Chien-Chun Chen

Electron tomography at 2.4-angstrom resolution

Transmission electron microscopy is a powerful imaging tool that has found broad application in materials science, nanoscience and biology. With the introduction of aberration-corrected electron lenses, both the spatial resolution and the image quality in transmission electron microscopy have been significantly improved and resolution below 0.5 ångströms has been demonstrated. To reveal the three-dimensional (3D) structure of thin samples, electron tomography is the method of choice, with cubic-nanometre resolution currently achievable. Discrete tomography has recently been used to generate a 3D atomic reconstruction of a silver nanoparticle two to three nanometres in diameter, but this statistical method assumes prior knowledge of the particle’s lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic-scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of an approximately ten-nanometre gold nanoparticle at 2.4-ångström resolution. Although we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified in three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic-scale resolution, but also to improve the spatial resolution and image quality in other tomography fields.

Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy

Microscopy has greatly advanced our understanding of biology. Although significant progress has recently been made in optical microscopy to break the diffraction-limit barrier, reliance of such techniques on fluorescent labeling technologies prohibits quantitative 3D imaging of the entire contents of cells. Cryoelectron microscopy can image pleomorphic structures at a resolution of 3–5 nm, but is only applicable to thin or sectioned specimens. Here, we report quantitative 3D imaging of a whole, unstained cell at a resolution of 50–60 nm by X-ray diffraction microscopy. We identified the 3D morphology and structure of cellular organelles including cell wall, vacuole, endoplasmic reticulum, mitochondria, granules, nucleus, and nucleolus inside a yeast spore cell. Furthermore, we observed a 3D structure protruding from the reconstructed yeast spore, suggesting the spore germination process. Using cryogenic technologies, a 3D resolution of 5–10 nm should be achievable by X-ray diffraction microscopy. This work hence paves a way for quantitative 3D imaging of a wide range of biological specimens at nanometer-scale resolutions that are too thick for electron microscopy.

Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities

Coherent diffraction imaging (CDI) is high-resolution lensless microscopy that has been applied to image a wide range of specimens using synchrotron radiation, X-ray free-electron lasers, high harmonic generation, soft X-ray lasers and electrons. Despite recent rapid advances, it remains a challenge to reconstruct fine features in weakly scattering objects such as biological specimens from noisy data. Here an effective iterative algorithm, termed oversampling smoothness (OSS), for phase retrieval of noisy diffraction intensities is presented. OSS exploits the correlation information among the pixels or voxels in the region outside of a support in real space. By properly applying spatial frequency filters to the pixels or voxels outside the support at different stages of the iterative process (i.e. a smoothness constraint), OSS finds a balance between the hybrid input-output (HIO) and error reduction (ER) algorithms to search for a global minimum in solution space, while reducing the oscillations in the reconstruction. Both numerical simulations with Poisson noise and experimental data from a biological cell indicate that OSS consistently outperforms the HIO, ER-HIO and noise robust (NR)-HIO algorithms at all noise levels in terms of accuracy and consistency of the reconstructions. It is expected that OSS will find application in the rapidly growing CDI field, as well as other disciplines where phase retrieval from noisy Fourier magnitudes is needed. The MATLAB (The MathWorks Inc., Natick, MA, USA) source code of the OSS algorithm is freely available from http://www.physics.ucla.edu/research/imaging.

Optical second-harmonic generation from a monolayer of centrosymmetric molecules adsorbed on silver

Abstract An increase in the optical second-harmonic signal arising from an electrochemically treated silver surface upon adsorption of a monolayer of the centrosymmetric molecule pyrazine is reported and an effective second-order non-linear polariz-ability for the adsorbed species deduced. These investigations illustrate the potential of second-harmonic generation in the elucidation of interfaces.

EQUILIBRIUM AND TRANSIENT STUDY OF ADSORPTION OF PYRIDINE ON SILVER IN AN ELECTROLYTIC SOLUTION

Abstract Surface-enhanced second-harmonic generation and surface-enhanced Raman scattering are used to study the adsorption of pyridine on silver in an electrolytic solution. The observed adsorption isotherms can be approximated by Langmuir curves, but the transient behaviors are difficult to understand.

Coherent diffraction microscopy at SPring-8: instrumentation, data acquisition and data analysis

An instrumentation and data analysis review of coherent diffraction microscopy at SPring-8 is given. This work will be of interest to those who want to apply coherent diffraction imaging to studies of materials science and biological samples.

Effect of extended surface plasmons on surface enhanced Raman scattering

Abstract Surface enhanced Raman scattering of pyridine adsorbed to weakly roughened silver films is studied using a well-characterized extended surface plasmon excitation. We show that the additional increase in the Raman signal associated with the extended surface plasmon is fully accounted for by the enhancement in the average macroscopic field.

Three-dimensional imaging of a phase object from a single sample orientation using an optical laser

, 224104 (2011)] purports a “matrix rank analysis” and anoptical experiment in support of the three-dimensional (3D) imaging technique called “ankylography.” However,the mathematical analysis does not appear to be conclusive, and the one used in the experiment is more a3D-supported scattering object of actually 2D complexity than a 3D-distributed scattering object of truly 3Dcomplexity. Consequently, the article provides little support to the “ankylography” technique.DOI: 10.1103/PhysRevB.86.226101 PACS number(s): 42

Atomic Electron Tomography: Probing 3D Structure and Material Properties at the Single-Atom Level

1. Dept. of Physics and Astronomy and California NanoSystems Institute, UCLA, CA, USA. 2. Dept. of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan. 3. NCEM, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 4. Dept. of Physics, University at Buffalo, the State University of New York, Buffalo, NY, USA. 5. Nanoscale Physics Research Laboratory, School of Physics and Astronomy, University of Birmingham, Edgbaston, Birmingham, UK. 6. National Center for Computational Sciences, ORNL, Oak Ridge, TN, USA. 7. Computer Science and Mathematics Division, ORNL, Oak Ridge, TN, USA. 8. Center for Nanophase Materials Sciences, ORNL, Oak Ridge, TN, USA. 9. Dept. of Physics, University of Nebraska at Omaha, Omaha, NE, USA.

Determination of three-dimensional atomic positions from tomographic reconstruction using ensemble empirical mode decomposition

Tomographic reconstruction from a tilt series of electron micrographs has raised great interest in materials, chemical, and condensed matters science because of its capability of revealing 3D local atomic structures within nanomaterials. Previous breakthroughs have demonstrated that the positions of individual atoms can not only be visualized but also determined by combining a scanning transmission electron microscope with a high-angle annular dark-field detector, equally sloped tomography, and the filtering/denoising method. However, the filtering/denoising approach—whether imposed on 2D projections or 3D reconstruction—raises concerns regarding the robustness of image processing, the accuracy of atomic positions, and the artificial atoms introduced during filtering. In this article, we report a general method that overcomes these limitations. By removing unphysical oscillations in 2D projections through ensemble empirical mode decomposition and applying a standard Wiener filter to the 3D reconstruction, we are able to determine atomic structures with higher accuracy.