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Chemical Imaging Initiative

Delivering New Capabilities for In Situ, Molecular-Scale Imaging

Frequency resolved TERS images of laser-irradiated region

Duets by Molecules and Plasmons

Scientists examine the information content in nanoscale chemical images

Light waves trapped on a metal's surface can interrogate the nearby molecules about their chemical identity through the molecule's characteristic vibrations, which act as fingerprints. Scientists at Pacific Northwest National Laboratory (PNNL) "saw" the interaction between the molecules and the trapped light waves or surface plasmons. Their fundamental endeavor could lead to breakthroughs in interpreting ultrasensitive chemical images for characterizing new materials with potential uses in catalysis and energy conversion.

(January 2015)

Ocean wave

How Sea Spray Particles Evolve in the Atmosphere

Carbon-rich chemicals coat sea salt particles, altering their structure and possibly changing the atmosphere

When ocean waves make bursting whitecaps or crash against the shores, tiny particles of sea spray enter the atmosphere. Once airborne, the particles are quickly coated by organic chemicals. The chemicals, emitted by diverse sources, cause the particles to evolve, according to scientists at Lawrence Berkeley and PNNL. Using complementary chemical imaging techniques, they found that when temperature and humidity rise, reactions within particles create organic salts. These reacted particles, when chilled, become glass-like lumps.

(January 2015)

Galya Orr

Galya Orr Selected for Editorial Advisory Board

Dr. Galya Orr has been asked to be a member of the editorial advisory board of Chemical Research in Toxicology, a peer-reviewed scientific journal published by the American Chemical Society. Orr is a senior research scientist and the Cell Isolation and System Analysis capability lead at EMSL. She is also a key collaborator on a Chemical Imaging Initiative project investigating the structure and dynamics of biological systems. The initiative is part of Pacific Northwest National Laboratory.

(December 2014)

Artistic representation of delta alumina

Weaving a Catalyst

Popular aluminum oxide created by interlacing different crystal forms

The exhaust system in your car and the plastic cup holding your drink, along with countless other products, rely upon reactions driven by catalysts supported on aluminum oxides. Characterizing these aluminum oxides or alumina has been challenging. For the first time, scientists at Pacific Northwest National Laboratory and FEI Company obtained an atomically resolved view of delta alumina. The team showed that the oxide is two crystal forms or variants woven together.

(November 2014)

Atom probe tomography results

Arun Devaraj, Daniel Perea Featured in Chemical & Engineering News Article on Seeing Atoms

Arun Devaraj and Daniel Perea, Pacific Northwest National Laboratory, were interviewed about their chemical imaging research for Mitch Jacoby's cover story in Chemical & Engineering News.

(October 2014)

Laser excites material, produces APT information

Taking Back the Angels' Share of Atoms

Non-uniform evaporation prevents scientists from seeing every atom on a surface

On the surface of a battery's electrode, a material that stores wind energy, or on nearly any other surface, scientists can use atom probe tomography to identify and locate almost every atom. But some atoms evaporate non-uniformly before they are identified-reminiscent of the angels' share, the amount of wine or whiskey volume lost to evaporation during barrel aging. Scientists at Pacific Northwest National Laboratory and the University of Rouen revealed which atoms evaporate in mixed materials, where there are many different types of atoms. They managed this feat by correlating data from three techniques, accounting for all of the atoms and determining how atoms were evaporating from APT.

(September 2014)

Electron beam choice and electron microscopy experiments

Seeing Clearly Through a Liquid

Designing controlled, reproducible experiments in an in situ liquid stage

Using in situ liquid transmission electron microscopy to probe nanomaterials is a difficult task for scientists, as electron beams perturb the sample and induce artifacts. At Pacific Northwest National Laboratory and University of California, Davis, scientists demonstrated that the choice of electron beam energy has a strong effect that goes far beyond merely increasing the concentration of reducing radicals. They also found that when compared to solid samples, radicals formed in the liquid phase are more mobile, and ultimately dictate the choice of electron microscopy imaging mode.

(September 2014)

Layla Mehdi

Layla Mehdi Receives Scholarship for Microscopy Conference

Congratulations to materials postdoctoral researcher Layla Mehdi, who received a Robert P. Apkarian Memorial Scholarship to attend the Microscopy & Microanalysis (M&M) 2014 Annual Meeting August 3-7 in Hartford, Connecticut. She presented a poster titled "Direct Observation of Li2O2 Nucleation and Growth with In-Situ Liquid ec-(S)TEM," research developed under the Joint Center for Energy Storage Research project.

(September 2014)

Artistic rendering of nanoparticles' attack

Watching Nanoparticles Swim

Researchers collaborate to see particles in real time in their native environment

Like sharks hunting their prey, soft nanoparticles should quickly navigate through the body's waters and attack cancerous cells, destroying the diseased tissue and leaving the rest alone. That's the goal. The challenge is understanding how the particle behaves in liquids, something most microscopes don't handle. Thanks to fortuitous discussions as part of the initial formation of the PREMIER Network, scientists studying the particles at the University of California at San Diego and the University of Pittsburgh teamed up with microscopists at Pacific Northwest National Laboratory (PNNL) and, together, they obtained clear images of the particles moving liquids.

(August 2014)

Aluminum EXAFS and zeolite structure

Creating a GPS for Aluminum Ions

New approach pinpoints locations in simple zeolite catalysts

Employing a combination of methods devised at Pacific Northwest National Laboratory and the Swiss Light Source, scientists determined the distribution of aluminum ions in zeolites, which are widely used by industry. In the first example of this approach, the scientists analyzed two chemical compositions of a structural variant. They found that the aluminum atoms, which are critical to the catalytic activity, preferentially replace silicon atoms at certain sites.

(August 2014)


2014 PNWAVS Symposium To Be Held in Conjunction with PREMIER Network Meeting

The 25th Annual Symposium of the Pacific Northwest AVS Science and Technology Society will be held in conjunction with the Pooled Resources for Electron Microscopy Informatics Education and Research, or PREMIER, Network meeting on September 16-19. The meeting will be held at EMSL in Richland, Washington.
(July 2014)

Analyst journal cover

New Imaging Approach Accurately Measures Lipid and Metabolite Distributions in Biological Samples

Mass spectrometry technique could lead to answers about how cells interact

To understand how cells converse, scientists at Pacific Northwest National Laboratory and Oregon Health & Science University designed an approach that accurately determines the spatial location of molecules and quantifies lipids and metabolites in biological samples. The new approach efficiently accounts for signal suppression or matrix effect (see sidebar) that may significantly alter molecules’ distributions obtained in mass spectrometry imaging experiments. Compensation for matrix effects is achieved by adding appropriate internal standards to the solvent used in nano-DESI imaging.
(July 2014)

Julia Laskin

Julia Laskin Receives Laboratory Director's Science and Engineering Achievement Award

Congratulations to Dr. Julia Laskin on receiving a 2014 Laboratory Director’s Science and Engineering Achievement Award. The award recognizes Laskin for her fundamental contributions to mass spectrometry, in particular for her research involving ion collisions with surfaces.

(July 2014)


PNNL Team Wins R&D 100 Award for SALVI

A small window to the world of liquid interfaces has won an R&D 100 Award for a team of PNNL researchers. Xiao-Ying Yu, Zihua Zhu, Bingwen Liu, Martin Iedema and Matthew Marshall of PNNL and collaborators James Cowin and Li Yan developed the System for Analysis at the Liquid Vacuum Interface (SALVI), a novel innovation that allows a new level of molecular insight and liquid analysis that can be deployed in a range of instruments.

(July 2014)

SALVI technology

Window into Liquid Analysis Earns PNNL an R&D 100 Award

SALVI enables real-time imaging of liquid samples by more than one analytical instrument

Many studies rely on knowing precisely how solids and liquids interact on a molecular level, but liquids evaporate in the vacuum of certain powerful scientific instruments. PNNL developed SALVI, or the System for Analysis at the Liquid Vacuum Interface, that for the first time allows these instruments to image liquid samples in real time. R&D Magazine honored SALVI’s research team with a 2014 R&D 100 award. The magazine selects the 100 most innovative scientific and technological breakthroughs of the year.

(July 2014)

cobalt tem

Cobalt Migrates and Forms Islands in Two-Metal Catalysts

Chemical imaging technique provides insights for materials used in fuel production

Direct observation of atomic-level process of a platinum-cobalt nanoparticle catalyst reveals that the cobalt is far from stationary. A collaborative study including scientists at Pacific Northwest National Laboratory shows the cobalt migrates from deep inside the nanoparticle to the surface when surrounded by oxygen. When placed in hydrogen gas, the cobalt migrates back inside the nanoparticle, leaving a thin layer of platinum on the particle's surface.
(June 2014)

cartoon and image of STEM and electrolyte sample

Degradation Mechanisms Uncovered in Li-Ion Battery Electrolytes

In situ scanning transmission electron microscopy helps characterize stability, degradation

A team led by Pacific Northwest National Laboratory scientists has uncovered information about high-demand batteries that could improve their performance and longevity. The scientists characterized the stability and interconnected degradation mechanisms in electrolytes commonly used for lithium-ion, or Li-ion, batteries. They obtained detailed chemical imaging data using an environmental liquid stage in a scanning transmission electron microscope (STEM). The detailed characterization offered by liquid-stage STEM can provide unique insights into electrolyte behavior, either for use in future in situ battery studies or to test new electrolytes, winnowing the library of candidate solutions for further characterization and reducing the experimental time spent on less effective electrolytes.

(March 2014)


By Losing Their Shape, Material Fails Batteries

Scientists show that too many electrons at the lithiation front in silicon are a problem

As every cell phone owner knows, lithium-ion batteries fade, holding less energy after each charge. This fading relates to electron-rich regions forming in the electrodes, according to scientists at Pacific Northwest National Laboratory and three universities.

(March 2014)

Ilke Arslan, portrait

Ilke Arslan Joins Microscopy & Microanalysis Editorial Board

Congratulations to Dr. Ilke Arslan, Pacific Northwest National Laboratory, on joining the editorial board for Microscopy & Microanalysis. The journal provides original research articles on imaging and compositional analysis to biologists, materials scientists, and others interested in microscopy. The publication is the official journal of the Microscopy Society of America and eight other societies.

(March 2014)

cover of Analyst journal

In Situ Chemical Imaging at the Sub-Biofilm-Scale Now Possible

Provides new look at naturally wet microbial community behavior

A multidisciplinary team at Pacific Northwest National Laboratory is the first to demonstrate imaging of a biofilm's chemical components as they form in hydrated biological samples, rather than from frozen or dried samples. They used a surface technique called time-of-flight secondary ion mass spectrometry to study complex microbiological processes, such as chemical attachment of microbes to surfaces to form biofilms. The work used PNNL's vacuum-compatible liquid probe.

(February 2014)

XFEL images of bacteriorhodopsin proteins

Superbright and Fast X-rays Image Single Layer of Proteins

Newest method for determining a protein's shape based on XFEL technology significantly broadens number and type of proteins that researchers can study

Using a unique form of X-ray diffraction called diffract-before-destroy imaging, an international team of scientists led by Pacific Northwest National Laboratory and Lawrence Livermore National Laboratory proved it is possible to study individual monolayers of protein. Previously, X-ray techniques were unable to collect diffraction in the forward or transmitted direction unless proteins stacked into large crystals. The Department of Energy's X-ray Free-Electron Laser (a.k.a. the Linac Coherent Light Source) produces exceptionally bright and fast X-rays that can take a picture rivaling conventional methods with a sheet of proteins just one protein molecule thick. The technique opens the door to learning details of the proteins, aiding understanding of how they cause disease or toxicity.

(February 2014)

particle size distribution curve

Watching Nanoparticles Grow

New approach shows particles and ensembles follow different growth patterns, explaining a frustrating discrepancy in experimental results

Individual silver nanoparticles in solutions typically grow through single atom attachment, but importantly, when they reach a certain size they can link with other particles, according to scientists at Pacific Northwest National Laboratory, the University of California, Davis, and Florida State University. This seemingly simple result has shifted a long-held scientific paradigm that did not consider kinetic models when explaining how nanoparticle ensembles formed. Greater understanding of mesoscale interactions in nanoparticles provides more precision in material synthesis, bringing us closer to tailored materials for catalysis, energy storage, and other uses.

(February 2014)

electrodes in TEM wet cell

Batteries as They Are Meant To Be Seen

In the search for long-lasting, inexpensive rechargeable batteries, researchers develop more realistic methods to study the materials in action

Researchers at a host of universities and national laboratories including Pacific Northwest National Laboratory have developed a way to microscopically view battery electrodes while they are bathed in wet electrolytes, mimicking realistic conditions inside actual batteries. While life sciences researchers regularly use transmission electron microscopy to study wet environments, this time scientists have applied it successfully to rechargeable battery research.

(January 2014)

Cartoon of E Probe

Microfluidic Probe Allows Real-Time Imaging of Electrode-Liquid Electrolyte Interface

New probe also couples electrochemistry and imaging approaches to observe interface kinetics

A new microfluidic probe developed by PNNL scientists provides dynamic chemical imaging of the electrode-electrolyte interface in situ. Using this probe, the scientists showed the molecular composition of the reaction products and intermediate species at different stages of the redox cycle in situ using—for the first time—a surface imaging technique that operates in a vacuum.

(January 2014)

Kleese Van Dam Quoted in Genetic Engineering & Biotechnology News

In the January 2014 issue of Genetic Engineering & Biotechnology News, PNNL's Kerstin Kleese van Dam, an associate division director in CSMD and Technical Lead of the Scientific Data Management Group, is featured as part of an article highlighting the upcoming Big Data and Analytics in Life Sciences Forum, hosted by the International Quality & Productivity Center in Boston on January 27-28, 2014.

Kerstin Kleese van Dam discusses big data. 

In the article, "Big Data Expected to Impact Pharma R&D," which also examined how to manage, and benefit from, the vast amounts of data affecting pharmaceutical development, Kleese van Dam is quoted describing the work of the Chemical Imaging, Future Power Grid and Analysis in Motion initiatives at PNNL in creating tools that address this confluence of volume, rate and heterogeneity of informatics data. Notably, she explained the role of three data paradigms that PNNL uses to simultaneously organize and interpret data throughout the research process: always on analysis, analysis in motion and analytics at the edge.

Kleese van Dam will present "Case Study: Advances in Predictive Analytics" at the Big Data and Analytics in Life Sciences Forum on Tuesday, January 28 at 1:30 PM.

(January 2014)

photo of Devaraj and Campbell

Arun Devaraj interviewed by EMSL Director Allison Campbell

Pacific Northwest National Laboratory material scientist Dr. Arun Devaraj was interviewed in December by EMSL director Dr. Allison Campbell about his work using atom probe tomography for PNNL’s Chemical Imaging Initiative. The video is available at

(December 2013)

Ilke Arslan featured in DOE Pulse

The November 18 issue of DOE Pulse featured Dr. Ilke Arslan of Pacific Northwest National Laboratory. The article discusses how this diplomat's daughter, who completed her doctoral degree at the age of 25, applies the fundamentals of physics to change the scientific community's view of nanoparticles. Her research is working towards the goal of providing a clear view of a working catalyst in real time, in three dimensions, and at the atomic scale. Arlsan's imaging work is providing fundamental answers for her teammates in PNNL's Chemical Imaging Initiative and Institute for Integrated Catalysis.

Read the DOE Pulse article "Ilke Arslan: A catalyst for clarity."

(November 2013)

x-ray energy-dispersive spectroscopy maps of LMNO cathode

The Character of a Cathode

Nickel segregation, cation spatial distribution, and tightly integrated phases occur in pristine battery material

To prevent fading in a layered lithium cathode that has promise for heavy duty transportation use, scientists at Pacific Northwest National Laboratory, FEI Company, and Argonne National Laboratory obtained a definitive view of a pristine cathode. Controversy has encircled this material, a.k.a., LMNO cathode. Some state it's a solid solution; others, a composite. To address this debate, the team used a suite of instruments and determined the material is a composite with tightly integrated phases where the surface contains higher concentrations of nickel, low concentration of oxygen, and electron-rich manganese. Obtaining this type of clarityaround the fundamentals of the cathodeis necessary if scientists are toimprove the cycle life and capacity of the resulting battery.

(November 2013)

Ilke Arslan

Ilke Arslan Presents at National Academy of Sciences' Kavli Symposium

Congratulations to Dr. Ilke Arslan at Pacific Northwest National Laboratory on being chosen to attend the 25th U.S. Kavli Frontiers of Science Symposium. This invite-only National Academy event is designed to foster discussions among high-profile young scientists across a wide range of disciplines. Between 80 and 100 scientists under the age of 45 are asked to attend. They are chosen from those who have prestigious awards and honors or are nominated by Academy members or other participants.

Arslan is well known for bringing her physics expertise to chemical imaging and catalysis. She won research fellowships from the Royal Society USA and the National Science Foundation. She received a U.S. Presidential Early Career Award for Scientists and Engineers. She is also a Microscopy Society of America tour speaker.

(November 2013)

Patricia Abellan Earns International Award for Doctoral Thesis

Congratulations to Dr. Patricia Abellan at Pacific Northwest National Laboratory on receiving the Microscopy Society of Spain's Best Ph.D. Thesis in Materials Science award. Her research shows how strain state and interface structure in oxide nanostructured materials grown by a solution route changed the material's superconductivity, magnetism and other properties. She also discovered a novel mechanism for lattice parameter relaxation. She is currently conducting work for the Chemical Imaging Initiative and DOE's EMSL.
(October 2013)

Cathode material nanoparticle

New Technique Efficiently Resolves Chemistry of Nanoparticles

Elements clearly identified on 3D map

A new technique developed by scientists at PNNL and FEI Company lets scientists efficiently resolve elements’ locations in three dimensions. The technique combines scanning transmission electron microscopy and X-ray energy dispersive spectrometry with a new detector arrangement and a brighter electron beam. The result: the fastest, cleanest view yet of the elements’ placement on a sample smaller than a single blood cell. The team applied this technique to a lithium-rich nickel-based material that could be part of tomorrow’s batteries and discovered how nickel was segregating away from other elements on the material’s surface. Their results, published in Ultramicroscopy, is the journal’s most downloaded article in the last 90 days
(September 2013)

Analyzing the Status of Oxide Surface Photochemical Reactivity

Invited review shows power of scanning tunneling microscopy to understand and control the surface photochemistry of oxide materials

In their invited review, Dr. Michael Henderson and Dr. Igor Lyubinetsky at Pacific Northwest National Laboratory show that scanning probe microscopy techniques, in particular scanning tunneling microscopy, allow scientists to understand fundamental interactions that are key to our energy future.
(July 2013)

James De Yoreo

De Yoreo Receives Outstanding Materials Science Award

Congratulations to Dr. James De Yoreo, Pacific Northwest National Laboratory, on earning the 2013 American Association for Crystal Growth Award for his foundational insights into the processes underlying biomineralization and biomolecular assembly.
(June 2013)

Arslan's Research Graces the North American Catalysis Society Meeting's Program

Congratulations to Dr. Ilke Arslan, Pacific Northwest National Laboratory, on having her scientific image chosen as the cover art for the North American Catalysis Society meeting. The image depicts the morphological changes of a layered zeolite before and after delamination. Delamination of stacked zeolite sheets provides more accessible surface area where bulky molecules can react -- important for the petrochemical industry.

(June 2013)

New Imaging Tool Directly Measures Liquid Surfaces

Basic scientific insights of interest for energy storage, environmental cleanup

A unique chemical imaging tool readily and reliably presents volatile liquids to scientific instruments, according to a team including Pacific Northwest National Laboratory. These instruments require samples be held in a vacuum, which is often incompatible with hydrocarbons and other liquids. Designed and built at PNNL, this one-of-a-kind sample holder continuously pumps the liquid through a gold-coated microfluidic chamber. The extremely narrow channel provides high linear velocity at the detection window and helps overcome the liquids' tendency to vaporize. Instruments access the liquid via an open viewing port. Tests with electron microscopes and mass spectrometers prove the device can operate continuously for up to 8 hours. Further, the device handles complex liquids.
(May 2013)

Nigel Browning Commentary in Nature Chemistry

Nigel Browning
Nigel Browning serves as the Chief Science Officer on PNNL's Chemical Imaging Initiative

A commentary by Dr. Nigel Browning, the Chief Science Officer for the Chemical Imaging Initiative at Pacific Northwest National Laboratory, was recently published in Nature Chemistry. The commentary featured recent four-dimensional electron microscopy (4D-EM) work done by the research group of Nobel prize winning scientist Ahmed Zewail. Browning highlighted the wealth of new information 4D-EM has revealed about how electronic phase transitions occur in individual nanoparticles, how the particle-to-particle variability changes the speed and magnitude of the transition, and how interactions between nanoparticles control the ensemble-average response of the system. The power of 4D-EM to image structural dynamics on the scale of a few hundred nanoseconds and allow the switching dynamics to be quantified makes a unique contribution to the study of nanostructures. A broad class of electronic phase transitions in individual nanomaterials can now be studied directly using 4D-EM.

(April 2013)

Researchers have long wanted to "see" chemical, materials, and biochemical processes, in time and space, with enough detail to determine what is occurring at the molecular level. But, they lack the tools to reach this level of clarity. Instead, they must infer what is happening from secondary sources and mathematical models.

The Pacific Northwest National Laboratory is developing the tools and techniques to generate images of chemicals, materials, and biological molecules at the nanometer scale through its Chemical Imaging Initiative. (A nanometer is the length of two hydrogen atoms side by side.)

Achieving molecular-scale clarity requires molecules to be examined in situ—exactly as they are rather than in an intermediate state. Data from two or more experimental tools are needed to adequately describe the molecules, so computational tools are being developed to integrate the data streams.

This level of information will allow scientists and engineers to move from observing chemical, materials, and biological processes to controlling them.

Technical challenges include the following

Develop light-source-based x-ray and vacuum ultraviolet probes coupled with laboratory-based imaging capabilities for three-dimensional tomographic, structural, and element-specific molecular-level probes that would significantly enhance imaging capabilities. Use of these new techniques, for example, could potentially provide an atomic-resolution, in situ "movie" of a functioning photocatalyst or clear characterizations of nanoporous materials and their active sites for batteries and biomolecules.

Develop coupled optical, electron, ion, and scanned probe microscopies to understand chemical and biological transformations and mechanisms. Use of these new techniques could produce useful insights into the mineral-fluid interface in supercritical CO2 or the lifecycle of molecular machinery in microorganisms and microbial communities, among others.

Chemical Imaging Initiative

Talks, Proposals and Publications

Fundamental & Computational Sciences Directorate




Nigel Browning
Initiative Lead

Lou Terminello
Initiative Advisor

Wayne Hess
Science Theme 1 Co-Lead

Kerstin Kleese van-Dam
Science Theme 1 Co-Lead

Scott E. Baker
Science Theme 2 Co-Lead

Theva Thevuthasan
Science Themes 2 and 3 Co-Lead

Alex Guenther
Science Theme 3 Co-Lead

Edmond Hui
Project Leader


Julie Wiley


Project Administration


CII Funding