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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↗

Characterization of Static Recrystallization of a Ni-Cr-Mo-Based C276 Superalloy in Two-Stage Isothermal Compression

In order to clarify the microstructure evolution characteristics during holding period after slight degree of deformation for a Ni-Cr-Mo-based C276 superalloy, two-stage isothermal compression tests have been performed at the temperature range of 1000-1150 °C and the strain rate range of 0.1-5 s{sup −1}. The stress–strain curves and microstructure observation infer that both static recovery (SRV) and static recrystallization (SRX) took place during the holding period when the specimens were deformed at 1100-1150 °C and only SRV occurred in the specimens that deformed at the temperatures lower than 1100 °C. The softening effects increase with the increasing temperature and deformation degree, while the influence of strain rate seems less pronounced because of the limited stored energy resulted from the small deformation. The grain boundary characteristics, analyzed using electron backscatter diffraction technique, indicate that high densities of twins and Σ3 grain boundaries form associated with the nucleation and growth of SRX grains. Finally, the recrystallization during and after deformation, i.e., dynamic recrystallization, SRX and metadynamic recrystallization, was discussed concurrently.

36 MATERIALS SCIENCE↗

Neutron diffraction: a primer

Because of the neutron’s special properties, neutron diffraction may be considered one of the most powerful techniques for structure determination of crystalline and related matter. Neutrons can be released from nuclear fission, from spallation processes, and also from low-energy nuclear reactions, and they can then be used in powder, time-of-flight, texture, single crystal, and other techniques, all of which are perfectly suited to clarify crystal and magnetic structures. With high neutron flux and sufficient brilliance, neutron diffraction also excels for diffuse scattering, for in situ and operando studies as well as for high-pressure experiments of today’s materials. For these, the wave-like neutron’s infinite advantage (isotope specific, magnetic) is crucial to answering important scientific questions, for example, on the structure and dynamics of light atoms in energy conversion and storage materials, magnetic matter, or protein structures. In this primer, we summarize the current state of neutron diffraction (and how it came to be), but also look at recent advances and new ideas, e.g., the design of new instruments, and what follows from that.

36 MATERIALS SCIENCE↗

Spatial dynamics of lithiation and lithium plating during high-rate operation of graphite electrodes

The principal inhibitor of fast charging lithium ion cells is the graphite negative electrode, where favorable conditions for lithium plating occur at high charge rates, causing accelerated degradation and safety concerns. The local response of graphite, both at the electrode and particle level, when exposed to fast charging conditions of around 6C is not well understood. Consequently, the conditions that lead to the onset of lithium plating, as well as the local dynamics of lithium plating and stripping, have also remained elusive. Here, we use high-speed (100 Hz) pencil-beam X-ray diffraction to repeatedly raster along the depth of a 101 μm thick graphite electrode in 3 μm steps during fast (up to 6C) charge and discharge conditions. Consecutive depth profiles from separator to current collector were each captured in 0.5 seconds, giving an unprecedented spatial and temporal description of the state of the electrode and graphite's staging dynamics during high rate conditions. The electrode is preferentially activated near the separator, and the non-uniformity increases with rate and is influenced by free-energy barriers between graphite's lithiation stages. The onset of lithium plating and stripping was quantified, occurring only within the first 15 μm from the separator. The presence of lithium plating changed the behavior of the underlying graphite, such as causing co-existence of LiC 6 and graphite in the fully discharged state. Finally, the staging behavior of graphite at different rates was quantified, revealing a high dependency on rate and drastic hysteresis between lithiation and delithiation.

25 ENERGY STORAGE↗

Dynamics and Structure of Molten Neodymium Titanate

Binary rare earth titanates can be vitrified using levitation melt quenching, and their glasses are promising for optical applications. To better understand their thermophysical properties and dynamics, we have used molecular dynamics (MD) and empirical potential structure refinement (EPSR) to simulate molten neodymium titanate, 83TiO 2 –17Nd 2 O 3 . The models are compared with high-energy synchrotron X-ray diffraction of the melt structure over 1060–1960 K and thermophysical property measurements of electrostatically levitated droplets over 1500–2200 K. As temperature increases, the network periodicity increases and the correlation length decreases, both in monotonic trends that suggest continuous structural evolution through the melt and supercooled liquid regimes. At 1900 K, the mean Ti–O and Nd–O coordination numbers are 5.8(5) and 6.7(5), compared to the glass, 5.72(6) and 7.70(26). The equilibrium melting point is measured as 1860(20) K, over 100 K higher than previous estimates. Viscosity data from MD are in good agreement with experimental measurements. The dynamic propensity of Nd is similar to that of the network-forming Ti, suggesting that Nd does not participate as a conventional modifier. The viscosity of this fragile liquid is likely controlled by the breaking of cation–oxygen bonds and rearrangements of Ti–O polyhedra.

molecular dynamics↗

Solute effects upon dislocation motion and recovery in Mg alloys (Final Report)

The objective the research was to develop a firmer understanding of the interactions between substitutional solute atoms and dislocations within Mg alloys. These interactions govern the absolute and relative mobilities of various types of dislocations in Mg (e.g., basal < a>, non-basal < a>, and pyramidal < c+a>). Furthermore, they have an impact on dislocation recovery processes (e.g., cross-glide, climb, rearrangement, and annihilation). Ultimately, solute-dislocation interactions strongly impact a) strain hardening, b) strain rate sensitivity, c) plastic anisotropy of textured polycrystals, d) texture evolution, e) dislocation substructures evolution, and even f) recrystallization behavior. It is broadly known that Mg alloys exhibit poor low temperature formability. Since formability is largely governed by properties (a) – (c) in this list, it is critical to develop a better understanding of solute-dislocation interactions, if one hopes to improve the situation. While the theory of static solute strengthening is well developed, especially for alloys with face centered cubic (FCC) crystal structures, there are outstanding questions related to applications to hexagonal close packed (HCP) crystal structures and dynamic strain aging (DSA) in materials of various structures. DSA has far-reaching implications for metal formability and, in the case of Mg alloys, appears to correlate with the so-called rare-earth (RE) texture which has been shown to benefit formability. The Portevin-Le Chatelier (PLC) effect, and associated negative strain rate sensitivity, occur at higher temperatures (>100℃) in Mg alloys as compared with similar Al alloys, even though they have similar melting points and solute diffusivities. Our preliminary research has shown that modern, physics-based models of DSA can be tuned to describe the behavior of Mg alloys if a rather higher activation enthalpy is assumed for cross-core diffusivity. While this partially explains the delay in DSA to higher temperatures, it is also hypothesized that this delay is due in part to the intrinsically more thermally activated (rate sensitive) nature of non-basal < a> dislocation motion which is required for macroscopic flow of Mg alloys, whereas octahedral slip in many FCC metals like aluminum is essentially athermal at room temperature. It was originally proposed to employ a combination of in-situ diffraction-based experimental characterization to validate existing theory. It was envisioned to perform in-situ transmission electron microscopy (TEM) to assess individual dislocation behavior and in-situ high-energy X-ray diffraction (HEXRD) techniques which were showing great promise for elucidating collective dislocation behavior, 2 including recovery, especially if the contributions to various forms of diffraction peak broadening (𝜂𝜂,𝜔𝜔,and 2𝜃𝜃) can be effectively integrated. Finally, it was envisioned to perform discrete dislocation dynamics (DDD) modeling approaches to aide in the interpretation of both TEM and HEXRD experiments. In the end, mechanical tests were performed on more complex Mg alloys which exhibited evidence of dynamic strain aging, and this led to the establishment of another project. Mechanical test data obtained at McMaster University served as the basis of an assessment of the applicability of Bazinski’s “stress equivalence” theory of solute strengthening to polycrystalline alloys of Mg. Although we did not succeed in applying the approach to Mg alloys, we did develop expertise with the HEXRD approach using a BCC, β-Ti alloy and demonstrated numerous new capabilities that may be applied to any polycrystalline material in collaboration with researchers at CHESS and around the world: (1) assessment of details of the elastoplastic transition (yielding) using a combination of HEXRD and full-field polycrystal plasticity modeling, (2) the first-ever experimental observation of strong stress rotation within the individual grains of a polycrystalline material, and (3) a comprehensive analysis of the grain-level dislocation density evolution based upon diffraction peak broadening along 𝜂𝜂,𝜔𝜔,and 2𝜃𝜃 directions. This final aspect allowed us to confirm that dislocations were gliding on multiple plane types and not restricted to {110} type planes, and it also provided clues as to why some grains were unloading during straining, with surprising implications for our understanding of the effects of geometrically necessary dislocations (GNDs). Finally, graduate student, Mohammed Shabana, developed a MATLAB code which confirmed the conclusions of Prof. Catalin Picu (Rensallear Polytechnic Institute, RPI) regarding the effect of solute-trapped, forest dislocations on the breaking stress of Lomer lock junctions in FCC metal alloys. He applied the same anisotropic line-tension model to a variety of dislocation junction configurations and found an inconsistency in the widely cited results of Dupuy and Fivel regarding the Hirth Lock, and he outlined an approach to extend these finding to HCP Mg alloys that we are still pursuing with discretionary fundings at UVA.

36 MATERIALS SCIENCE↗

Ultrafast visualization of incipient plasticity in dynamically compressed matter

Plasticity is ubiquitous and plays a critical role in material deformation and damage; it inherently involves the atomistic length scale and picosecond time scale. A fundamental understanding of the elastic-plastic deformation transition, in particular, incipient plasticity, has been a grand challenge in high-pressure and high-strain-rate environments, impeded largely by experimental limitations on spatial and temporal resolution. Here, we report femtosecond MeV electron diffraction measurements visualizing the three-dimensional (3D) response of single-crystal aluminum to the ultrafast laser-induced compression. We capture lattice transitioning from a purely elastic to a plastically relaxed state within 5 ps, after reaching an elastic limit of ~25 GPa. Our results allow the direct determination of dislocation nucleation and transport that constitute the underlying defect kinetics of incipient plasticity. Large-scale molecular dynamics simulations show good agreement with the experiment and provide an atomic-level description of the dislocation-mediated plasticity.

36 MATERIALS SCIENCE↗

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗

Metal–Ligand Based Mechanophores Enhance Both Mechanical Robustness and Electronic Performance of Polymer Semiconductors

The backbone of diketopyrrolopyrrole-thiophene-vinylene-thiophene-based polymer semiconductors (PSCs) is modified with pyridine (Py) or bipyridine ligands to complex Fe(II) metal centers, allowing the metal–ligand complexes to act as mechanophores and dynamically crosslink the polymer chains. Here, mono- and bi-dentate ligands are observed to exhibit different degrees of bond strengths, which subsequently affect the mechanical properties of these Wolf-type-II metallopolymers. The counter ion also plays a crucial role, as it is observed that Py-Fe mechanophores with non-coordinating BPh 4 – counter ions (Py-FeB) exhibit better thin film ductility with lower elastic modulus, as compared to the coordinating chloro ligands (Py-FeC). Interestingly, besides mechanical robustness, the electrical charge carrier mobility can also be enhanced concurrently when incorporating Py-FeB mechanophores in PSCs. This is a unique observation among stretchable PSCs, especially that most reports to date describe a decreased mobility when the stretchability is improved. Next, it is determined that improvements to both mobility and stretchability are correlated to the solid-state molecular ordering and dynamics of coordination bonds under strain, as elucidated via techniques of grazing-incidence X-ray diffraction and X-ray absorption spectroscopy techniques, respectively. This study provides a viable approach to enhance both the mechanical and the electronic performance of polymer-based soft devices.

36 MATERIALS SCIENCE↗

Deuteration as a Means to Tune Crystallinity of Conducting Polymers

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied in this paper experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of the dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton–proton and deuteron–deuteron motions but not of the proton–deuteron motion. Thus and finally, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anomalous Nanoscale Optoacoustic Phonon Mixing in Nematic Mesogens

Recent inelastic X-ray scattering (IXS) experiments on mesogens have shown entirely new capabilities with regards to their nanoscale phonon-assisted heat management. Mesogens such as nematic liquid crystals (LCs) are appealing systems for study because their structure and morphology can easily be tuned. We report on Q-resolved ultra-high-resolution IXS, X-ray diffraction, and THz time-domain spectroscopy experiments combined with large-scale all-atom molecular dynamics simulations on the dynamic properties of 5CB LCs. For the first time, we observe a strong mixing of phonon excitations originating from independent in-phase and out-of-phase van-der-Waals-mediated displacement patterns. The coexistence of transverse acoustic and optical modes of 5CB LCs at near room temperature is revealed through the emergent transverse phonon gap and THz light–phonon coupling taking place within the same energy range. Moreover, our experimental observations are supported by analysis showing correlations of spontaneous fluctuations of LCs on picosecond time scales. These findings are significant for the design of a new generation of soft molecular vibration-sensitive nanoacoustic and optomechanical applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Monitoring a Silent Phase Transition in CH 3 NH 3 PbI 3 Solar Cells via Operando X-ray Diffraction

The relatively modest temperature of the tetragonal-to-cubic phase transition in CH 3 NH 3 PbI 3 perovskite is likely to occur during real world operation of CH 3 NH 3 PbI 3 solar cells. In this work, we simultaneously monitor the structural phase transition of the active layer along with solar cell performance as a function of the device operating temperature. The tetragonal to cubic phase transition is observed in the working device to occur reversibly at temperatures between 60.5 and 65.4 degrees C. In these operando measurements, no discontinuity in the device performance is observed, indicating electronic behavior that is insensitive to the structural phase transition. Here, this decoupling of device performance from the change in long-range order across the phase transition suggests that the optoelectronic properties are primarily determined by the local structure in CH 3 NH 3 PbI 3 . That is, while the average crystal structure as probed by X-ray diffraction shows a transition from tetragonal to cubic, the local structure generally remains well characterized by uncorrelated, dynamic octahedral rotations that order at elevated temperatures but are unchanged locally.

14 SOLAR ENERGY↗

A database of synthetic inelastic neutron scattering spectra from molecules and crystals

Abstract Inelastic neutron scattering (INS) is a powerful tool to study the vibrational dynamics in a material. The analysis and interpretation of the INS spectra, however, are often nontrivial. Unlike diffraction, for which one can quickly calculate the scattering pattern from the structure, the calculation of INS spectra from the structure involves multiple steps requiring significant experience and computational resources. To overcome this barrier, a database of INS spectra consisting of commonly seen materials will be a valuable reference, and it will also lay the foundation of advanced data-driven analysis and interpretation of INS spectra. Here we report such a database compiled for over 20,000 organic molecules and over 10,000 inorganic crystals. The INS spectra are obtained from a streamlined workflow, and the synthetic INS spectra are also verified by available experimental data. The database is expected to greatly facilitate INS data analysis, and it can also enable the utilization of advanced analytics such as data mining and machine learning. Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Probing the pathway of an ultrafast structural phase transition to illuminate the transition mechanism in Cu 2 S

Disentangling the primary order parameter from secondary order parameters in phase transitions is critical to the interpretation of transition mechanisms in strongly correlated systems and quantum materials. Here in this work, we present a study of structural phase transition pathways in superionic Cu 2 S nanocrystals that exhibit intriguing properties. Utilizing ultrafast electron diffraction techniques sensitive to both the momentum-space and the time-domain, we distinguish the dynamics of crystal symmetry breaking and lattice expansion in this system. We are able to follow the transient states along the transition pathway, and so observe the dynamics of both the primary and secondary order parameters. Based on these observations, we argue that the mechanism of structural phase transition in Cu 2 S is dominated by the electron-phonon coupling. Lastly, this mechanism advances the understanding from previous results, where the focus was solely on dynamic observations of the lattice expansion.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Generation regimes of an Nd : YAG laser with mode locking by a travelling-wave acousto-optic modulator and spherical mirror

The lasing regimes of a diode-pumped Nd : YAG laser with mode locking by a spherical mirror and a travelling-wave acousto-optic modulator (SMAOM method) are investigated. The lasing dynamics at mode spacing detuning from the doubled operating modulator frequency and with a change in the diffraction modulator efficiency is studied. The results of measuring the pulse duration and the frequency spectrum of output radiation are presented. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Se diffusion in CdTe thin films for photovoltaics

Manipulating CdSeTe bandgrading to enhance photocurrent and carrier lifetime is an essential part of high-performance CdTe photovoltaics (PVs). Here, we examine Se diffusion kinetics in single-crystal and polycrystalline CdTe during deposition, thermal annealing, and CdCl 2 treatments. Se distributions are determined by dynamic secondary-ion-mass spectroscopy and Auger electron spectroscopy depth profiling and coupled with electron backscatter diffraction images of the crystalline structure. Effective bulk and grain boundary diffusion coefficients are determined by analytical models and discussed in the context of processing and film morphology. Se is found to diffuse in CdTe at much higher rates during CdCl 2 treatments than with thermal processing alone. GB diffusion also occurs at a significantly faster rate than bulk diffusion. As a result of these two effects, the near interface bulk and GB Se diffusion during CdCl 2 treatments dominates the bandgrading profiles in CdTe PVs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Atomistic three-dimensional coherent x-ray imaging of nonbiological systems

We computationally study the resolution limits for three-dimensional coherent x-ray diffractive imaging of heavy, nonbiological systems using Ar clusters as a prototype. We treat electronic and nuclear dynamics on an equal footing and remove the frozen-lattice approximation often used in electronic damage studies. We explore the achievable resolution as a function of pulse parameters (fluence level, pulse duration, and photon energy) and particle size. The contribution of combined lattice and electron dynamics is not negligible even for 2 fs pulses, and the Compton scattering is less deleterious than in biological systems for atomic-scale imaging. Although free-electron scattering represents a significant background, we find that recovery of the original structure is in principle possible with 3 angstrom resolution for particles of 11 nm diameter.

47 OTHER INSTRUMENTATION↗