Quiet Wing

EMSL’s Quiet Wing supports a wide range of research areas, including climate, biological, environmental and energy systems, of importance to the Department of Energy. It is among the most advanced quiet laboratories in the world for high-resolution imaging capabilities.

The Quiet Wing is a unique research environment housing a suite of ultrasensitive microscopy and scanning instruments. It was designed to help accelerate critical science by allowing state-of-the-art ultrasensitive microscopy equipment to operate at optimal resolution. A temperature-controlled facility, the wing’s design eliminates or reduces to a minimum the vibrations, acoustics and electromagnetic noise that can interfere with the resolution of ultrasensitive scientific instrumentation.

The 9,500-square-foot facility features eight quiet laboratory cells and a sample preparation area. The wing currently houses seven microscopy instruments and has room for one more. These microscopes are just a few of the extensive suite of microscopy instruments at EMSL available for scientific inquiry.

EMSL's microscopy capabilities, including those in the Quiet Wing, are available to the scientific community at typically no cost for openly published research. Scientists gain access to instruments and collaborate with onsite microscopy experts through a peer-reviewed proposal process. Learn more about becoming an EMSL user.

Learn more about each instrument and the science it advances on EMSL's YouTube channel and watch the video below on the Quiet Wing.

Related information:

Instruments

The JEOL JEM-3000SFF was designed for high-resolution cryogenic transmission electron microscopy (cryo-EM) of biological samples and expands EMSL/...
EMSL's ultra-high vacuum, low-temperature scanning probe microscope instrument, or UHV LT SPM, is the preeminent system dedicated to surface...
Custodian(s): Igor Lyubinetsky
EMSL's environmental transmission electron microscope (ETEM) is a state-of-the-art, Cs-corrected field emission gun (FEG) scanning transmission...
Custodian(s): Libor Kovarik
Type of Instrument:
Microscope
The Helium Ion Microscope promises to advance biological, geochemical, biogeochemical, and surface/interface studies using its combined surface...
EMSL's aberration-corrected Titan 80-300™ scanning/transmission electron microscope (S/TEM) provides high-resolution imaging with sub-angstrom...
Custodian(s): Chongmin Wang, Scott Lea

Science Highlights

Posted: October 07, 2014
The Science Steam reforming is a method for converting biomass-derived light hydrocarbons and aromatics into a mixture of carbon monoxide and...
Posted: August 03, 2014
The Science Nanocatalysts consisting of two metals can offer superior performance compared with those made up of only one metal, so they are widely...
Posted: April 15, 2014
Scientists at EMSL and Pacific Northwest National Laboratory are studying energy storage devices to make them last longer and be able to be...
Posted: March 12, 2014
The Science Lithium-sulfur batteries are promising options for electric vehicles and for storing renewable energy because they can store a lot of...
Posted: March 05, 2014
Lithium-ion batteries fade because the materials lose their structure in response to charging and discharging. This fading relates to electron-rich...

EMSL’s Quiet Wing supports a wide range of research areas, including climate, biological, environmental and energy systems, of importance to the Department of Energy. It is among the most advanced quiet laboratories in the world for high-resolution imaging capabilities.

The Quiet Wing is a unique research environment housing a suite of ultrasensitive microscopy and scanning instruments. It was designed to help accelerate critical science by allowing state-of-the-art ultrasensitive microscopy equipment to operate at optimal resolution. A temperature-controlled facility, the wing’s design eliminates or reduces to a minimum the vibrations, acoustics and electromagnetic noise that can interfere with the resolution of ultrasensitive scientific instrumentation.

The 9,500-square-foot facility features eight quiet laboratory cells and a sample preparation area. The wing currently houses seven microscopy instruments and has room for one more. These microscopes are just a few of the extensive suite of microscopy instruments at EMSL available for scientific inquiry.

EMSL's microscopy capabilities, including those in the Quiet Wing, are available to the scientific community at typically no cost for openly published research. Scientists gain access to instruments and collaborate with onsite microscopy experts through a peer-reviewed proposal process. Learn more about becoming an EMSL user.

Learn more about each instrument and the science it advances on EMSL's YouTube channel and watch the video below on the Quiet Wing.

Related information:

Molecular Selectivity of Brown Carbon Chromophores.

Abstract: 

Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

Citation: 
Laskin J, A Laskin, S Nizkorodov, PJ Roach, PA Eckert, MK Gilles, B Wang, HJ Lee, and Q Hu.2014."Molecular Selectivity of Brown Carbon Chromophores."Environmental Science & Technology 48(20):12047-12055. doi:10.1021/es503432r
Authors: 
J Laskin
A Laskin
S Nizkorodov
PJ Roach
PA Eckert
MK Gilles
B Wang
HJ Lee
Q Hu
Volume: 
48
Issue: 
20
Pages: 
12047-12055
Publication year: 
2014

Proteogenomic characterization of human colon and rectal cancer.

Abstract: 

We analyzed proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) and performed integrated proteogenomic analyses. Protein sequence variants encoded by somatic genomic variations displayed reduced expression compared to protein variants encoded by germline variations. mRNA transcript abundance did not reliably predict protein expression differences between tumors. Proteomics identified five protein expression subtypes, two of which were associated with the TCGA "MSI/CIMP" transcriptional subtype, but had distinct mutation and methylation patterns and associated with different clinical outcomes. Although CNAs showed strong cis- and trans-effects on mRNA expression, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. Our analyses identified HNF4A, a novel candidate driver gene in tumors with chromosome 20q amplifications. Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords novel insights into cancer biology.

Citation: 
Zhang B, J Wang, X Wang, J Zhu, Q Liu, Z Shi, MC Chambers, LJ Zimmerman, KF Shaddox, S Kim, S Davies, S Wang, P Wang, C Kinsinger, R Rivers, H Rodriguez, R Townsend, M Ellis, SA Carr, DL Tabb, RJ Coffey, R Slebos, and D Liebler.2014."Proteogenomic characterization of human colon and rectal cancer."Nature 513(7518):382-387. doi:10.1038/nature13438
Authors: 
B Zhang
J Wang
X Wang
J Zhu
Q Liu
Z Shi
MC Chambers
LJ Zimmerman
KF Shaddox
S Kim
S Davies
S Wang
P Wang
C Kinsinger
R Rivers
H Rodriguez
R Townsend
M Ellis
SA Carr
DL Tabb
RJ Coffey
R Slebos
D Liebler
Facility: 
Instruments: 
Volume: 
513
Issue: 
7518
Pages: 
382-387
Publication year: 
2014

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

Ion-induced swelling of ODS ferritic alloy MA957 tubing to 500 dpa.

Abstract: 

In order to study the potential swelling behavior of the ODS ferritic alloy MA957 at very high dpa levels, specimens were prepared from pressurized tubes that were unirradiated archives of tubes previously irradiated in FFTF to doses as high at 110 dpa. These unirradiated specimens were irradiated with 1.8 MeV Cr+ ions to doses ranging from 100 to 500 dpa and examined by transmission electron microscopy. No coinjection of helium or hydrogen was employed. It was shown that compared to several ferritic/martensitic steels irradiated in the same facility, these tubes were rather resistant to void swelling, reaching a maximum value of only 4.5% at 500 dpa and 450°C. In this fine-grained material, the distribution of swelling was strongly influenced by the presence of void denuded zones along the grain boundaries.

Citation: 
Toloczko MB, FA Garner, V Voyevodin, VV Bryk, OV Borodin, VV Melnichenko, and AS Kalchenko.2014."Ion-induced swelling of ODS ferritic alloy MA957 tubing to 500 dpa."Journal of Nuclear Materials 453(1-3):323-333. doi:10.1016/j.jnucmat.2014.06.011
Authors: 
MB Toloczko
FA Garner
V Voyevodin
VV Bryk
OV Borodin
VV Melnichenko
AS Kalchenko
Volume: 
453
Issue: 
Pages: 
323-333
Publication year: 
2014

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

Grain boundary depletion and migration during selective oxidation of Cr in a Ni-5Cr binary alloy exposed to high-temperature

Abstract: 

High-resolution microscopy of a high-purity Ni-5Cr alloy exposed to 360°C hydrogenated water reveals intergranular selective oxidation of Cr accompanied by local Cr depletion and diffusion-induced grain boundary migration (DIGM). The corrosion-product oxide consists of a porous, interconnected network of Cr2O3 platelets with no further O ingress into the metal ahead. Extensive grain boundary depletion of Cr (to <0.05at.%) is observed typically 20–100 nm wide as a result of DIGM and reaching depths of many micrometers beyond the oxidation front.

Citation: 
Schreiber DK, MJ Olszta, and SM Bruemmer.2014."Grain boundary depletion and migration during selective oxidation of Cr in a Ni-5Cr binary alloy exposed to high-temperature hydrogenated water."Scripta Materialia 89:41-44. doi:10.1016/j.scriptamat.2014.06.022
Authors: 
DK Schreiber
MJ Olszta
SM Bruemmer
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Competing retention pathways of uranium upon reaction with Fe(II).

Abstract: 

Biogeochemical retention processes, including adsorption, reductive precipitation, and incorporation into host minerals, are important in contaminant transport, remediation, and geologic deposition of uranium. Recent work has shown that U can become incorporated into iron (hydr)oxide minerals, with a key pathway arising from Fe(II)-induced transformation of ferrihydrite, (Fe(OH)3•nH2O) to goethite (α-FeO(OH)); this is a possible U retention mechanism in soils and sediments. Several key questions, however, remain unanswered regarding U incorporation into iron (hydr)oxides and this pathway’s contribution to U retention, including: (i) the competitiveness of U incorporation versus reduction to U(IV) and subsequent precipitation of UO2; (ii) the oxidation state of incorporated U; (iii) the effects of uranyl aqueous speciation on U incorporation; and, (iv) the mechanism of U incorporation. Here we use a series of batch reactions conducted at pH ~7, [U(VI)] from 1 to 170 μM, [Fe(II)] from 0 to 3 mM, and [Ca] at 0 or 4 mM) coupled with spectroscopic examination of reaction products of Fe(II)-induced ferrihydrite transformation to address these outstanding questions. Uranium retention pathways were identified and quantified using extended x-ray absorption fine structure (EXAFS) spectroscopy, x-ray powder diffraction, x-ray photoelectron spectroscopy, and transmission electron microscopy. Analysis of EXAFS spectra showed that 14 to 89% of total U was incorporated into goethite, upon reaction with Fe(II) and ferrihydrite. Uranium incorporation was a particularly dominant retention pathway at U concentrations ≤ 50 μM when either uranyl-carbonato or calcium-uranyl-carbonato complexes were dominant, accounting for 64 to 89% of total U. With increasing U(VI) and Fe(II) concentrations, U(VI) reduction to U(IV) became more prevalent, but U incorporation remained a functioning retention pathway. These findings highlight the potential importance of U(V) incorporation within iron oxides as a retention process of U across a wide range of biogeochemical environments and the sensitivity of uranium retention processes to operative (bio)geochemical conditions.

Citation: 
Massey MS, JS Lezama Pacheco, M Jones, ES Ilton, JM Cerrato, JR Bargar, and S Fendorf.2014."Competing retention pathways of uranium upon reaction with Fe(II)."Geochimica et Cosmochimica Acta 142:166-185. doi:10.1016/j.gca.2014.07.016
Authors: 
MS Massey
JS Lezama Pacheco
M Jones
ES Ilton
JM Cerrato
JR Bargar
S Fendorf
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Improved protocol to purify untagged amelogenin - Application to murine amelogenin containing the equivalent P70 → T point

Abstract: 

Amelogenin is the predominant extracellular protein responsible for converting carbonated hydroxyapatite into dental enamel, the hardest and most heavily mineralized tissue in vertebrates. Despite much effort, the precise mechanism by which amelogenin regulates enamel formation is not fully understood. To assist efforts aimed at understanding the biochemical mechanism of enamel formation, more facile protocols to purify recombinantly expressed amelogenin, ideally without any tag to assist affinity purification, are advantageous. Here we describe an improved method to purify milligram quantities of amelogenin that exploits its high solubility in 2% glacial acetic acid under conditions of low ionic strength. The method involves heating the frozen cell pellet for two 15 min periods at ~70 ºC with two minutes of sonication in between, dialysis twice in 2% acetic acid (1:250 v/v), and reverse phase chromatography. A further improvement in yield is obtained by resuspending the frozen cell pellet in 6 M guanidine hydrochloride in the first step. The acetic acid heating method is illustrated with a murine amelogenin containing the corresponding P70T point mutation observed in an human amelogenin associated with amelogenesis imperfecta (P71T), while the guanidine hydrochloride heating method is illustrated with wild type murine amelogenin (M180). The self-assembly properties of P71T were probed by NMR chemical shift perturbation studies as a function of protein (0.1 to 1.8 mM) and NaCl (0 to 367 mM) concentration. Relative to similar studies with wild type murine amelogenin, P71T self-associates at lower protein or salt concentrations with the interactions initiated near the N-terminus.

Citation: 
Buchko GW, and WJ Shaw.2015."Improved protocol to purify untagged amelogenin - Application to murine amelogenin containing the equivalent P70 ? T point mutation observed in human amelogenesis imperfecta."Protein Expression and Purification 105(1):14-22. doi:10.1016/j.pep.2014.09.020
Authors: 
GW Buchko
WJ Shaw
Instruments: 
Volume: 
105
Issue: 
1
Pages: 
14-22
Publication year: 
2015

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

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