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. See a complete list of Microscopy instruments.

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.

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.

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

The Asylum MFP-3D BIO is a versatile atomic force microscope (AFM) that combines molecular resolution imaging and picoNewton force-based...
Custodian(s): Kevin M. Rosso
Housed in EMSL's Radiochemistry Annex, the field emission electron microprobe (EMP) enables chemical analysis and imaging of radionuclides with high...
Custodian(s): Bruce Arey
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
The JEOL JEM-3000SFF was designed for high-resolution cryogenic transmission electron microscopy (cryo-EM) of biological samples and expands EMSL/...
This time-lapse fluorescence microscope with single molecule detection sensitivity is used to follow individual molecules or organelles in their...
Custodian(s): Galya Orr

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...
Dealuminated zeolite HY was used to support Ir(CO)2 complexes formed from Ir(CO)2(C5H7O2). Infrared and X-ray absorption spectra and atomic-...
We record sequences of Raman spectra at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated with 4,4’-...
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: January 13, 2015
The Science Lithium (Li) metal has long been considered one of the most attractive anode materials, but large-scale application of high-energy...
Posted: December 09, 2014
The Science Rechargeable lithium ion batteries are common in portable electronics and in some vehicles, but they cannot store enough energy for 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: 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’...

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. See a complete list of Microscopy instruments.

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.

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.

Iridium Complexes and Clusters in Dealuminated Zeolite HY: Distribution between Crystalline and Impurity Amorphous Regions.

Abstract: 

Dealuminated zeolite HY was used to support Ir(CO)2 complexes formed from Ir(CO)2(C5H7O2). Infrared and X-ray absorption spectra and atomic-resolution electron microscopy images identify these complexes, and the images and 27Al NMR spectra identify impurity amorphous regions in the zeolite where the iridium is more susceptible to aggregation than in the crystalline regions. The results indicate a significant stability limitation of metal in amorphous impurity regions of zeolites.

Citation: 
Martinez-Macias C, P Xu, SJ Hwang, J Lu, CY Chen, ND Browning, and BC Gates.2014."Iridium Complexes and Clusters in Dealuminated Zeolite HY: Distribution between Crystalline and Impurity Amorphous Regions."ACS Catalysis 4(8):2662–2666. doi:10.1021/cs5006426
Authors: 
C Martinez-Macias
P Xu
SJ Hwang
J Lu
CY Chen
ND Browning
BC Gates
Instruments: 
Volume: 
Issue: 
Pages: 
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

Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2.

Abstract: 

Photosynthetic microbes are of emerging interest as production organisms in biotechnology because they can grow autotrophically using sunlight, an abundant energy source, and CO2, a greenhouse gas. Important traits for such microbes are fast growth and amenability to genetic manipulation. Here we describe Synechococcus elongatus UTEX 2973, a unicellular cyanobacterium capable of rapid autotrophic growth, comparable to heterotrophic industrial hosts such as yeast. Synechococcus 2973 can be readily transformed for facile generation of desired knockout and knock-in mutations. Genome sequencing coupled with global proteomics studies revealed that Synechococcus 2973 is a close relative of the widely studied cyanobacterium Synechococcus elongatus PCC 7942, an organism that grows more than two times slower. A small number of nucleotide changes are the only significant differences between the genomes of these two cyanobacterial strains. Thus, our study has unraveled genetic determinants necessary for rapid growth of cyanobacterial strains of significant industrial potential.

Citation: 
Yu J, ML Liberton, P Cliften, R Head, JM Jacobs, RD Smith, DW Koppenaal, JJ Brand, and HB Pakrasi.2015."Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2."Scientific Reports 5:8132. doi:10.1038/srep08132
Authors: 
Yu J
ML Liberton
P Cliften
R Head
JM Jacobs
RD Smith
DW Koppenaal
JJ Br
HB Pakrasi
Facility: 
Volume: 
Issue: 
Pages: 
Publication year: 
2015

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

Vibronic Raman Scattering at the Quantum Limit of Plasmons.

Abstract: 

We record sequences of Raman spectra at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated with 4,4’-dimercaptostilbene (DMS). A 2D correlation analysis of the recorded trajectories reveals that the observable vibrational states can be divided into sub-sets. The first set comprises the totally symmetric vibrations of DMS (ag) that are neither correlated with each other nor to the fluctuating background, which is assigned to the signature of charge transfer plasmons tunneling through DMS. The second set consists of bu vibrations, which are correlated both with each other and with the continuum. Our findings are rationalized on the basis of the charge-transfer theory of Raman scattering, and illustrate how the tunneling plasmons modulate the vibronic coupling term from which the intensities of the bu states are derived.

Citation: 
El-Khoury PZ, and WP Hess.2014."Vibronic Raman Scattering at the Quantum Limit of Plasmons."Nano Letters 14(7):4114-4118. doi:10.1021/nl501690u
Authors: 
PZ El-Khoury
WP Hess
Facility: 
Volume: 
14
Issue: 
7
Pages: 
4114-4118
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

Formation of Interfacial Layer and Long-Term Cylability of Li-O-2 Batteries.

Abstract: 

Extended cycling of the Li-O2 battery under full discharge/charge conditions is achievable upon selection of appropriate electrode materials and cycling protocol. However, the decomposition of the side products also contribute to the observed good cycling behavior of high capacity Li-O2 batteries. Quantitative analyses of the discharge and charge products reveals a quick switch from the predominant formation of Li2O2 to the predominant formation of side products during the first a few cycles of the Li-O2 batteries. After the switch, cycling stabilizes with a repeatable formation of Li2O2/side products at ~1:2 ratio. CNTs/Ru composite electrodes exhibits lower charge voltage and deliver 50 full discharge-charge cycles without sharp capacity drop. Ru coated glass carbon electrode can lead to more than 500 cycles without change in its cycling profiles. The better understanding on Li-O2 reaction processes developed in this work may lead to the further improvement on the long term cycling behavior of high capacity Li-O2 batteries.

Citation: 
Nasybulin EN, W Xu, BL Mehdi, EC Thomsen, MH Engelhard, RC Masse, P Bhattacharya, M Gu, WD Bennett, Z Nie, CM Wang, ND Browning, and J Zhang.2014."Formation of Interfacial Layer and Long-Term Cylability of Li-O-2 Batteries."ACS Applied Materials & Interfaces 6(16):14141-14151. doi:10.1021/am503390q
Authors: 
EN Nasybulin
W Xu
BL Mehdi
EC Thomsen
MH Engelhard
RC Masse
P Bhattacharya
M Gu
WD Bennett
Z Nie
CM Wang
ND Browning
J Zhang
Facility: 
Instruments: 
Volume: 
6
Issue: 
16
Pages: 
14141-14151
Publication year: 
2014

Detailed Characterization of Particulates Emitted by Pre-Commercial Single-Cylinder Gasoline Compression Ignition Engine.

Abstract: 

Gasoline Compression Ignition (GCI) engines have the potential to achieve high fuel efficiency and to significantly reduce both NOx and particulate matter (PM) emissions by operating under dilute partially-premixed conditions. This low temperature combustion strategy is dependent upon direct-injection of gasoline during the compression stroke and potentially near top dead center (TDC). The timing and duration of the in-cylinder injections can be tailored based on speed and load to create optimized conditions that result in a stable combustion. We present the results of advanced aerosol analysis methods that have been used for detailed real-time characterization of PM emitted from a single-cylinder GCI engine operated at different speed, load, timing, and number and duration of near-TDC fuel injections. PM characterization included 28 measurements of size and composition of individual particles sampled directly from the exhaust and after mass and/or mobility classification. We use these data to calculate particle effective density, fractal dimension, dynamic shape factors in free-molecular and transition flow regimes, average diameter of primary spherules, number of spherules, and void fraction of soot agglomerates.

Citation: 
Zelenyuk A, P Reitz, ML Stewart, D Imre, P Loeper, C Adams, M Andrie, D Rothamer, DE Foster, K Narayanaswamy, PM Najt, and AS Solomon.2014."Detailed Characterization of Particulates Emitted by Pre-Commercial Single-Cylinder Gasoline Compression Ignition Engine."Combustion and Flame 161(8):2151-2164. doi:10.1016/j.combustflame.2014.01.011
Authors: 
A Zelenyuk
P Reitz
ML Stewart
D Imre
P Loeper
C Adams
M Andrie
D Rothamer
DE Foster
K Narayanaswamy
PM Najt
AS Solomon
Volume: 
161
Issue: 
8
Pages: 
2151-2164
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

Pages