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At least 1,333 records · Page 74

Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time‐Resolved X‐Ray Solution Scattering and Markov State Modeling

Understanding protein folding pathways is crucial to deciphering the principles of protein structure and function. Here, the unfolding dynamics of the 35‐residue villin headpiece (HP35) and a norleucine‐substituted variant (2F4K) using a combination of experimental and computational techniques is investigated. Time‐resolved X‐ray solution scattering coupled with equilibrium molecular dynamics simulations and Markov state modeling reveals distinct unfolding mechanisms between the two variants: HP35 and 2F4K. Specifically, HP35 exhibits a two‐state unfolding process, whereas an intermediate state is identified for the 2F4K mutant. A Markov state model constructed from simulations is used to map atomic‐level transitions to experimental observations, providing insights into the role of sequence variations in modulating folding pathways. The findings underscore the importance of integrating experimental and computational approaches to unravel protein unfolding mechanisms between heterogenous structural ensembles.

Nijhawan, Adam K. [Department of Chemistry Northwe↗

Toward accurate measurement of electromagnetic field by retrieving and refining the center position of non-uniform diffraction disks in Lorentz 4D-STEM

Recent advancement in scanning transmission electron microscopy (STEM) allows the use of 4D-STEM, a technique that captures an electron diffraction pattern at each scan point in STEM, to measure electrostatic and magnetic potential and field in materials. However, accurate measurement, separation of the magnetic and electric signals, and removal of artifacts remain challenging, especially in the presence of complex non-uniform diffraction contrast within the disks. In this work, based on dynamic simulations of 4D-STEM patterns built upon superstructures consisting of millions of atoms to account for different sample thickness and edge geometries, we show how the shape and intensity distribution of the central disk are affected by multiple scattering. We propose a robust refinement procedure through iteration of the spin-sensitive peak position of the disk-center in the circular Hough transform filtered images from experimental Lorentz 4D-STEM dataset after minimizing the possible artifacts, such as those due to the change of thickness, dynamic scattering, and scanning process. We verify that caution must be taken as in practice the rigid-disk-shift model used to reconstruct induction maps can easily break down due to disk-protrusion when there exists a nonconstant phase gradient or thickness within the width of the probe. Through quantitative analysis and comparing experiment with calculation the effect of the non-spin-related intensity distribution inside the disk as well as that causes the disk shift due to the intensity-protrusion can be removed, and high-quality magnetic field mapping is possible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Carbon Coating Influence on the Formation of Percolating Electrode Networks for Silicon Anodes

Previous studies have demonstrated that chemical vapor deposition carbon coating on silicon (Si@C) can enhance the electrochemical performance of lithium-ion batteries with Si-based anodes. However, the underlying mechanisms contributing to this improvement have not been fully explored. Here, we address this knowledge gap by applying a suite of characterization methods to evaluate Si@C anodes prepared by reducing acetylene on ball-milled Si particles. Raman mapping measurements show that the C coating (<5 nm thick) enables a homogeneous Si and carbon distribution during the slurry casting process, thereby promoting Si utilization during cycling. The coating’s microstructure and morphology were evaluated using X-ray photoelectron spectroscopy (XPS), scanning transmission electron microscopy, and neutron reflectivity experiments. Electrochemical impedance spectroscopy measurements upon cycling indicate that carbon coating also reduces the overall resistance as benchmarked against bare Si anodes. Galvanostatic cycling in half-cell studies revealed higher initial Coulombic efficiency and specific capacities with increasing carbon coating time. However, solid electrolyte interphase (SEI) investigations using XPS showed that the coated and uncoated samples have very similar characteristics, suggesting that the SEI may only play a minor role in enhancing the performance of Si@C. Full-cell evaluation of the Si electrodes was consistent with half-cell results relating to performance and SEI properties, further supporting the conclusion that electronic and ionic percolation, enabled by effective electrode manufacturing, are the dominant factors contributing to the favorable performance of Si@C.

25 ENERGY STORAGE↗

Single Nanoflake Photoelectrochemistry Reveals Intrananoflake Doping Heterogeneity That Explains Ensemble-Level Photoelectrochemical Behavior

Transition metal dichalcogenide (TMD) nanoflake thin films are attractive electrode materials for photoelectrochemical (PEC) solar energy conversion and sensing applications, but their photocurrent quantum yields are generally lower than those of bulk TMD electrodes. The poor PEC performance has been primarily attributed to enhanced charge carrier recombination at exposed defect and edge sites introduced by the exfoliation process. Here, a single nanoflake PEC approach reveals how an alternative effect, doping heterogeneity, limits ensemble-level PEC performance. Photocurrent mapping and local photocurrent–potential (i–E) measurements of MoS 2 nanoflakes exfoliated from naturally occurring bulk crystals revealed the presence of n- and p-type domains within the same nanoflake. Interestingly, the n- and p-type domains in the natural MoS 2 nanoflakes were equally efficient for iodide oxidation and tri-iodide reduction (IQE values exceed 80%). At the single domain-level, the natural MoS 2 nanoflakes were nearly as efficient as nanoflakes exfoliated from synthetic n-type MoS 2 crystals. Single domain-level i–E measurements explain why natural MoS 2 nanoflakes exhibit an n-type to p-type photocurrent switching effect in ensemble-level measurements: the n- and p-type diode currents from individual domains oppose each other upon illuminating the entire nanoflake, resulting in zero photocurrent at the switching potential. Furthermore, the doping heterogeneity effect is likely due to nonideal stoichiometry, where p-type domains are S-rich according to XPS measurements. Although this doping heterogeneity effect limits photoanode or photocathode performance, these findings open the possibility to synthesize efficient TMD nanoflake photocatalysts with well-defined lateral p- and n-type domains for enhanced charge separation.

14 SOLAR ENERGY↗

Chemical Evolution in Silicon–Graphite Composite Anodes Investigated by Vibrational Spectroscopy

Silicon–graphite composites are under development for the next generation of high-capacity lithium-ion anodes, and vibrational spectroscopy is a powerful tool to identify the different mechanisms that contribute to performance loss. With alloy anodes, the underlying causes of cell failure are significantly different in half-cells with lithium metal counter electrodes compared to full cells with standard cathodes. However, most studies which take advantage of vibrational spectroscopy have only examined half-cells. In this work, a combination of FTIR and Raman spectroscopy describes several factors that lead to degradation in full pouch cells with LiNi 0.5 Mn 0.3 Co 0.2 O 2 (NMC532) cathodes. The spectroscopic signatures evolve after longer term cycling compared to the initial formation cycles. Several side-reactions that consume lithium ions have clear FTIR signatures, and comparison to a library of reference compounds facilitates identification. Raman microspectroscopy combined with mapping shows that the composite anodes are not homogeneous but segregate into graphite-rich and silicon-rich phases. Lithiation does not proceed uniformly either. A basis analysis of Raman maps identifies electrochemically inactive regions of the anodes. In conclusion, the spectroscopic results presented here emphasize the importance of improving electrode processing and SEI stability to enable practical composite anodes with high silicon loadings.

25 ENERGY STORAGE↗

Absolute contrast estimation for soft X-ray photon fluctuation spectroscopy using a variational droplet model

Abstract X-ray photon fluctuation spectroscopy using a two-pulse mode at the Linac Coherent Light Source has great potential for the study of quantum fluctuations in materials as it allows for exploration of low-energy physics. However, the complexity of the data analysis and interpretation still prevent recovering real-time results during an experiment, and can even complicate post-analysis processes. This is particularly true for high-spatial resolution applications using CCDs with small pixels, which can decrease the photon mapping accuracy resulting from the large electron cloud generation at the detector. Droplet algorithms endeavor to restore accurate photon maps, but the results can be altered by their hyper-parameters. We present numerical modeling tools through extensive simulations that mimic previous x-ray photon fluctuation spectroscopy experiments. By modification of a fast droplet algorithm, our results demonstrate how to optimize the precise parameters that lift the intrinsic counting degeneracy impeding accuracy in extracting the speckle contrast. These results allow for an absolute determination of the summed contrast from multi-pulse x-ray speckle diffraction, the modus operandi by which the correlation time for spontaneous fluctuations can be measured.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nanoscale mapping of plasmon and exciton in ZnO tetrapods coupled with Au nanoparticles

Metallic nanoparticles can be used to enhance optical absorption or emission in semiconductors, thanks to a strong interaction of collective excitations of free charges (plasmons) with electromagnetic fields. Herein we present direct imaging at the nanoscale of plasmon-exciton coupling in Au/ZnO nanostructures by combining scanning transmission electron energy loss and cathodoluminescence spectroscopy and mapping. The Au nanoparticles (~30 nm in diameter) are grown in-situ on ZnO nanotetrapods by means of a photochemical process without the need of binding agents or capping molecules, resulting in clean interfaces. Interestingly, the Au plasmon resonance is localized at the Au/vacuum interface, rather than presenting an isotropic distribution around the nanoparticle. Moreover, on the contrary, a localization of the ZnO signal has been observed inside the Au nanoparticle, as also confirmed by numerical simulations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Tracking ion intercalation into layered Ti 3 C 2 MXene films across length scales

Enhancing the energy stored and power delivered by layered materials relies strongly on improved understanding of the intricate interplay of electrolyte ions, solvents, and electrode interactions as well as the role of confinement. Here we report a highly integrated study with multiscale theory/modelling and experiments to track the intercalation of aqueous Li + , Na + , K + , Cs + , and Mg 2+ ions into Ti 3 C 2 MXene. The integrated analysis of experiments assisted by theory/modelling allows for a deep understanding of energy storage processes highlighting the importance of the dynamics of cations, their positionings between MXene sheets, their effects on mechanical properties and capacitive energy storage. Computational simulations and operando calorimetry measurements prove the processes involving cation dehydration and H+ rehydration, showing a good correlation for heat variations between experiments and theory. Operando liquid AFM mapped energy dissipation of ions appears non-uniformly across the MXene surface, indicating heterogeneities of ions inside the MXene and confirming partially the ion behaviour obtained in theory. We directly demonstrate that the average distance between the cation and MXene surface follows a modified two-sided Helmholtz model when plotted versus the open circuit potential capacitance, revealing a different electrical double layer mechanism in confinement. This new fundamental understanding lays the foundation for improved functional devices utilizing electrodes and membranes made of two-dimensional materials.

36 MATERIALS SCIENCE↗

Thermoelectric transport properties of diamond-like Cu{sub 1−x}Fe{sub 1+x}S{sub 2} tetrahedral compounds

Polycrystalline samples with the composition of Cu{sub 1−x}Fe{sub 1+x}S{sub 2} (x = 0, 0.01, 0.03, 0.05, 0.1) were synthesized by a melting-annealing-sintering process. X-ray powder diffraction reveals all the samples are phase pure. The backscattered electron image and X-ray map indicate that all elements are distributed homogeneously in the matrix. The measurements of Hall coefficient, electrical conductivity, and Seebeck coefficient show that Fe is an effective n-type dopant in CuFeS{sub 2}. The electron carrier concentration of Cu{sub 1−x}Fe{sub 1+x}S{sub 2} is tuned within a wide range leading to optimized power factors. The lattice phonons are also strongly scattered by the substitution of Fe for Cu, leading to reduced thermal conductivity. We use Debye approximation to model the low temperature lattice thermal conductivity. It is found that the large strain field fluctuation introduced by the disordered Fe ions generates extra strong phonon scatterings for lowered lattice thermal conductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Spatially resolved and observer-free experimental quantification of spatial resolution in tomographic images

We present a novel framework and experimental method for the quantification of spatial resolution of a tomography system. The framework adopts the “black box” view of an imaging system, considering only its input and output. The tomography system is locally stimulated with a step input, viz., a sharp edge. The output, viz., the reconstructed images, is analysed by Fourier decomposition of their spatial frequency components, and the local limiting spatial resolution is determined using a cut-off threshold. At no point is an observer involved in the process. The framework also includes a means of translating the quantification region in the imaging space, thus creating a spatially resolved map of objectively quantified spatial resolution. As a case-study, the framework is experimentally applied using a gaseous propane phantom measured by a well-established chemical species tomography system. A spatial resolution map consisting of 28 regions is produced. In isolated regions, the indicated performance is 4-times better than that suggested in the literature and varies by 57% across the imaging space. A mechanism based on adjacent but non-interacting beams is hypothesised to explain the observed behaviour. The mechanism suggests that, as also independently concluded by other methods, a geometrically regular beam array maintains maximum objectivity in reconstructions. We believe that the proposed framework, methodology, and findings will be of value in the design and performance evaluation of tomographic imaging arrays and systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Grad–Shafranov equilibria via data-free physics informed neural networks

A large number of magnetohydrodynamic (MHD) equilibrium calculations are often required for uncertainty quantification, optimization, and real-time diagnostic information, making MHD equilibrium codes vital to the field of plasma physics. In this paper, we explore a method for solving the Grad–Shafranov equation by using physics-informed neural networks (PINNs). For PINNs, we optimize neural networks by directly minimizing the residual of the partial differential equation as a loss function. We show that PINNs can accurately and effectively solve the Grad–Shafranov equation with several different boundary conditions, making it more flexible than traditional solvers. This method is flexible as it does not require any mesh and basis choice, thereby streamlining the computational process. We also explore the parameter space by varying the size of the model, the learning rate, and boundary conditions to map various tradeoffs such as between reconstruction error and computational speed. Additionally, we introduce a parameterized PINN framework, expanding the input space to include variables such as pressure, aspect ratio, elongation, and triangularity in order to handle a broader range of plasma scenarios within a single network. Parameterized PINNs could be used in future work to solve inverse problems such as shape optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

THE COORDINATED RADIO AND INFRARED SURVEY FOR HIGH-MASS STAR FORMATION. II. SOURCE CATALOG

The CORNISH project is the highest resolution radio continuum survey of the Galactic plane to date. It is the 5 GHz radio continuum part of a series of multi-wavelength surveys that focus on the northern GLIMPSE region (10 Degree-Sign < l < 65 Degree-Sign ), observed by the Spitzer satellite in the mid-infrared. Observations with the Very Large Array in B and BnA configurations have yielded a 1.''5 resolution Stokes I map with a root mean square noise level better than 0.4 mJy beam{sup -1}. Here we describe the data-processing methods and data characteristics, and present a new, uniform catalog of compact radio emission. This includes an implementation of automatic deconvolution that provides much more reliable imaging than standard CLEANing. A rigorous investigation of the noise characteristics and reliability of source detection has been carried out. We show that the survey is optimized to detect emission on size scales up to 14'' and for unresolved sources the catalog is more than 90% complete at a flux density of 3.9 mJy. We have detected 3062 sources above a 7{sigma} detection limit and present their ensemble properties. The catalog is highly reliable away from regions containing poorly sampled extended emission, which comprise less than 2% of the survey area. Imaging problems have been mitigated by down-weighting the shortest spacings and potential artifacts flagged via a rigorous manual inspection with reference to the Spitzer infrared data. We present images of the most common source types found: H II regions, planetary nebulae, and radio galaxies. The CORNISH data and catalog are available online at http://cornish.leeds.ac.uk.

79 ASTRONOMY AND ASTROPHYSICS↗

Transforming microseismic clouds into near real-time visualization of the growing hydraulic fracture

SUMMARY Microseismic observations during unconventional reservoir stimulation are typically seen as a proxy for clusters of hydraulic fractures and the extent of the stimulated reservoir. Such straightforward interpretation is often misleading and fails to provide a physically reasonable image of the fracturing process. This paper demonstrates the application of a physics-based machine learning algorithm which enables a rapid and accurate fracture mapping from the microseismic data. Our training and validation data set relies on a history-matched geomechanical modelling workflow implemented in GEOS software for the Hydraulic Fracturing Test Site 1 (HFTS-1) project. For this study we augmented the simulated fracture growth through geostatistical modelling of induced seismicity, so that the synthetic microseismic catalogue matches the main statistical properties of the field observations. We formulated the problem of mapping the actual fracture in the clutter of events to parallel common video segmentation workflows: several past video frames (microseismic density snapshots) are passed through a deep convolutional network to classify whether a given voxel is associated with a fracture or intact rock. We found that for accurate fracture mapping, the network’s input and architecture must be augmented to incorporate the fluid injection parameters (pressure, rate, concentration of proppant, and location of the perforation within the cluster). The error rate for the network reached as little as 10 per cent of the fracture area, while a conventional microseismic interpretation approach yielded ∼300 per cent. Our approach also yields must faster predictions than conventional methods (minutes instead of weeks), and could enable engineers to make rapid decisions regarding engineering parameters (pumping rate, viscosity) in real time during stimulation.

58 GEOSCIENCES↗

How do supernova remnants cool? – I. Morphology, optical emission lines, and shocks

ABSTRACT Supernovae (SNe) inject ∼1051 erg in the interstellar medium, thereby shocking and heating the gas. A substantial fraction of this energy is later lost via radiative cooling. We present a post-processing module for the flash code to calculate the cooling radiation from shock-heated gas using collisional excitation data from mappings v. When applying this tool to a simulated SN remnant (SNR), we find that most energy is emitted in the EUV. However, optical emission lines ([O iii], [N ii], [S ii], H α, H β) are usually best observable. Our shock detection scheme shows that [S ii] and [N ii] emissions arise from the thin shell surrounding the SNR, while [O iii], H $\rm \alpha$, and H $\rm \beta$ originate from the volume-filling hot gas inside the SNR bubble. We find that the optical emission lines are affected by the SNR’s complex structure and its projection on to the plane of the sky because the escaping line luminosity can be reduced by 10–80 per cent due to absorption along the line of sight. Additionally, the subtraction of contaminating background radiation is required for the correct classification of an SNR on the oxygen or sulphur BPT diagrams. The electron temperature and density obtained from our synthetic observations match well with the simulation but are very sensitive to the assumed metallicity.

Astronomy & Astrophysics↗

Wave-packet manipulation of He Rydberg states by a seeded free-electron laser

We report a two-dimensional pump-control-probe spectroscopic study of the dynamics of singly excited He Rydberg-state wave packets with a seeded extreme ultraviolet (XUV) free-electron laser (FEL) source. A pair of coherent XUV pulses, defined by their coarse time separation and relative phase, created and manipulated the wave packets. The He atoms were postionized by infrared (IR) pulses, and the ion yield was measured as a function of XUV phase and IR arrival time. We tagged and sorted the relative phase of the XUV pulse pair on a single-shot basis by fitting each FEL spectrum with a suitable function that accounts for nonidealities of the XUV pulse pairs, associated with the seeding process; more generally, the fit returns the time-dependent electric field of the FEL spectra. The experimental two-dimensional maps of ion yields, measured as a function of IR (probe) delay and of XUV (pump-control) phase, were compared with the solution of the first-order time-dependent Schrödinger equation for this field. Despite the fact that the experimental conditions imply strong excitation, beyond the approximations of first-order perturbation theory, the simulated map satisfactorily reproduces the experimental one for temporally well-separated pulses. We show that by selecting data at appropriate values of pump-control phase, we enhance or suppress the amplitude of chosen wave-packet components consisting of two or more Rydberg states. When the temporal overlap of the pulse pair cannot be neglected, the phase reconstruction is underdetermined, and we provide a simplified comparison between data and simulations. Published by the American Physical Society 2024

Dumergue, Mathieu (ORCID:0000000236984406)↗

Photoluminescence Imaging of Large-Grain CdTe for Grain Boundary Characterization

In this work, we use photoluminescence (PL) imaging to characterize CdTe grain boundary recombination. We use a silicon megapixel camera and green (532 nm) laser diodes for excitation. A microscope objective lens system is used for high spatial resolution and a field of view down to 190 um x 190 um. PL images of large-grain (5 to 50 um) CdTe samples show grain boundary and grain interior features that vary with processing conditions. PL images of samples in the as-deposited state show distinct dark grain boundaries that suggest high excess carrier recombination. A CdCl2 treatment leads to PL images with very little distinction at the grain boundaries, which illustrates the grain boundary passivation properties. Other process conditions are also shown, along with comparisons of PL images to high spatial resolution time-resolved PL carrier lifetime maps.

14 SOLAR ENERGY↗

Scalable Algorithms for Distributed-Memory Adaptive Mesh Refinement

This paper presents scalable algorithms and data structures for adaptive mesh refinement computations. We describe a novel mesh restructuring algorithm for adaptive mesh refinement computations that uses a constant number of collectives regardless of the refinement depth. To further increase scalability, we describe a localized hierarchical coordinate-based block indexing scheme in contrast to traditional linear numbering schemes, which incur unnecessary synchronization. In contrast to the existing approaches which take O(P) time and storage per process, our approach takes only constant time and has very small memory footprint. With these optimizations as well as an efficient mapping scheme, our algorithm is scalable and suitable for large, highly-refined meshes. We present strong-scaling experiments up to 2k ranks on Cray XK6, and 32k ranks on IBM Blue Gene/Q.

Langer, Akhil↗