Microscopy

Advancement in energy, environment and biology research relies heavily on micro-, nano- and atomic-scale chemical and structural imaging. Many microscopy instruments have high-resolution imaging capabilities including complementary chemical, structural and phase information, in-situ imaging in native environments and imaging of dynamic processes with high temporal-resolution.

Resources and Techniques

  • Nanoscale and sub-nanoscale imaging allows users to elucidate chemical processes and acquire structural data for a variety of samples such as nanostructures and cell-surface proteins.
  • Tomography yields three-dimensional reconstruction of transmission electron microscopy images generated for biological samples as well as for soft materials and samples with 3D structural heterogeneity.
  • Environmental particle analysis offers knowledge about non-volatile atmospheric particle composition and hydration properties using high-pressure scanning electron microscopy equipped with energy-dispersive x-ray analysis capability.
  • Environmental mode imaging techniques enable sample preservation to eliminate extensive preparation procedures that can introduce artifacts and make possible live-cell imaging and in situ imaging in liquids or controlled gas environments with high resolution microscopy.
  • Dynamic imaging capability enables real-time studies of nanosecond-scale dynamic processes with unprecedented spatial resolution, such as protein-protein interactions, with contrast at the single-molecule level.

In 2014, EMSL anticipates debuting its Dynamic Transmission Electron Microscope (DTEM) for the broad scientific community. It will enable dynamic in suit observation of cellular systems and components at near-atomic spatial resolution and nanosecond time resolution.

Quiet Wing for Advanced Microscopy
Seven microscopes are housed in the Quiet Wing, a space specially designed to reduce external factors, such as vibrations and electromagnetic fields, that can impede capture of high-resolution images. Read more about the Quiet Wing and its instrumentation.

Additonal Information:

Description

Capability Details

• Electron microscopes with tomography, cryo, scanning, photoemission and high-resolution (sub-nanometer) imaging capabilities
• Focused ion beam/scanning electron microscopes for specialized sample preparation and three-dimensional topographic and chemical imaging
• Nuclear magnetic resonance microscopy with 10-40-_m resolution to study the anatomy, metabolism and transport processes of live cell cultures, biofilms and tissue samples
• Dual Raman confocal microscope for analysis of radiological samples
• Single-molecule fluorescence tools to study molecular interactions in real time
• Scanning probe microscopy with capabilities ranging from examination of dynamic nanoscale processes in condensed environments to high resolution studies of catalysis materials in ultra-high vacuum.

 

Instruments

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
Type of Instrument:
Microscope
EMSL's ultra-high vacuum, variable-temperature scanning probe microscope system, or UHV VT SPM, is a state-of-the-art surface science tool...
Custodian(s): Igor Lyubinetsky
The LEAP® 4000 XHR local electrode atom probe tomography instrument enabled the first-ever comprehensive and accurate 3-D chemical imaging studies...
Custodian(s): Arun Devaraj, Daniel Perea
This FEI Tecnai T-12 cryo-transmission electron microscope (TEM) complements EMSL's broader microscopy suite and JEOL 2010 analytical high-...
Custodian(s): Alice Dohnalkova
The environmental scanning electron microscope (ESEM) is a new-generation SEM that can image samples under controlled environments and temperatures...
Custodian(s): Alexander Laskin, Scott Lea

Publications

Electrochemical performance of the existing state-of-the art capacitors is not very high, key scientific barrier is that its charge storage mechanism...
The metallic compound MnBi is a promising rare-earth-free permanent magnet material. Compare to other rare-earth-free candidates, MnBi stands out for...
We report on ab initio molecular dynamics simulations of Ca-rich montmorillonite systems, in different hydration states in the presence of...
In H2 fuel cells, performance depends on factors controlling turnover frequency and energy efficiency in the electrocatalytic oxidation of H2. Nature...
Understanding hydrogen formation on TiO2 surfaces is of great importance as it could provide fundamental insight into water splitting for hydrogen...

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: September 22, 2014
Phototrophs are organisms that use sunlight to convert inorganic materials to organic materials. Researchers are studying these organisms’...
Posted: September 15, 2014
Knowing the distribution of atoms on the surfaces of electrodes or other materials could benefit the development of longer lasting batteries and...
Posted: September 08, 2014
The Science The formation of ice crystals in the atmosphere strongly affects cloud dynamics, cloud radiative properties and the water vapor budget,...
Posted: September 08, 2014
Scientists have found it difficult to probe nanomaterials in liquids when using in situ liquid transmission electron microscopy, or TEM, and...

Advancement in energy, environment and biology research relies heavily on micro-, nano- and atomic-scale chemical and structural imaging. Many microscopy instruments have high-resolution imaging capabilities including complementary chemical, structural and phase information, in-situ imaging in native environments and imaging of dynamic processes with high temporal-resolution.

Resources and Techniques

  • Nanoscale and sub-nanoscale imaging allows users to elucidate chemical processes and acquire structural data for a variety of samples such as nanostructures and cell-surface proteins.
  • Tomography yields three-dimensional reconstruction of transmission electron microscopy images generated for biological samples as well as for soft materials and samples with 3D structural heterogeneity.
  • Environmental particle analysis offers knowledge about non-volatile atmospheric particle composition and hydration properties using high-pressure scanning electron microscopy equipped with energy-dispersive x-ray analysis capability.
  • Environmental mode imaging techniques enable sample preservation to eliminate extensive preparation procedures that can introduce artifacts and make possible live-cell imaging and in situ imaging in liquids or controlled gas environments with high resolution microscopy.
  • Dynamic imaging capability enables real-time studies of nanosecond-scale dynamic processes with unprecedented spatial resolution, such as protein-protein interactions, with contrast at the single-molecule level.

In 2014, EMSL anticipates debuting its Dynamic Transmission Electron Microscope (DTEM) for the broad scientific community. It will enable dynamic in suit observation of cellular systems and components at near-atomic spatial resolution and nanosecond time resolution.

Quiet Wing for Advanced Microscopy
Seven microscopes are housed in the Quiet Wing, a space specially designed to reduce external factors, such as vibrations and electromagnetic fields, that can impede capture of high-resolution images. Read more about the Quiet Wing and its instrumentation.

Additonal Information:

Effect of Composition and Heat Treatment on MnBi Magnetic Materials.

Abstract: 

The metallic compound MnBi is a promising rare-earth-free permanent magnet material. Compare to other rare-earth-free candidates, MnBi stands out for its high intrinsic coercivity (Hci) and its large positive temperature coefficient. Several groups have demonstrated that the Hci of MnBi compound in thin film or in powder form can exceed 12 kOe and 26 kOe at 300 K and 523 K, respectively. Such steep increase in Hci with increasing temperature is unique to MnBi. Consequently, MnBi is a highly sought-after hard phase for exchange coupling nanocomposite magnets. The reaction between Mn and Bi is peritectic, so Mn tends to precipitate out of the MnBi liquid during the solidification process. As result, the composition of the Mn-Bi alloy with the largest amount of the desired LTP (low temperature phase) MnBi and highest saturation magnetization will be over-stoichiometric and rich in Mn. The amount of additional Mn required to compensate the Mn precipitation depends on solidification rate: the faster the quench speed, the less Mn precipitates. Here we report a systematic study of the effect of composition and heat treatments on the phase contents and magnetic properties of Mn-Bi alloys. In this study, Mn-Bi alloys with 14 compositions were prepared using conventional metallurgical methods such as arc melting and vacuum heat treatment, and the obtained alloys were analyzed for compositions, crystal structures, phase content, and magnetic properties. The results show that the composition with 55 at.% Mn exhibits the highest LTP MnBi content and the highest magnetization. The sample with this composition shows >90 wt.% LTP MnBi content. Its measured saturation magnetization is 68 emu/g with 2.3 T applied field at 300 K; its coercivity is 13 kOe and its energy product is 12 MGOe at 300 K. A bulk magnet fabricated using this powder exhibits an energy product of 8.2 MGOe.

Citation: 
Cui J, JP Choi, E Polikarpov, ME Bowden, W Xie, G Li, Z Nie, N Zarkevich, MJ Kramer, and DD Johnson.2014."Effect of Composition and Heat Treatment on MnBi Magnetic Materials."Acta Materialia 79:374-381. doi:10.1016/j.actamat.2014.07.034
Authors: 
J Cui
JP Choi
E Polikarpov
ME Bowden
W Xie
G Li
Z Nie
N Zarkevich
MJ Kramer
DD Johnson
Volume: 
Issue: 
Pages: 
Publication year: 
2014

In Situ One-Step Synthesis of Hierarchical Nitrogen-Doped Porous Carbon for High Performance Supercapacitors.

Abstract: 

Electrochemical performance of the existing state-of-the art capacitors is not very high, key scientific barrier is that its charge storage mechanism wholly depends on adsorption of electrolyte on electrode. We present a novel method for the synthesis of nitrogen -doped porous carbons and address the drawback by precisely controlling composition and surface area. Nitrogen-doped porous carbon was synthesized using a self-sacrificial template technique without any additional nitrogen and carbon sources. They exhibited exceptionally high capacitance (239 Fg-1) due to additional pseudocapacitance originating from doped nitrogen. Cycling tests showed no obvious capacitance decay even after 10,000 cycles, which meets the requirement of commercial supercapacitors. Our method is simple and highly efficient for the production of large quantities of nitrogen-doped porous carbons.

Citation: 
Jeon JW, R Sharma, P Meduri, BW Arey, HT Schaef, J Lutkenhaus, JP Lemmon, PK Thallapally, MI Nandasiri, BP McGrail, and SK Nune.2014."In Situ One-Step Synthesis of Hierarchical Nitrogen-Doped Porous Carbon for High Performance Supercapacitors."ACS Applied Materials & Interfaces 6(10):7214-7222. doi:10.1021/am500339x
Authors: 
JW Jeon
R Sharma
P Meduri
BW Arey
HT Schaef
J Lutkenhaus
JP Lemmon
PK Thallapally
MI Nasiri
BP McGrail
SK Nune
Instruments: 
Volume: 
6
Issue: 
10
Pages: 
7214-7222
Publication year: 
2014

Microstructural Response of Variably Hydrated Ca-Rich Montmorillonite to Supercritical CO2.

Abstract: 

We report on ab initio molecular dynamics simulations of Ca-rich montmorillonite systems, in different hydration states in the presence of supercritical CO2. Analysis of the molecular trajectories provides estimates of the relative H2O:CO2 ratio per interspatial cation. The vibrational density of states in direct comparison with dipole moment derived IR spectra for these systems provide unique signatures that can used to follow molecular transformation. In a co-sequestration scenario, these signatures could be used to identify the chemical state and fate of Sulfur compounds. Interpretation of CO2 asymmetric stretch shift is given based on a detailed analysis of scCO2 structure and intermolecular interactions of the intercalated species. Based on our simulations, smectites with higher charge interlayer cations at sub-single to single hydration states should be more efficient in capturing CO2, while maintaining caprock integrity. This research would not have been possible without the support of the office of Fossil Energy, Department of Energy. The computational resources were made available through a user proposal of the EMSL User facility, 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: 
Lee MS, BP McGrail, and VA Glezakou.2014."Microstructural Response of Variably Hydrated Ca-Rich Montmorillonite to Supercritical CO2."Environmental Science & Technology 48(15):8612-8619. doi:10.1021/es5005889
Authors: 
MS Lee
BP McGrail
VA Glezakou
Instruments: 
Volume: 
48
Issue: 
15
Pages: 
8612-8619
Publication year: 
2014

Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs.

Abstract: 

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521.

Citation: 
Parenteau MN, LL Jahnke, JD Farmer, and SL Cady.2014."Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs."Astrobiology 14(6):, doi:10.1089/ast.2013.1122
Authors: 
MN Parenteau
LL Jahnke
JD Farmer
SL Cady
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Structures and Stabilities of (MgO)n Nanoclusters.

Abstract: 

Global minima for (MgO)n structures were optimized using a tree growth−hybrid genetic algorithm in conjunction with MNDO/MNDO/d semiempirical molecular orbital calculations followed by density functional theory geometry optimizations with the B3LYP functional. New lowest energy isomers were found for a number of (MgO)n clusters. The most stable isomers for (MgO)n (n > 3) are 3-dimensional. For n < 20, hexagonal tubular (MgO)n structures are more favored in energy than the cubic structures. The cubic structures and their variations dominate after n = 20. For the cubic isomers, increasing the size of the cluster in any dimension improves the stability. The effectiveness of increasing the size of the cluster in a specific dimension to improve stability diminishes as the size in that dimension increases. For cubic structures of the same size, the most compact cubic structure is expected to be the more stable cubic structure. The average Mg−O bond distance and coordination number both increase as n increases. The calculated average Mg−O bond distance is 2.055 Å at n = 40, slightly smaller than the bulk value of 2.104 Å. The average coordination number is predicted to be 4.6 for the lowest energy (MgO)40 as compared to the bulk value of 6. As n increases, the normalized clustering energy ΔE(n) for the (MgO)n increases and the slope of the ΔE(n)vs n curve decreases. The value of ΔE(40) is predicted to be 150 kcal/mol, as compared to the bulk value ΔE(∞) = 176 kcal/mol. The electronic properties of the clusters are presented and the reactive sites are predicted to be at the corners.

Citation: 
Chen M, AR Felmy, and DA Dixon.2014."Structures and Stabilities of (MgO)n Nanoclusters."Journal of Physical Chemistry A 118(17):3136-3146. doi:10.1021/jp412820z
Authors: 
M Chen
AR Felmy
DA Dixon
Instruments: 
Volume: 
118
Issue: 
17
Pages: 
3136-3146
Publication year: 
2014

Physical Properties of Ambient and Laboratory-Generated Secondary Organic Aerosol.

Abstract: 

The size and thickness of organic aerosol particles collected by impaction in five field campaigns were compared to those of laboratory generated secondary organic aerosols (SOA). Scanning transmission x-ray microscopy (STXM) was used to measure the total carbon absorbance (TCA) by individual particles as a function of their projection areas on the substrate. Because they flatten less upon impaction, particles with higher viscosity and surface tension can be identified by a steeper slope on a plot of TCA vs. size. The slopes of the ambient data are statistically similar indicating a small range of average viscosities and surface tensions across five field campaigns. Steeper slopes were observed for the plots corresponding to ambient particles, while smaller slopes were indicative of the laboratory generated SOA. This comparison indicates that ambient organic particles have higher viscosities and surface tensions than those typically generated in laboratory SOA studies.

Citation: 
O'Brien RE, A Neu, SA Epstein, A MacMillan, B Wang, ST Kelly, S Nizkorodov, A Laskin, RC Moffet, and MK Gilles.2014."Physical Properties of Ambient and Laboratory-Generated Secondary Organic Aerosol."Geophysical Research Letters 41(2):4347-4353. doi:10.1002/2014GL060219
Authors: 
RE O'Brien
A Neu
SA Epstein
A MacMillan
B Wang
ST Kelly
S Nizkorodov
A Laskin
RC Moffet
MK Gilles
Facility: 
Volume: 
41
Issue: 
2
Pages: 
4347-4353
Publication year: 
2014

Oxidative Remobilization of Technetium Sequestered by Sulfide-Transformed Nano Zerovalent Iron.

Abstract: 

The dissolution of Tc(IV) sulfide and concurrent transformation of sulfidated ZVI during 2 oxidation were examined. Kinetic data obtained with 10 mL batch reactors showed that Tc(VII) 3 reduced by sulfidated nZVI has significantly slower reoxidation rates than Tc(VII) reduced by 4 nZVI only. In a 50 mL batch reactor, initial inhibition of Tc(IV) dissolution was apparent and 5 lasted until 120 hours at S/Fe = 0.112, presumably due to the redox buffer capacity of FeS. This 6 is evidenced by the parallel trends in oxidation-reduction potentials (ORP) and Tc dissolution 7 kinetics. Mӧssbauer spectra and micro X-ray diffraction of S/Fe = 0.112 suggested the 8 persistence of FeS after 24-h oxidation although X-ray photoelectron spectroscopy indicated 9 substantial surface oxidation. After 120-h oxidation, all characterizations showed complete 10 oxidation of FeS, which further indicates that FeS inhibits Tc oxidation. X-ray absorption 11 spectroscopy for S/Fe = 0.011 showed significantly increasing percentage of TcS2 in the solid 12 phase after 24-h oxidation, indicating TcS2 is more resistant to oxidation than TcO2. At S/Fe = 13 0.112, the XAS results revealed significant transformation of Tc speciation from TcS2 to TcO2 14 after 120-h oxidation at S/Fe = 0.112. Given that no apparent Tc dissolution occurred during this 15 period, the speciation transformation might play a secondary role in hindering Tc oxidation, 16 especially as redox buffer capacity approached depletion.

Citation: 
Fan D, R Anitori, BM Tebo, PG Tratnyek, JS Lezama Pacheco, RK Kukkadapu, L Kovarik, MH Engelhard, and ME Bowden.2014."Oxidative Remobilization of Technetium Sequestered by Sulfide-Transformed Nano Zerovalent Iron."Environmental Science & Technology 48(13):7409-7417. doi:10.1021/es501607s
Authors: 
D Fan
R Anitori
BM Tebo
PG Tratnyek
JS Lezama Pacheco
RK Kukkadapu
L Kovarik
MH Engelhard
ME Bowden
Instruments: 
Volume: 
48
Issue: 
13
Pages: 
7409-7417
Publication year: 
2014

Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams.

Abstract: 

High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral resolution are needed to enable this. In this report, we employed Bi3 bombardment time-of-flight (Bi3 ToF-SIMS) and C60 bombardment Fourier transform ion cyclotron resonance secondary ion mass spectrometry (C60 FTICR-SIMS) to image Dictyostelium discoideum aggregation streams. Nearly 300 lipid species were identified from the aggregation streams. High resolution mass spectrometry imaging (FTICR-SIMS) enabled the generation of multiple molecular ion maps at the nominal mass level and provided good coverage for fatty acyls, prenol lipids, and sterol lipids. The comparison of Bi3 ToF-SIMS and C60 FTICR-SIMS suggested that while the first provides fast, high spatial resolution molecular ion images, the chemical complexity of biological samples warrants the use of high resolution analyzers for accurate ion identification.

Citation: 
Debord JD, DF Smith, CR Anderton, RM Heeren, L Pasa-Tolic, RH Gomer, and FA Fernandez-Lima.2014."Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams."PLoS One 9(6):e99319. doi:10.1371/journal.pone.0099319
Authors: 
JD Debord
DF Smith
CR Anderton
RM Heeren
L Pasa-Tolic
RH Gomer
FA Fernez-Lima
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

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