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.

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

Li-rich and Mn-rich (LMR) layered structured materials are very promising cathodes for high-energy lithium-ion batteries. However, their fundamental...
The recent development of in situ liquid stages for (scanning) transmission electron microscopes now makes it possible for us to study the details of...
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional...
In mass spectrometry (MS)-based proteomics, accurate estimation of statistical signicance of peptide and protein identications is desired for...
The Stopping and Range of Ions in Matter (SRIM) code has been widely used to predict nuclear stopping power and angular distribution of ion-solid...

Science Highlights

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...
Posted: August 29, 2014
The goal is for the soft nanoparticles to move through the body and attack cancerous cells, destroying only the diseased tissue. The challenge is to...

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.

Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates.

Abstract: 

An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

Citation: 
Chaka AM, and AR Felmy.2014."Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates."Journal of Physical Chemistry A 118(35):7469-7488. doi:10.1021/jp500271n
Authors: 
AM Chaka
AR Felmy
Instruments: 
Volume: 
118
Issue: 
35
Pages: 
7469-7488
Publication year: 
2014

In Situ Electrochemical Transmission Electron Microscopy for Battery Research.

Abstract: 

The recent development of in situ liquid stages for (scanning) transmission electron microscopes now makes it possible for us to study the details of electrochemical processes under operando conditions. As electrochemical processes are complex, care must be taken to calibrate the system before any in situ/operando observations. In addition, as the electron beam can cause effects that look similar to electrochemical processes at the electrolyte/electrode interface, an understanding of the role of the electron beam in modifying the operando observations must also be understood. In this paper we describe the design, assembly, and operation of an in situ electrochemical cell, paying particular attention to the method for controlling and quantifying the experimental parameters. The use of this system is then demonstrated for the lithiation/delithiation of silicon nanowires.

Citation: 
Mehdi BL, M Gu, LR Parent, W Xu, EN Nasybulin, X Chen, RR Unocic, P Xu, DA Welch, P Abellan, J Zhang, J Liu, CM Wang, I Arslan, JE Evans, and ND Browning.2014."In Situ Electrochemical Transmission Electron Microscopy for Battery Research."Microscopy and Microanalysis 20(2):484-492. doi:10.1017/S1431927614000488
Authors: 
BL Mehdi
M Gu
LR Parent
W Xu
EN Nasybulin
X Chen
RR Unocic
P Xu
DA Welch
P Abellan
J Zhang
J Liu
CM Wang
I Arslan
JE Evans
ND Browning
Facility: 
Volume: 
20
Issue: 
2
Pages: 
484-492
Publication year: 
2014

Mitigating Voltage Fade in Cathode Materials by Improving the Atomic Level Uniformity of Elemental Distribution.

Abstract: 

Li-rich and Mn-rich (LMR) layered structured materials are very promising cathodes for high-energy lithium-ion batteries. However, their fundamental structure and voltage fading mechanisms are far from being well understood. Here we report the first evidence on the reduced voltage and energy fade of LMR cathode by improving the atomic level spatial distribution of the chemical species. LMR cathode (Li[Li0.2Ni0.2M0.6]O2) prepared by co-precipitation and sol-gel methods are dominated by R-3m phase and show significant Ni-segregation at the surface of the particles. They exhibit large voltage-fade and fast capacity degradation. In contrast, LMR cathode prepared by hydrothermal assisted method is dominated by C2/m phase and minimal Ni-segregation. It also demonstrates much smaller voltage-fade and excellent capacity retention. The fundamental correlation between the atomic level spatial distribution of the chemical species and the functional stability of the materials found in this work also guide the design of other functional materials with enhanced stabilities.

Citation: 
Zheng J, M Gu, A Genc, J Xiao, P Xu, X Chen, Z Zhu, W Zhao, L Pullan, CM Wang, and J Zhang.2014."Mitigating Voltage Fade in Cathode Materials by Improving the Atomic Level Uniformity of Elemental Distribution."Nano Letters 14(5):2628-2635. doi:10.1021/nl500486y
Authors: 
J Zheng
M Gu
A Genc
J Xiao
P Xu
X Chen
Z Zhu
W Zhao
L Pullan
CM Wang
J Zhang
Facility: 
Instruments: 
Volume: 
14
Issue: 
5
Pages: 
2628-2635
Publication year: 
2014

Optical, physical, and chemical properties of springtime aerosol over Barrow Alaska in 2008.

Abstract: 

Airborne observations from four flights during the 2008 Indirect and Semi-Direct Aerosol Campaign (ISDAC) are used to examine some cloud-free optical, physical, and chemical properties of aerosol particles in the springtime Arctic troposphere. The number concentrations of particles larger than 0.12 μm (Na>120), important for light extinction and cloud droplet formation, ranged from 15 to 2260 cm−3, with the higher Na>120 cases dominated by measurements from two flights of long-range transported biomass burning (BB) aerosols. The two other flights examined here document a relatively clean aerosol and an Arctic Haze aerosol impacted by larger particles largely composed of dust. For observations from the cleaner case and the BB cases, the particle light scattering coefficients at low relative humidity (RH<20%) increased nonlinearly with increasing Na>120, driven mostly by an increase in mean sizes of particles with increasing Na>120 (BB cases). For those three cases, particle light absorption coefficients also increased nonlinearly with increasing Na>120 and linearly with increasing submicron particle volume concentration. In addition to black carbon, brown carbon was estimated to have increased light absorption coefficients by 27% (450 nm wavelength) and 14% (550 nm) in the BB cases. For the case with strong dust influence, the absorption relative to submicron particle volume was small compared with the other cases. There was a slight gradient of Passive Cavity Aerosol Spectrometer Probe (PCASP) mean volume diameter (MVD) towards smaller sizes with increasing height, which suggests more scavenging of the more elevated particles, consistent with a typically longer lifetime of particles higher in the atmosphere. However, in approximately 10% of the cases, the MVD increased (>0.4 μm) with increasing altitude, suggesting transport of larger fine particle mass (possibly coarse particle mass) at high levels over the Arctic. This may be because of transport of larger particles at higher elevations and relatively slow deposition to the surface.

Citation: 
Shantz NC, I Gultepe, E Andrews, A Zelenyuk, M Earle, AM MacDonald, PS Liu, and WR Leaitch.2014."Optical, physical, and chemical properties of springtime aerosol over Barrow Alaska in 2008."International Journal of Climatology 34(10):3125-3138. doi:10.1002/joc.3898
Authors: 
NC Shantz
I Gultepe
E Andrews
A Zelenyuk
M Earle
AM MacDonald
PS Liu
WR Leaitch
Instruments: 
Volume: 
34
Issue: 
10
Pages: 
3125-3138
Publication year: 
2014

Direct Evidence of Lithium-Induced Atomic Ordering in Amorphous TiO2 Nanotubes .

Abstract: 

In this paper, we report the first direct chemical and imaging evidence of lithium-induced atomic ordering in amorphous TiO2 nanomaterials and propose new reaction mechanisms that contradict the many works in the published literature on the lithiation behavior of these materials. The lithiation process was conducted in situ inside an atomic resolution transmission electron microscope. Our results indicate that the lithiation started with the valence reduction of Ti4+ to Ti3+ leading to a LixTiO2 intercalation compound. The continued intercalation of Li ions in TiO2 nanotubes triggered an amorphous to crystalline phase transformation. The crystals were formed as nano-islands and identified to be Li2Ti2O4 with cubic structure (a = 8.375 Å). The tendency for the formation of these crystals was verified with density functional theory (DFT) simulations. The size of the crystalline islands provides a characteristic length scale (∼5 nm) at which the atomic bonding configuration has been changed within a short time period. This phase transformation is associated with local inhomogeneities in Li distribution. On the basis of these observations, a new reaction mechanism is proposed to explain the first cycle lithiation behavior in amorphous TiO2 nanotubes.

Citation: 
Gao Q, M Gu, A Nie, F Mashayek, CM Wang, GM Odegard, and R Shahbazian-Yassar.2014."Direct Evidence of Lithium-Induced Atomic Ordering in Amorphous TiO2 Nanotubes ."Chemistry of Materials 26(4):1660-1669. doi:10.1021/cm403951b
Authors: 
Q Gao
M Gu
A Nie
F Mashayek
CM Wang
GM Odegard
R Shahbazian-Yassar
Instruments: 
Volume: 
26
Issue: 
4
Pages: 
1660-1669
Publication year: 
2014

In Situ Observation of Directed Nanoparticle Aggregation During the Synthesis of Ordered Nanoporous Metal in Soft Templates.

Abstract: 

The prevalent approach to developing new nanomaterials is a trial-and-error process of iteratively altering synthesis procedures and then characterizing the resulting nanostructures. This is fundamentally limited in that the growth processes that occur during synthesis can be inferred only from the final synthetic structure. Directly observing real-time nanomaterial growth provides unprecedented insight into the relationship between synthesis conditions and product evolution and facilitates a mechanistic approach to nanomaterial development. Here, we use in situ liquid-stage scanning transmission electron microscopy to observe the growth of mesoporous palladium in a solvated block copolymer (BCP) template under various synthesis conditions, and we ultimately determined a refined synthesis procedure that yields extended structures with ordered pores. We found that after sufficient drying time of the casting solvent (tetrahydrofuran, THF), the BCP assembles into a rigid, cylindrical micelle array with a high degree of short-range order but poor long-range order. Upon slowing the THF evaporation rate using a solvent-vapor anneal step, the long-range order was greatly improved. The electron beam induces nucleation of small particles in the aqueous phase around the micelles. The small particles then flocculate and grow into denser structures that surround, but do not overgrow, the micelles, forming an ordered mesoporous structure. The microscope observations revealed that pore disorder can be addressed prior to metal reduction and is not invariably induced by the Pd growth process itself, allowing for more rapid optimization of the synthetic method.

Citation: 
Parent LR, DB Robinson, PJ Cappillino, RJ Hartnett, P Abellan, JE Evans, ND Browning, and I Arslan.2014."In Situ Observation of Directed Nanoparticle Aggregation During the Synthesis of Ordered Nanoporous Metal in Soft Templates."Chemistry of Materials 26(3):1426-1433. doi:10.1021/cm4035209
Authors: 
LR Parent
DB Robinson
PJ Cappillino
RJ Hartnett
P Abellan
JE Evans
ND Browning
I Arslan
Instruments: 
Volume: 
26
Issue: 
3
Pages: 
1426-1433
Publication year: 
2014

A study of ZnxZryOz mixed oxides for direct conversion of ethanol to isobutene.

Abstract: 

ZnxZryOz mixed oxides were studied for direct conversion of ethanol to isobutene. Reaction conditions (temperature, residence time, ethanol molar fraction, steam to carbon ratio), catalyst composition, and pretreatment conditions were investigated, aiming at high-yield production of isobutene under industrially relevant conditions. An isobutene yield of 79% was achieved with an ethanol molar fraction of 8.3% at 475 °C on fresh Zn1Zr8O17 catalysts. Further durability and regeneration tests revealed that the catalyst exhibited very slow deactivation via coking formation with isobutene yield maintained above 75% for more than 10 h time-on-stream. More importantly, the catalysts activity in terms of isobutene yield can be readily recovered after in situ calcination in air at 550 °C for 2.5 h. XRD, TPO, IR analysis of adsorbed pyridine (IR-Py), and nitrogen sorption have been used to characterize the surface physical/chemical properties to correlate the structure and performance of the catalysts.

Citation: 
Liu C, J Sun, C Smith, and Y Wang.2013."A study of ZnxZryOz mixed oxides for direct conversion of ethanol to isobutene."Applied Catalysis. A, General 467:91-97. doi:10.1016/j.apcata.2013.07.011
Authors: 
C Liu
J Sun
C Smith
Y Wang
Facility: 
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2013

Angular Distribution and Recoil Effect for 1 MeV Au+ Ions through a Si3N4 Thin Foil .

Abstract: 

The Stopping and Range of Ions in Matter (SRIM) code has been widely used to predict nuclear stopping power and angular distribution of ion-solid collisions. However, experimental validation of the predictions is insufficient for slow heavy ions in nonmetallic compounds. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) is applied to determine the angular distribution of 1 MeV Au ions after penetrating a Si3N4 foil with a thickness of ~100 nm. The exiting Au ions are collected by a Si wafer located ~14 mm behind the Si3N4 foil, and the resulting 2-dimensional distribution of Au ions on the Si wafer is measured by ToF-SIMS. The SRIM-predicted angular distribution of Au ions through the Si3N4 thin foil is compared with the measured results, indicating that SRIM slightly overestimates the nuclear stopping power by up to 10%. In addition, thickness reduction of the suspended Si3N4 foils induced by 1 MeV Au ion irradiation is observed with an average loss rate of ~107 atom/ion.

Citation: 
Jin K, Z Zhu, S Manandhar, J Liu, CH Chen, V Shutthanandan, S Thevuthasan, WJ Weber, and Y Zhang.2014."Angular Distribution and Recoil Effect for 1 MeV Au+ Ions through a Si3N4 Thin Foil ."Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 332:346-350. doi:10.1016/j.nimb.2014.02.093
Authors: 
K Jin
Z Zhu
S Manhar
J Liu
CH Chen
V Shutthanan
S Thevuthasan
WJ Weber
Y Zhang
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Spectral probabilities of top-down tandem mass spectra.

Abstract: 

In mass spectrometry (MS)-based proteomics, accurate estimation of statistical signicance of peptide and protein identications is desired for determining whether they are actually correct. Probabilistic models, such as the generating function method, have been successfully applied to compute statistical signicance of peptide-spectrum matches (PSMs) in bottom-up MS, but it is limited to PSMs of short peptides without post-translational modications (PTMs). Recently, top-down MS has be- come available in many laboratories, which often identies intact proteins with PTMs. In this paper, we propose an extended generating function (EGF) method for accurately computing statistical signicance of protein- spectrum matches (PrSMs) with PTMs.

Citation: 
Liu X, MW Segar, SC Li, and S Kim.2014."Spectral probabilities of top-down tandem mass spectra."BMC Genomics 15(Supp 1):Article No. S9. doi:10.1186/1471-2164-15-S1-S9
Authors: 
X Liu
MW Segar
SC Li
S Kim
Facility: 
Instruments: 
Volume: 
Issue: 
Pages: 
Publication year: 
2014

Assessment of Controlling Processes for Field-Scale Uranium Reactive Transport under Highly Transient Flow Conditions.

Abstract: 

This paper presents the results of a comprehensive model-based analysis of a uranium tracer test conducted at the U.S Department of Energy Hanford 300 Area (300A) IFRC site. A three-dimensional multi-component reactive transport model was employed to assess the key factors and processes that control the field-scale uranium reactive transport. Taking into consideration of relevant physical and chemical processes, the selected conceptual/numerical model replicates the spatial and temporal variations of the observed U(VI) concentrations reasonably well in spite of the highly complex field conditions. A sensitivity analysis was performed to interrogate the relative importance of various processes and factors for reactive transport of U(VI) at the field-scale. The results indicate that multi-rate U(VI) sorption/desorption, U(VI) surface complexation reactions, and initial U(VI) concentrations were the most important processes and factors controlling U(VI) migration. On the other hand, cation exchange reactions, the choice of the surface complexation model, and dual-domain mass transfer processes, which were previously identified to be important in laboratory experiments, played less important roles under the field-scale experimental condition at the 300A site. However, the model simulations also revealed that the groundwater chemistry was relatively stable during the uranium tracer experiment and therefore presumably not dynamic enough to appropriately assess the effects of ion exchange reaction and the choice of surface complexation models on U(VI) sorption and desorption. Furthermore, it also showed that the field experimental duration (16 days) was not sufficiently long to precisely assess the role of a majority of the sorption sites that were accessed by slow kinetic processes within the dual domain model. The sensitivity analysis revealed the crucial role of the intraborehole flow that occurred within the long-screened monitoring wells and thus significantly affected both field-scale measurements and simulated U(VI) concentrations as a combined effect of aquifer heterogeneity and highly dynamic flow conditions. Overall, this study, which provides one of the few detailed and highly data-constrained uranium transport simulations, highlights the difference in controlling processes between laboratory and field scale that prevent a simple direct upscaling of laboratory-scale models.

Citation: 
Ma R, C Zheng, C Liu, J Greskowiak, H Prommer, and JM Zachara.2014."Assessment of Controlling Processes for Field-Scale Uranium Reactive Transport under Highly Transient Flow Conditions."Water Resources Research 50(2):1006-1024. doi:10.1002/2013WR013835
Authors: 
Ma R
C Zheng
C Liu
J Greskowiak
H Prommer
JM Zachara
Instruments: 
Volume: 
50
Issue: 
2
Pages: 
1006-1024
Publication year: 
2014

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