Frontier methods in coherent X-ray diffraction for high-resolution structure determination

Electron scattering beyond the independent atom model: Quantum fluctuation of the Coulomb potential

In the past century, electron scattering has mostly served as a powerful tool to measure the microscopic structure of gases, liquids, and solids in either a static or time-resolved manner. One common basis for these works is the independent atom model, which directly relates electron scattering signals to the atomic structure of matter. In this perspective, we explore the information content of electron scattering that goes beyond the independent atom model. We show that the small-angle limit of the electron scattering signal encodes the quantum mechanical fluctuation of the long-range Coulomb potential. This quantum fluctuation, described by the second moment of the dipole operator, is the root cause of the intermolecular van der Waals forces.

Oxidation-induced three-dimensional morphological changes in Ni nanoparticles observed by coherent X-ray diffraction imaging

Three-dimensional structures of Ni nanoparticles undergoing significant morphological changes on oxidation were observed non-destructively using coherent X-ray diffraction imaging. The Ni particles were oxidized into Ni₁O₁ while forming pores of various sizes internally. For each Ni nanoparticle, one large void was identified at a lower corner near the interface with the substrate. The porosity of the internal region of the agglomerated Ni oxide was about 38.4%. Regions of high NiO density were mostly observed at the outer crust of the oxide or at the boundary with the large voids. This research expands our understanding of general catalytic reactions with direct observation of oxidation-induced nanoscale morphological changes.

Phase separated bi-metallic PtNi nanoparticles formed by pulsed laser dewetting

We present morphological and compositional analysis of phase-separated Pt-Ni alloy nanoparticles (NPs) formed by ns pulsed laser dewetting. The PtNi NPs obtained by the pulsed laser dewetting consist of phase-separated multiple domains including Pt₃Ni, PtNi and PtNi₃ phases with various crystal orientations as revealed by transmission electron microscopy, which is in contrast to thermal dewetting resulting NPs of a uniform composition. A three-dimensional (3D) electron density map of a dewetted PtNi NP obtained using the coherent x-ray diffraction microscopy elucidates the 3D morphology of Pt- and Ni-rich regions together with a nano-cavity formed during the pulsed laser irradiation.

Data-driven challenges and opportunities in crystallography

Structural biology is in the midst of a revolution fueled by faster and more powerful instruments capable of delivering orders of magnitude more data than their predecessors. This increased pace in data gathering introduces new experimental and computational challenges, frustrating real-time processing and interpretation of data and requiring long-term solutions for data archival and retrieval. This combination of challenges and opportunities is driving the exploration of new areas of structural biology, including studies of macromolecular dynamics and the investigation of molecular ensembles in search of a better understanding of conformational landscapes. The next generation of instruments promises to yield even greater data rates, requiring a concerted effort by institutions, centers and individuals to extract meaning from every bit and make data accessible to the community at large, facilitating data mining efforts by individuals or groups as analysis tools improve.

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data

Hybrid approaches for the modeling of macromolecular complexes that combine computational molecular mechanics simulations with experimental data are discussed. Experimental data for biological molecular structures are often low-resolution, and thus, do not contain enough information to determine the atomic positions of molecules. This is especially true when the dynamics of large macromolecules are the focus of the study. However, computational modeling can complement missing information. Significant increase in computational power, as well as the development of new modeling algorithms allow us to model structures of biological macromolecules reliably, using experimental data as references. We review the basics of molecular mechanics approaches, such as atomic model force field, and coarse-grained models, molecular dynamics simulation and normal mode analysis and describe how they could be used for flexible fitting hybrid modeling with experimental data, especially from cryo-EM and SAXS.

Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core-shell architecture were used as a model system for proof-of-principle coherent diffractive single-particle imaging experiments. To deal with the heterogeneity of the core-shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core-shell architecture.

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge

Precise localization of nanoparticles within a cell is crucial to the understanding of cell-particle interactions and has broad applications in nanomedicine. Here, we report a proof-of-principle experiment for imaging individual functionalized nanoparticles within a mammalian cell by correlative microscopy. Using a chemically-fixed HeLa cell labeled with fluorescent core-shell nanoparticles as a model system, we implemented a graphene-oxide layer as a substrate to significantly reduce background scattering. We identified cellular features of interest by fluorescence microscopy, followed by scanning transmission X-ray tomography to localize the particles in 3D, and ptychographic coherent diffractive imaging of the fine features in the region at high resolution. By tuning the X-ray energy to the Fe L-edge, we demonstrated sensitive detection of nanoparticles composed of a 22 nm magnetic Fe3O4 core encased by a 25-nm-thick fluorescent silica (SiO2) shell. These fluorescent core-shell nanoparticles act as landmarks and offer clarity in a cellular context. Our correlative microscopy results confirmed a subset of particles to be fully internalized, and high-contrast ptychographic images showed two oxidation states of individual nanoparticles with a resolution of ~16.5 nm. The ability to precisely localize individual fluorescent nanoparticles within mammalian cells will expand our understanding of the structure/function relationships for functionalized nanoparticles.