Effect of lattice mismatch and shell thickness on strain in core@shell nanocrystals
Abstract not provided
Gamler, Jocelyn T.L.↗
SEARCH · Engineering Papers
Results for “atomic resolution”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Electron inelastic mean free path in water
Liquid phase transmission electron microscopy (LPTEM) is rapidly developing as a powerful tool for probing processes in liquid environments with close to atomic resolution. Knowledge of the water thickness is needed for reliable interpretation and modelling of analytical studies in LPTEM, and is particularly essential when using thin liquid layers, required for achieving the highest spatial resolutions. Furthermore, the log-ratio method in electron energy-loss spectroscopy (EELS) is often applied in TEM to quantify the sample thickness, which is measured relative to the inelastic mean free path ( λ IMFP ). However, λ IMFP itself is dependent on sample material, the electron energy, and the convergence and divergence angles of the microscope electronoptics. Here, we present a detailed quantitative analysis of the λ IMFP of water as functions of the EELS collection angle ( β ) at 120 keV and 300 keV in a novel nanochannel liquid cell. We observe good agreement with earlier studies conducted on ice, but find that the most widely used theoretical models significantly underestimate λ IMFP of water. We determine an adjusted average energy-loss term E m, water , and characteristic scattering angle θ E, water that improve the accuracy. The results provide a comprehensive knowledge of the λ IMFP of water (or ice) for reliable interpretation and quantification of observations in LPTEM and cryo-TEM studies.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins
Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro-Michael process. Furthermore, this series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON–OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Plastic recognition and electrogenic uniport translocation of 1 st -, 2 nd -, and 3 rd -row transition and post-transition metals by primary-active transmembrane P 1B-2 -type ATPase pumps
Transmembrane P 1B -type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn(II)-pumps of the P 1B-2 -type subclass, in addition to Zn 2+ , select diverse metals (Pb 2+ , Cd 2+ and Hg 2+ ) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn(II)-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a “multi-probe” approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray absorption spectroscopy (XAS), we demonstrate that Zn(II)-pumps are electrogenic uniporters that preserve the transport mechanism with 1 st -, 2 nd - and 3 rd -row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Surfactant-like peptide gels are based on cross-β amyloid fibrils
Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form supramolecular hydrogels. These peptides have been explored extensively as substrates for the creation of functional materials since a wide variety of amphipathic sequences can be prepared from commonly available amino acid precursors. The self-assembly behavior of surfactant-like peptides has been compared to that observed for small molecule amphiphiles in which nanoscale phase separation of the hydrophobic domains drives the self-assembly of supramolecular structures. Here, we investigate the relationship between sequence and supramolecular structure for a pair of bola-amphiphilic peptides, Ac-KLIIIK-NH 2 (L2) and Ac-KIIILK-NH 2 (L5). Despite similar length, composition, and polar sequence pattern, L2 and L5 form morphologically distinct assemblies, nanosheets and nanotubes, respectively. Cryo-EM helical reconstruction was employed to determine the structure of the L5 nanotube at near-atomic resolution. Rather than displaying self-assembly behavior analogous to conventional amphiphiles, the packing arrangement of peptides in the L5 nanotube displayed steric zipper interfaces that resembled those observed in the structures of β-amyloid fibrils. Like amyloids, the supramolecular structures of the L2 and L5 assemblies were sensitive to conservative amino acid substitutions within an otherwise identical amphipathic sequence pattern. This study highlights the need to better understand the relationship between sequence and supramolecular structure to facilitate the development of functional peptide-based materials for biomaterials applications.
Das, Abhinaba [Emory University, Atlanta, GA (Unit↗
Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis
Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted intensities are affected by partiality. To tackle these issues, one established procedure is that of splitting the data into time bins, and averaging the multiple measurements of equivalent reflections within each bin. This binning and averaging often involve a loss of information. Here, we propose an alternative approach, which we call low-pass spectral analysis (LPSA). In this method, the data are projected onto the subspace defined by a set of trigonometric functions, with frequencies up to a certain cutoff. This approach attenuates undesirable high-frequency features and facilitates retrieving the underlying dynamics. A time-lagged embedding step can be included prior to subspace projection to improve the stability of the results with respect to the parameters involved. Subsequent modal decomposition allows to produce a low-rank description of the system's evolution. Using a synthetic time-evolving model with incomplete and partial observations, we analyze the LPSA results in terms of quality of the retrieved signal, as a function of the parameters involved. We compare the performance of LPSA to that of a range of other sophisticated data analysis techniques. We show that LPSA allows to achieve excellent dynamics reconstruction at modest computational cost. Finally, we demonstrate the superiority of dynamics retrieval by LPSA compared to time binning and merging, which is, to date, the most commonly used method to extract dynamical information from TR-SFX data.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
59 BASIC BIOLOGICAL SCIENCES↗
Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein
Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Scaling and merging time-resolved pink-beam diffraction with variational inference
Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often difficult. Extracting small, time-dependent changes in signal is frequently a bottleneck for practitioners. Recent work demonstrated this challenge can be addressed when merging redundant observations by a statistical technique known as variational inference (VI). However, the variational approach to time-resolved data analysis requires identification of successful hyperparameters in order to optimally extract signal. In this case study, we present a successful application of VI to time-resolved changes in an enzyme, DJ-1, upon mixing with a substrate molecule, methylglyoxal. We present a strategy to extract high signal-to-noise changes in electron density from these data. Furthermore, we conduct an ablation study, in which we systematically remove one hyperparameter at a time to demonstrate the impact of each hyperparameter choice on the success of our model. We expect this case study will serve as a practical example for how others may deploy VI in order to analyze their time-resolved diffraction data.
47 OTHER INSTRUMENTATION↗
Addressing the sensitivity of signals from solid/liquid ambient pressure XPS (APXPS) measurement
Ambient pressure XPS has demonstrated its great potential in probing the solid/liquid interface, which is a central piece in electrocatalytic, corrosion, and energy storage systems. Additionally, despite the advantage of ambient pressure XPS being a surface sensitive characterization technique, the ability of differentiating the surface adsorbed species (~Å scale) and bulk electrolyte (~10 nm scale) in the spectrum depends on the delicate balance between bulk solution concentration (C), surface coverage (θ), bulk liquid layer thickness (L), and inelastic mean free path (λ) as a function of photon energy. By investigating a model system of gold dissolving in a bromide solution, the connection between theoretical prediction at the atomic resolution and macroscopic observable spectrum is established.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Theory and application of the vector pair correlation function for real-space crystallographic analysis of order/disorder correlations from STEM images
Deviations of local structure and chemistry from the average crystalline unit cell are increasingly recognized to have a significant influence on the properties of many technologically important materials. Here, we present the vector pair correlation function (vPCF) as a new real-space crystallographic analysis method, which can be applied to atomic-resolution scanning transmission electron microscopy (STEM) images to quantify and analyze structural order/disorder correlations. Our STEM-based vPCFs have several advantages over radial PCFs and/or 3D pair distribution functions from x-ray total scattering: vPCFs explicitly retain crystallographic orientation information, are spatially resolved, can be applied directly on a sublattice basis, and are suitable for any material that can be imaged with STEM. To show the utility of our approach, we measure partial vPCFs in Ba 5 SmSn 3 Nb 7 O 30 (BSSN), a tetragonal tungsten bronze (TTB) structured complex oxide. Many TTBs are known to be classical or relaxor ferroelectrics, and these properties have been correlated with the presence of superlattice ordering. BSSN, specifically, exhibits relaxor behavior and an incommensurate structural modulation. From the vPCF data, we observe that, of the cation sites, only the Ba (A2) sublattice is structurally modulated. We then infer the local modulation vector and reveal a marked anisotropy in its correlation length. Finally, short-range correlated polar displacements on the B2 cation sites are observed. This work introduces the vPCF as a powerful real-space crystallography technique, which enables direct, robust quantification of short-to-long range order on a sublattice-specific basis and is applicable to a wide range of complex material types.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystal structure and magnetic properties in semiconducting Eu 3-δ Zn x Sn y As 3 with Eu-Eu dimers
Magnetic structure and crystal symmetry, which primarily determine the time-reversal and inversion symmetry, may give rise to numerous exotic quantum phenomena in magnetic semiconductors and semimetals when arranged in different patterns. Here, a new layered magnetic semiconductor, Eu 3-δ Zn x Sn y As 3 , was discovered and high-quality single crystals were grown using the Sn flux. According to structural characterization by x-ray diffraction and atomic-resolution scanning transmission electron microscopy, Eu 3-δ Zn x Sn y As 3 is found to crystallize in a hexagonal symmetry with the space group P6 3 /mmc (No. 194). After examining different specimens, we conclude that their stoichiometry is fixed at ~Eu 2.6 Zn 0.65 Sn 0.85 As 3 , which meets the chemical charge balance. Eu 3-δ Zn x Sn y As 3 is composed of septuple (Eu 1-δ Sn y As 2 )-Eu-(Zn x As)-Eu sequences. The shortest Eu–Eu distance in the system is between two Eu layers separated by Zn x As along the c-axis. Magnetization measurement shows an antiferromagnetic ordering in Eu 3-δ Zn x Sn y As 3 at T N ~ 12 K, where the magnetic easy-axis is along the c-axis, and Mössbauer spectroscopy observes magnetic hyperfine splitting on Eu and Sn at 6 K. Magnetic anisotropy is significantly different from the ones along the ab-plane in other layered Eu-based magnetic semimetals. Heat capacity measurements confirm the magnetic transition around 12 K. Electrical resistivity measurement indicates semiconductor behavior with a band gap of ~0.86 eV. Finally, various Eu-based magnetic semiconductors could provide a tunable platform to study potential topological and magnetic properties.
36 MATERIALS SCIENCE↗
Formation of tubular conduction channel in a SiGe(P)/Si core/shell nanowire heterostructure
Realizing a tubular conduction channel within a one-dimensional core–shell nanowire (NW) enables better understanding of quantum phenomena and exploration of electronic device applications. Herein, we report the growth of a SiGe(P)/Si core/shell NW heterostructure using a chemical vapor deposition coupled with vapor–liquid–solid growth mechanism. The entire NW heterostructure behaves as a p-type semiconductor, which demonstrates that the high-density carriers are confined within the 4 nm-thick Si shell and form a tubular conduction channel. These findings are confirmed by both calculations and the gate-dependent current–voltage ( I d – V g ) characteristics. Atomic resolution microscopic analyses suggest a coherent epitaxial core/shell interface where strain is released by forming dislocations along the axial direction of the NW heterostructure. Additional surface passivation achieved via growing a SiGe(P)/Si/SiGe core/multishell NW heterostructure suggests potential strategies to enhance the tubular carrier density, which could be further modified by improving multishell crystallinity and structural design.
36 MATERIALS SCIENCE↗
Atomic-scale in situ observation of electron beam and heat induced crystallization of Ge nanoparticles and transformation of Ag@Ge core-shell nanocrystals
Crystallization of amorphous materials by thermal annealing has been investigated for numerous applications in the fields of nanotechnology, such as thin-film transistors and thermoelectric devices. The phase transition and shape evolution of amorphous germanium (Ge) and Ag@Ge core–shell nanoparticles with average diameters of 10 and 12 nm, respectively, were investigated by high-energy electron beam irradiation and in situ heating within a transmission electron microscope. The transition of a single Ge amorphous nanoparticle to the crystalline diamond cubic structure at the atomic scale was clearly demonstrated. Depending on the heating temperature, a hollow Ge structure can be maintained or transformed into a solid Ge nanocrystal through a diffusive process during the amorphous to crystalline phase transition. Selected area diffraction patterns were obtained to confirm the crystallization process. In addition, the thermal stability of Ag@Ge core–shell nanoparticles with an average core of 7.4 and a 2.1 nm Ge shell was studied by applying the same beam conditions and temperatures. The results show that at a moderate temperature (e.g., 385 °C), the amorphous Ge shell can completely crystallize while maintaining the well-defined core–shell structure, while at a high temperature (e.g., 545 °C), the high thermal energy enables a freely diffusive process of both Ag and Ge atoms on the carbon support film and leads to transformation into a phase segregated Ag–Ge Janus nanoparticle with a clear interface between the Ag and Ge domains. In conclusion, this study provides a protocol as well as insight into the thermal stability and strain relief mechanism of complex nanostructures at the single nanoparticle level with atomic resolution.
36 MATERIALS SCIENCE↗
Chirality reversal of magnetic solitons in chiral Cr 1/3 TaS 2
Ferromagnetism in two-dimensional (2D) materials provides an ideal platform to study emergent electromagnetic phenomena in low dimensions for future spintronics. In magnetic-element intercalated transition metal dichalcogenides, topologically nontrivial spin textures, such as chiral helimagnetic spin states and chiral soliton lattices, are realized due to the chiral lattice distortions induced by intercalated magnetic ions. Consequently, the magnetic chirality is predictably determined by the sign of antisymmetric exchange interaction (or Dzyaloshinskii–Moriya interaction, DMI) vector that is coupled to the underlying crystal chirality. Here, using cryogenic Lorentz phase microscopy, we directly observed the chirality reversal behavior of the chiral soliton lattices in Cr 1/3 TaS 2 across the structural defects. We show that a partial 1 T stacking in 2H-TaS 2 locally reduces DMI, leading to magnetic chirality reversal with direct atomic resolution imaging. Furthermore, our experimental results show that manipulation of stacking sequence provides a viable way to control the chirality of topologically nontrivial soliton lattices in 2D magnets.
2D materials↗
All polymer microfluidic chips—A fixed target sample delivery workhorse for serial crystallography
The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around “workhorse” for serial crystallography measurements. In conclusion, this Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.
59 BASIC BIOLOGICAL SCIENCES↗
Quick-connect scanning tunneling microscope head with nested piezoelectric coarse walkers
To meet changing research demands, new scanning tunneling microscope (STM) features must constantly evolve. We describe the design, development, and performance of a modular plug-in STM, which is compact and stable. The STM head is equipped with a quick-connect socket that is matched to a universal connector plug, enabling it to be transferred between systems. This head can be introduced into a vacuum system via a load-lock and transferred to various sites equipped with the connector plug, permitting multi-site STM operation. Its design allows for reliable operation in a variety of experimental conditions, including a broad temperature range, ultra-high vacuum, high magnetic fields, and closed-cycle pulse-tube cooling. The STM’s compact size is achieved by a novel nested piezoelectric coarse walker design, which allows for large orthogonal travel in the X, Y, and Z directions, ideal for studying both bulk and thin film samples ranging in size from mm to μm. Its stability and noise tolerance are demonstrated by achieving atomic resolution under ambient conditions on a laboratory desktop with no vibrational or acoustic isolation. The operation of the nested coarse walkers is demonstrated by successful navigation to a μm-sized 2D sample.
Instruments & Instrumentation↗
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗