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Chemical Imaging Initiative

Current Projects

Projects to develop coupled optical, electron, ion, and scanned probe microscopies to understand chemical and biological transformations and mechanisms are as follows.

Thrust Area 1: Nanoscale Molecular Imaging

Project 1.1: Correlative High-Resolution Imaging and Spectroscopy to Characterize the Structure and Biogeochemical Function of Microbial Biofilms
Principal Investigator:
Matthew Marshall
Team Members: Jim Fredrickson, Alice Dohnalkova, Erin Miller, and Zihua Zhu (Pacific Northwest National Laboratory); Carolyn Larabell and David Shuh (Lawrence Berkeley National Laboratory); and Ken Kemner (Argonne National Laboratory)

Direct examination has revealed that the majority of microorganisms in natural and engineered environments live in structured communities termed 'biofilms". In addition to microbial cells, biofilms are comprised of a poorly characterized organic matrix, commonly referred to as "extracellular polymeric substance" (EPS). EPS plays roles in facilitating microbial interactions and biogeochemical reactions, including extracellular electron transfer. This project is developing fundamental capabilities for enhanced visualization, compositional analysis, and functional characterization of biofilm EPS and a better understanding of EPS influences on biogeochemical reactions.

Project 1.2: Integrated Nano-Scale Imaging for Investigating Applications and Implications of Nanomaterials in the Living Cell
Principal Investigator:
Galya Orr
Team Members: Dehong Hu, Ana Tolic, Yumei Xie, Derek Hopkins and Jay Grate (Pacific Northwest National Laboratory); David Shuh and Tolek Tyliszczak (Lawrence Berkeley National Laboratory)

This project is developing new approaches to investigate individual nanoparticles and their interactions with living cells, providing the data needed to accelerate safe applications of nanotechnologies in industry and medicine. The unique properties of nanomaterials have made them popular for different uses, but the unknown impact on human health and the environment has limited the materials' use. Combining our experience in single-molecule fluorescence techniques and working with the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory, we are building super-resolution fluorescence imaging and x-ray tomography techniques to see 3D images of individual nanoparticles, proteins, and organelles in the intact cell with nanometer resolution.

Project 1.3: Chemical Imaging Analysis of Environmental Particles
Principal Investigator:
Alexander Laskin
Team Members: Alla Zelenyuk (Pacific Northwest National Laboratory); and Mary K. Gilles and Kevin Wilson (Lawrence Berkeley National Laboratory)

The project is establishing a unique analytical platform for comprehensive analysis of gas-particle reacting systems, and is contributing to our collective goal of achieving a fundamental understanding of the chemical composition, reaction mechanisms and kinetics of gas-particle transformations and heterogeneous chemistry pertinent to atmospheric and occupational environments. Despite their acknowledged importance, understanding of environmental particles is presently limited, and their environmental role cannot be quantitatively determined. This project focuses on laboratory studies that investigate the relationship between particle morphology, composition, formation, reactivity, and evaporation by developing novel methods for chemical imaging analysis.

Project 1.4: Integration of Molecular Imaging Techniques to Probe the Photoinduced Charge Transfer in Semiconductor Quantum Dots-Polymer Hybrid Solar Cells
Principal Investigator:
Ponnusamy Nachimuthu
Team Members: Ajay Karakoti, Shail Sanghavi, Theva Thevuthasan (Pacific Northwest National Laboratory); David Shuh (Lawrence Berkeley National Laboratory)

This project is integrating molecular imaging and spectroscopy capabilities to advance the fundamental understanding of the photo-induced charge transfer in hybrid solar cells, which convert sunlight directly into electricity. In particular, the team is studying the concentration and size-dependent distribution of the CdSe quantum dots in conductive polymer films, the chemical and electronic structure interactions and their influence on the photo-induced charge transfer and the efficiency of the hybrid solar cells.

Project 1.5: XES Nanoprobe for Hard X-Ray Region
Principal Investigator:
Nancy Hess
Team Members: Kyle Alvine, Mark Bowden, John Fulton, Tamas Varga, John Lemmon (PNNL); Jerry Seidler (University of Washington); Steve Heald (Advanced Photon Source)

This project is building a high spatial resolution x-ray emission spectroscopy (XES) capability for in situ analysis of x-ray emission lines in the 5- to 10-keV range. The XES Nanoprobe capability will be demonstrated on two battery systems of scientific interest: sodium/nickel and nickel/lithium. The development of a low-cost, modular XES system at the Advanced Photon Source and ultimately at National Synchrotron Light Source 2 will be widely applicable to fundamental materials chemistry challenges.

Project 1.6: Imaging the Nucleation and Growth of Nanoparticles in Solution
Principal Investigator:
Ayman Karim
Team Members: Libor Kovarki, David Heldebrant (Pacific Northwest National Laboratory); Abhaya Datye (University of New Mexico); Anatoly Frenkel (Yeshiva University, Brookhaven National Laboratory)

This project is developing in situ tools with atomic-scale, millisecond time resolution to image the nucleation and growth of nanoparticles in solution. Atomic-scale, millisecond time-resolution imaging will advance the understanding of particle nucleation and growth mechanisms. This will enable the controlled synthesis and study of nanomaterials of well-defined size, shape and exposed surfaces. These nanomaterials are vital in enabling new material design and exploration.

Thrust Area 2: Near Nanometer In-House Imaging

Project 2.1: Site-Specific Atomic Resolution Probing of Structure-Property Relationship under Dynamic and/or Operando Conditions
Principal Investigator:
Chongmin Wang
Team Members: Libor Kovarik, Xiaolin Li, W Xu, Lax Saraf, R Dagle, Jun Liu, Don Baer, H Wan, Ja Hun Kwak, Janos Szanyi, Bernd Kabius, Charles HF Peden, Satya Kuchibhatla, Bruce Arey, Theva Thevuthasan, Shutta Shutthanandan, B Shelton, N Govind, A Andersen (PNNL), Ty Prosa (Cameca Inc.)

This project is developing chemical imaging capabilities that drive the atomic-level imaging and spectroscopic analysis of materials related to energy and environmental issues under in-situ/operando conditions, providing a general platform for design and discovery of new materials and catalysts with superior properties. The project will extend state-of-the-art aberration-corrected scanning transmission electron microscopy/transmission electron microscopy (STEM/TEM) and other complementary microscopy and spectroscopic imaging capabilities to new levels, enabling atomic-resolution imaging and spectroscopic analysis under dynamic operating conditions. It will develop new capabilities to enable complementary integration of site-specific atomic resolution structural and chemical information obtained from various techniques, including STEM/TEM, atom probe tomography and focused ion beam and scanning electron microscopy.

For more information on this project, check out these posters:

Project 2.2: Development of New Soft Ionization Mass Spectrometry Approaches for Spatial Imaging of Complex Chemical and Biological Systems
Principal Investigator:
Julia Laskin
Team Members: Ljiljana Pasa-Tolic, Patrick Roach, Errol Robinson, Don Smith, Zihua Zhu, Gordon Anderson, Jim Fredrickson, Matthew Marshall, Alice Dohnalkova, and Alexander Laskin (Pacific Northwest National Laboratory); Ron Heeren (Foundation for Fundamental Research on Matter); and Pieter Dorrestein (University of California, San Diego)

Mass spectrometry (MS) imaging of biological samples has recently gained momentum, mainly because of the development of soft ionization techniques and continued improvements in MS and secondary ion mass spectrometry (SIMS) instrumentation. This project is taking soft ionization, sensitivity and unsurpassed chemical specificity of MS to the nanoscale and applying novel tools for characterization of microbial biofilms. We are performing comprehensive MS characterization of extracellular material in biofilms of Shewanella oneidensis and obtaining detailed spatial profiles of chemical gradients generated at interfaces between biofilms and mineral surfaces using a variety of MS imaging approaches that target different classes of compounds.

Project 2.3: Facet-Specific Chemistry of Nanoscale Crystalline Alumina Using an Enhanced Scattering IR SNOM Instrument
Principal Investigator:
Scott Lea
Team Members: MS Taubman, MC Phillips, L Wang, and MA Henderson (PNNL) MB Raschke (University of Colorado-Boulder)

The project is combining atomic force microscopy with quantum cascade lasers to further develop the scattering infra-red near-field optical microscope (s-IR SNOM) being developed under EMSL's partner proposal. We are fully characterizing the capabilities of the new instrument using both quantum cascade lasers and the existing femtosecond pulsed oscillator/power oscillator laser chain. Our goal is to understand how best to expand the instrument's flexibility and resolution. The resulting instrumentation will be used to examine the distribution of Brønsted acid sites (OH groups) and determine the in-situ catalytic activity of the different crystal facets of γ-Al2O3.

Project 2.4: Quantitative Imaging of Atomic-Scale Chemistry Changes at Interfaces
Principal Investigator:
Nigel Browning
Team Members: Bruce Gates, Patricia Abellan, Ceren Aydin, Daniel Shelberg, Wen Tong, Hao Yang (University of California-Davis), Yuichi Ikuhara (University of Tokyo)

This project is developing a robust method to quantify atomic-scale changes in structure, composition, and bonding at interfaces. This research will use the advanced capabilities for chemical imaging under varied environmental conditions afforded by the new generation of aberration-corrected microscopes and in situ stages. The expected outcomes include developing robust statistical methods for reproducible and quantified image analysis/interpretation, applying methods to understand the interplay of structure-composition and properties at interfaces in functional oxides, and applying these statistical methods to investigate heterogeneous catalysts.

Project 2.5: Probing Structural Dynamics with High Spatial and Temporal Resolution
Principal Investigator:
Nigel Browning
Team Members: James Evans (PNNL and University of California-Davis), Bill Ristenpart, Roland Faller, Katie Jungjohann, David Welch, Taylor Woehl, Pinghong Xu (University of California, Davis)

This project is conducting the work to understand the structural dynamics in biological and/or nanomaterials systems on the ms to ns timescale. This research will use a unique aberration-corrected Dynamic TEM (DTEM), where a photoemission source will enable time-resolved images at/near atomic resolution. The expected outcomes include developing single-shot imaging with atomic spatial resolution for DTEM with in situ gas and liquid stages, testing the overall limits in spatio-temporal resolution for future ultrafast TEM designs, and developing the capability for imaging biological structures in their "live" hydrated state.

Thrust Area 3: Multi-modal Analysis and Integration Framework for Chemical Imaging

Project 3.1: A Multi-Modality Integration Framework for Chemical Imaging
Principal Investigator:
Kerstin Kleese van Dam
Team Members: James Carson, Abigail Corrigan, David Cowley, Daniel Einstein, Ian Gorton, Andrew Kuprat, Dongsheng Li, Guang Lin, Yan Liu, Patrick Paulson, Eric Stephan, Jian Yin, Julia Laskin, Matthew Marshall, Alice Dohnalkova (PNNL), Chao Yang (LBNL)

This project is developing a flexible, multi-modal integration framework that will allow the capture, formalization, and utilization of expert knowledge across the spectrum of chemical imaging technologies to facilitate user-driven analysis and integration of experimental technologies for accelerated knowledge creation and exploitation. The framework will enable the community to contribute their own tools as well as support their efforts by providing key technologies for data annotation, compression, reduction, reconstruction, registration, and segmentation to the community. This framework will be a first and world-leading in its capabilities.

Project 3.2: Synergistic Integration of Feature Recognition and Analysis for Chemical Imaging Data
Principal Investigator:
James Carson
Team Members: Andrew Kuprat, Kerstin Kleese-Van Dam, Matt Marshall, Alice Dohnalkova (PNNL)

The project is providing the foundation for unique research capabilities for performing image analysis and feature recognition of up to petascale spatial time-varying datasets. The primary outcome will be a toolkit design that links into the chemical imaging analysis pipeline. This toolkit will provide initial image analysis and feature recognition capabilities based on the identified needs of data collection instruments and applications. Importantly, the feature recognition will provide feedback to other steps in the pipeline, enhancing their capabilities. The tools and algorithms will be selected to be parallelized, enabling the potential to quickly provide feedback to the researcher and thus influence decision-making during the imaging process itself.

Project 3.3: Integrating Multimodal Chemical Imaging Instrumentation by Data Reduction and Resolution Merge
Principal Investigator:
Dongsheng Li
Team Members: Guang Lin, Jian Yin, Julia Laskin, Chongming Wang, Matt Marshall, Alice Dohnalkova (PNNL), Chao Yang (LBNL), and Somnath Ghosh (Johns Hopkins)

This project is developing the capabilities to integrate disparate images by data reduction and resolution merge. It will create high-resolution images that cover large areas of a sample. The expected outcomes include

  • Developing the capability to integrate multimodal imaging from different length scales
  • Developing a suite of tools for data integration
  • Establishing a bridge for hot spot identification, property prediction, etc.

Chemical Imaging Initiative

Talks, Proposals and Publications

Fundamental & Computational Sciences Directorate


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Chief Science Officer
Chemical Imaging

Chemical Physics & Analysis

Thrust Area 1

Thrust Area 2

Thrust Area 3

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Project Administration

2010 Archive

Speakers and Visitors

Talks by Chemical Imaging Staff