-Fe-OH]2+, based on Mössbauer measurements. During the severe hydrothermal aging (HTA) applied in this study, a majority of cationic Fe species convert to FeAlOx and clustered FeOx species, accompanied by severe dealumination of the SSZ-13 framework. The clustered FeOx species do not give a sextet Mössbauer spectrum, indicating that these are highly disordered. However, some Fe species in cationic positions remain after aging as determined from Mössbauer measurements and CO/NO FTIR titrations. NO/NH3 oxidation reaction tests reveal that dehydrated cationic Fe are substantially more active in catalyzing oxidation reactions than the hydrated ones. For NH3-SCR, enhancement of NO oxidation under ‘dry’ conditions promotes SCR rates below ~300 C. This is due mainly to contribution from the “fast” SCR channel. Above ~300 C, enhancement of NH3 oxidation under ‘dry’ conditions, however, becomes detrimental to NOx conversions. The HTA sample loses much of the SCR activity below ~300 C; however, above ~400 C much of the activity remains. This may suggest that the FeAlOx and FeOx species become active at such elevated temperatures. Alternatively, the high-temperature activity may be maintained by the remaining extra-framework cationic species. For potential practical applications, Fe/SSZ-13 may be used as a co-catalyst for Cu/CHA as integral aftertreatment SCR catalysts on the basis of the stable high temperature activity after hydrothermal aging. The authors gratefully acknowledge the US Department of Energy (DOE), Energy Efficiency and Renewable Energy, Vehicle Technologies Office for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.

Citation: 
Gao F, M Kollar, RK Kukkadapu, NM Washton, Y Wang, J Szanyi, and CHF Peden.2015."Fe/SSZ-13 as an NH3-SCR Catalyst: A Reaction Kinetics and FTIR/Mössbauer Spectroscopic Study."Applied Catalysis. B, Environmental 164:407-419. doi:10.1016/j.apcatb.2014.09.031
Authors: 
F Gao
M Kollar
RK Kukkadapu
NM Washton
Y Wang
J Szanyi
CHF Peden
Volume: 
Issue: 
Pages: 
Publication year: 
2015

Fe(II)-catalyzed Recrystallization of Goethite Revisited.

Abstract: 

Results from enriched 57Fe isotope tracer experiments have shown that atom exchange can occur between structural Fe in Fe(III) oxides and aqueous Fe(II) with no formation of secondary minerals or change in particle size or shape. Here we derive a mass balance model to quantify the extent of Fe atom exchange between goethite and aqueous Fe(II) that accounts for different Fe pool sizes. We use this model to reinterpret our previous work and to quantify the influence of particle size and pH on extent of goethite exchange with aqueous Fe(II). Consistent with our previous interpretation, substantial exchange of goethite occurred at pH 7.5 (≈ 90%) and we observed little effect of particle size between nanogoethite (81 x 11 nm) and microgoethite (590 x 42 nm). Despite ≈ 90% of the bulk goethite exchanging at pH 7.5, we found no change in mineral phase, particle size, crystallinity, or reactivity after reaction with aqueous Fe(II). At a lower pH of 5.0, no net sorption of Fe(II) was observed and significantly less exchange occurred accounting for less than the estimated proportion of surface Fe atoms in the particles. Particle size appears to influence the amount of exchange at pH 5.0 and we suggest that aggregation and surface area may play a role. Results from sequential chemical extractions indicate that 57Fe accumulates in extracted Fe(III) goethite components. Isotopic compositions of the extracts indicate that a gradient of 57Fe develops within the goethite with more accumulation of 57Fe occurring in the more easily extracted Fe(III) that may be nearer to the surface. We interpret our particle size, pH, and sequential extraction findings as consistent with the mechanism of interfacial electron transfer and bulk conduction previously proposed to explain the substantial Fe atom exchange observed in goethite in contact with aqueous Fe(II).

Citation: 
Handler R, AJ Frierdich, C Johnson, KM Rosso, B Beard, CM Wang, D Latta, A Neumann, TS Pasakarnis, WAPJ Premaratne, and M Scherer.2014."Fe(II)-catalyzed Recrystallization of Goethite Revisited."Environmental Science & Technology 48(19):11302-11311. doi:10.1021/es503084u
Authors: 
R Hler
AJ Frierdich
C Johnson
KM Rosso
B Beard
CM Wang
D Latta
A Neumann
TS Pasakarnis
WAPJ Premaratne
M Scherer
Volume: 
48
Issue: 
19
Pages: 
11302-11311
Publication year: 
2014

Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy.

Abstract: 

Long-range electron transfer (ET) plays a key role in many biological energy conversion and synthesis processes. We show that nonlinear spectroscopy with attosecond X-ray pulses provides a real time movie of the evolving oxidation states and electron densities around atoms, and can probe these processes with high spatial and temporal resolution. This is demonstrated in a simulation study of the stimulated X-ray Raman (SXRS) signals in Re-modified azurin, which had long served as a benchmark for long-range ET in proteins. Nonlinear SXRS signals are sensitive to the local electronic structure and should offer a novel window for long-range ET.

Citation: 
Zhang Y, J Biggs, N Govind, and S Mukamel.2014."Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy."The Journal of Physical Chemistry Letters 5(21):3656-3661. doi:10.1021/jz501966h
Authors: 
Y Zhang
J Biggs
N Govind
S Mukamel
Volume: 
5
Issue: 
21
Pages: 
3656-3661
Publication year: 
2014

In-Situ Transmission Electron Microscopy Probing of Native Oxide and Artificial Layers on Silicon Nanoparticles for Lithium Ion

Abstract: 

Surface modification of silicon nanoparticle via molecular layer deposition (MLD) has been recently proved to be an effective way for dramatically enhancing the cyclic performance in lithium ion batteries. However, the fundamental mechanism as how this thin layer of coating function is not known, which is even complicated by the inevitable presence of native oxide of several nanometers on the silicon nanoparticle. Using in-situ TEM, we probed in detail the structural and chemical evolution of both uncoated and coated silicon particles upon cyclic lithiation/delithation. We discovered that upon initial lithiation, the native oxide layer converts to crystalline Li2O islands, which essentially increases the impedance on the particle, resulting in ineffective lithiation/delithiation, and therefore low coulombic efficiency. In contrast, the alucone MLD coated particles show extremely fast, thorough and highly reversible lithiation behaviors, which are clarified to be associated with the mechanical flexibility and fast Li+/e- conductivity of the alucone coating. Surprisingly, the alucone MLD coating process chemically changes the silicon surface, essentially removing the native oxide layer and therefore mitigates side reaction and detrimental effects of the native oxide. This study provides a vivid picture of how the MLD coating works to enhance the coulombic efficiency and preserve capacity and clarifies the role of the native oxide on silicon nanoparticles during cyclic lithiation and delithiation. More broadly, this work also demonstrated that the effect of the subtle chemical modification of the surface during the coating process may be of equal importance as the coating layer itself.

Citation: 
He Y, DM Piper, M Gu, JJ Travis, SM George, SH Lee, A Genc, L Pullan, J Liu, SX Mao, J Zhang, C Ban, and CM Wang.2014."In-Situ Transmission Electron Microscopy Probing of Native Oxide and Artificial Layers on Silicon Nanoparticles for Lithium Ion Batteries."ACS Nano 8(11):11816-11823. doi:10.1021/nn505523c
Authors: 
He Y
DM Piper
M Gu
JJ Travis
SM George
SH Lee
A Genc
L Pullan
J Liu
SX Mao
J Zhang
C Ban
CM Wang
Volume: 
8
Issue: 
11
Pages: 
11816-11823
Publication year: 
2014

Enhancing the Lithiation Rate of Silicon Nanowires by the Inclusion of Tin.

Abstract: 

Silicon (Si) has a very high lithium storage capacity and is being explored as a negative electrode material in lithium-ion batteries (LIBs). Si nanowires can exhibit relatively stable performance for many cycles of charging; however, conductive carbon must often be added to the electrode layer to improve the rate capability due to the relatively low electrical conductivity of Si. The added carbon lowers the capacity of the electrode. Here, we show that the rate capability of Si in LIBs can be substantially enhanced by incorporating tin (Sn) into Si nanowires. The solubility of Sn in Si is very low (0.015 at%); yet, Sn used as a seed for supercritical fluid–liquid–solid (SFLS) growth can be trapped in Si nanowires with relatively high concentration (10 at%). Such Sn-containing Si nanowires and no added conductive carbon in the electrode layer, could be cycled in LIBs with high capacity (*1000 mA h g*1 over 100 cycles) at a current density of 2.8 A g*1 (1 C). Capacities exceeding that of graphite could still be reached at cycle rates as high as 2 C. Real-time in situ transmission electron microscopy (TEM) revealed that lithiation occurs five times faster in Si nanowires with significant amounts of Sn than in the Si nanowires without Sn, and twice as fast as in nanowires that were coated with carbon.

Citation: 
Bogart TD, X Lu, M Gu, CM Wang, and BA Korgel.2014."Enhancing the Lithiation Rate of Silicon Nanowires by the Inclusion of Tin."RSC Advances 4(79):42022-42028. doi:10.1039/c4ra07418a
Authors: 
TD Bogart
X Lu
M Gu
CM Wang
BA Korgel
Volume: 
4
Issue: 
79
Pages: 
42022-42028
Publication year: 
2014

Describing excited state relaxation and localization in TiO2 nanoparticles using TD-DFT.

Abstract: 

We have investigated the description of excited state relaxation in naked and hydrated TiO2 nanoparticles using Time-Dependent Density Functional Theory (TD-DFT) with three common hybrid exchange-correlation (XC) potentials; B3LYP, CAM-B3LYP and BHLYP. Use of TD-CAM-B3LYP and TD-BHLYP yields qualitatively similar results for all structures, which are also consistent with predictions of coupled cluster theory for small particles. TD-B3LYP, in contrast, is found to make rather different predictions; including apparent conical intersections for certain particles that are not observed with TD-CAM-B3LYP nor with TD-BHLYP. In line with our previous observations for vertical excitations, the issue with TD-B3LYP appears to be the inherent tendency of TD-B3LYP, and other XC potentials with no or a low percentage of Hartree-Fock Like Exchange, to spuriously stabilize the energy of charge-transfer (CT) states. Even in the case of hydrated particles, for which vertical excitations are generally well described with all XC potentials, the use of TD-B3LYP appears to result in CT-problems for certain particles. We hypothesize that the spurious stabilization of CT-states by TD-B3LYP even may drive the excited state optimizations to different excited state geometries than those obtained using TD-CAM-B3LYP or TD-BHLYP. Finally, focusing on the TD-CAM-B3LYP and TD-BHLYP results, excited state relaxation in naked and hydrated TiO2 nanoparticles is predicted to be associated with a large Stokes’ shift.

Citation: 
Berardo E, H Hu, HJJ van Dam, SA Shevlin, SM Woodley, K Kowalski, and MA Zwijnenburg.2014."Describing excited state relaxation and localization in TiO2 nanoparticles using TD-DFT."Journal of Chemical Theory and Computation 10(12):5538-5548. doi:10.1021/ct500787x
Authors: 
E Berardo
H Hu
HJJ van Dam
SA Shevlin
SM Woodley
K Kowalski
MA Zwijnenburg
Volume: 
10
Issue: 
12
Pages: 
5538-5548
Publication year: 
2014

Shell Model for Atomistic Simulation of Lithium Diffusion in Mixed Mn/Ti Oxides.

Abstract: 

Mixed Mn/Ti oxides present attractive physicochemical properties such as their ability to accommodate Li for application in Li-ion batteries. In this work, atomic parameters for Mn were developed to extend an existing shell model of the Li-Ti-O system and allow simulations of pure and lithiated Mn and mixed Mn/Ti oxide polymorphs. The shell model yielded good agreement with experimentally-derived structures (i.e. lattice parameters and inter-atomic distances) and represented an improvement over existing potential models. The shell model was employed in molecular dynamics (MD) simulations of Li diffusion in the 1×1 c direction channels of LixMn1 yTiyO2 with the rutile structure, where 0 ≤ x ≤ 0.25 and 0 ≤ y ≤ 1. In the infinite dilution limit, the arrangement of Mn and Ti ions in the lattice was found to have a significant effect on the activation energy for Li diffusion in the c channels due to the destabilization of half of the interstitial octahedral sites. Anomalous diffusion was demonstrated for Li concentrations as low as x = 0.125, with a single Li ion positioned in every other c channel. Further increase in Li concentration showed not only the substantial effect of Li-Li repulsive interactions on Li mobility but also their influence on the time dependence of Li diffusion. The results of the MD simulations can inform intrinsic structure-property relationships for the rational design of improved electrode materials for Li-ion batteries.

Citation: 
Kerisit SN, AM Chaka, TC Droubay, and ES Ilton.2014."Shell Model for Atomistic Simulation of Lithium Diffusion in Mixed Mn/Ti Oxides."Journal of Physical Chemistry C 118(42):24231-24239. doi:10.1021/jp506025k
Authors: 
SN Kerisit
AM Chaka
TC Droubay
ES Ilton
Volume: 
118
Issue: 
42
Pages: 
24231-24239
Publication year: 
2014

Etalon-induced Baseline Drift And Correction In Atom Flux Sensors Based On Atomic Absorption Spectroscopy.

Abstract: 

Atom flux sensors based on atomic absorption (AA) spectroscopy are of significant interest in thin film growth as they can provide unobtrusive, element specific, real-time flux sensing and control. The ultimate sensitivity and performance of the sensors are strongly affected by the long-term and short term baseline drift. Here we demonstrate that an etalon effect resulting from temperature changes in optical viewport housings is a major source of signal instability which has not been previously considered or corrected by existing methods. We show that small temperature variations in the fused silica viewports can introduce intensity modulations of up to 1.5%, which in turn significantly deteriorate AA sensor performance. This undesirable effect can be at least partially eliminated by reducing the size of the beam and tilting the incident light beam off the viewport normal.

Citation: 
Du Y, and SA Chambers.2014."Etalon-induced Baseline Drift And Correction In Atom Flux Sensors Based On Atomic Absorption Spectroscopy."Applied Physics Letters 105(16):163113(1)-163113(5). doi:10.1063/1.4898638
Authors: 
Du Y
SA Chambers
Volume: 
Issue: 
Pages: 
Publication year: 
2014

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