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Deconvoluting capping ligand influence on photophysical properties in tetrathiafulvalene-based diradicaloids
Tetrathiafulvalene-2,3,6,7-tetrathiolate (TTFtt) complexes are synthetically tunable and emit brightly in the near-infrared II region (NIR II, 1000–1700 nm).
AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids
Background The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use. Results We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes. Conclusions AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.
Datasets for Pty-co-SAXSNN: CNN-Based Deconvolution for Simultaneous X-ray Ptychography and SAXS
The data comprise a simulated 3D nanoparticle clathrate dataset and an experimental 3D PtychoSAXS dataset of a supercrystal colloidal clathrate assembly, which were used to evaluate our custom Pty-co-SAXSNN framework.
Hahn-Echo Assisted Deconvolution (HEAD)
This repository contains the Bruker pulse program for acquire 2D HEAD data in addition to the C++ program used for data processing. Data must be acquired with identical digital resolution in both dimensions. The resulting 2D spectrum is converted to a ASCII file using the Topspin 'totxt' command. This file can be handled by the HEAD_processing program.
Laue-DIALS: Open-source software for polychromatic x-ray diffraction data
Most x-ray sources are inherently polychromatic. Polychromatic (“pink”) x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure—ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.
Environmental Molecular Network (ENVnet) v1
Here, we present an approach that integrates mass difference based deconvolution with molecular networking to build a static reference network from all publicly available organic matter metabolomics datasets. This is accomplished using MS/MS deconvolution coupled with both recently reported (BUDDY) and novel machine learning algorithms to determine chemical formulas and perform MS/MS alignments (REM-BLINK).
STM/S Grid LDOS Data and Analysis Code for Deciphering Majorana Zero Modes in Topological Superconductor
This dataset provides raw millikelvin scanning tunneling microscopy/spectroscopy (STM/S) grid spectroscopy data and Python analysis scripts supporting the manuscript “Deciphering Majorana Zero Modes in Topological Superconductor FeTe0.55Se0.45 with Machine-Learning-Assisted Spectral Deconvolution.” The dataset includes a raw grid spectroscopy file acquired on FeTe0.55Se0.45 at 40 mK under magnetic field, together with Python/Jupytext analysis scripts used for STM/S data processing, visualization, spectral deconvolution, Lorentzian peak fitting, feature extraction, machine-learning-assisted clustering, and figure generation. These files support the analysis of vortex-core local density of states and the identification of zero-bias-peak-related spectral components from complex in-gap states. The dataset is intended to provide a citable archival record of the data and analysis code associated with the published manuscript and to support transparency and reproducibility of the reported STM/S and machine-learning workflow.
Temporal Explosion Source Processes of Declared Nuclear Tests in the Democratic People’s Republic of Korea
In this work we highlight a preliminary temporal source analysis of the six declared Democratic People's Republic of Korea (DPRK) nuclear tests. We use regional seismic data to estimate relative source time functions (RSTFs) via iterative time-domain deconvolution (Ammon, 2006; Pippin, 2022) of vertical-component ground motions recorded within 2000 km of the source region. Since RSTFs are ideally independent of site and propagation effects, their amplitude spectrum is equivalent to the source spectral ratio, but they also retain phase information. We compare observed RSTFs (in the time and frequency domains) with synthetic RSTFs derived from the Mueller & Murphy (1971) explosion source model. The resolution of these time functions varies, however, we generally obtain high-quality results within the limitations of the recording broadband instrumentation. The results indicate that this method effectively preserves source time-history information that can be used for temporal analysis of remote nuclear explosions. This preliminary analysis is intended to assess the viability of using time-domain deconvolution methods for extracting temporal source information.
Super Resolving Unrolled Neural Networks for Remote Sensing
In remote sensing systems, the capabilities of the system are constrained by the complex interactions between size, weight, and power (SWAP) of potential designs. In electro-optical (EO) systems, examples of these critical parameters include the system’s sensitivity and resolution. Those parameters can be increased by ever larger optical apertures and focal planes but at the cost of more SWAP. Multi-image super resolution (MISR) techniques allow resolution to be enhanced via computation rather than more sophisticated optical hardware. These algorithms combine multiple images together into a single, higher resolution image, trading temporal resolution and computation for spatial resolution. Fielded MISR techniques, such as Drizzle, can require several hundred images to create a single super resolved image, implying reduced temporal resolution, increased data acquisition load, and limiting mission applications. Iterative techniques, such as model-based image reconstruction and compressive sensing, have been shown to create super resolved images using fewer images than Drizzle. They do this by posing an optimization problem that balances accuracy between a highly accurate physical model and an image model. In the case of super resolution, the physical model is defined by the relation between low resolution input images and the desired high resolution output image. The image model encodes some assumptions about the super resolved image. These assumptions are meant to suppress reconstruction artifacts that arise due to deterministic physical model error, stochastic measurement noise, and potential undersampling. In practice, the performance of iterative methods are limited by imaging models compatible with optimization. Deep learning-based methods can effectively learn image models of arbitrary complexity, but lack the theoretical explainability and robustness of iterative techniques. Consensus equilibrium (CE) generalizes the iterative techniques beyond optimization, enabling blackbox algorithms such as traditional and neural image denoisers to be used as the image model. CE-based approaches retain much of the explainability and robustness of iterative techniques while allowing the expressiveness of machine learning image models to be used. Additionally, by unrolling iterations of CE with an embedded image denoiser, the image denoiser can be further trained and specialized to the specific application with potentially higher quality reconstructions. Under this project, we demonstrated the feasibility of training an unrolled neural network based upon CE. While we didn’t train one, we showed that the CE process is differentiable and its gradient can be tractably computed. We also explored the usage of a variants of CE akin to generative neural works. Most importantly, we applied the CE framework to a number of problems including non-blind deconvolution, upsampling, single-image super resolution, MISR, event-based sensing, and saturated deconvolution. Our MISR prototype creates high quality reconstructions with an order of magnitude fewer images than previous approaches and, critically, produces these reconstructions fast enough for practical usage.
Regularizing the linearly extrapolated BDF2 scheme for incompressible flows with time relaxation
This paper presents a highly-efficient finite element scheme for the time relaxation model (TRM). The efficiency is achieved through the second-order BDF2 time-stepping scheme with linear extrapolation (BDF2LE). The accuracy of the scheme is also greatly enhanced through the use of the divergence-free Scott-Vogeulis finite elements, and van Cittert approximate deconvolution. A complete finite element analysis is provided, which includes rigorous proofs for the stability, well-possessedness, and convergence of both velocity and pressure solutions. Furthermore, we also demonstrate that the inclusion of the linear time relaxation term preserves the long-time stability of the unregularized BDF2LE scheme. Finally, numerical experiments are presented that demonstrate the added stability and accuracy that time relaxation can provide.
Formation and Detriments of Residual Alkaline Compounds on High-Nickel Layered Oxide Cathodes
High-nickel layered oxides LiNi x M 1-x O 2 (x ≥ 0.9) have emerged as promising cathode materials for automotive batteries due to their high energy density and lower cost. However, the formation and accumulation of surface alkaline compounds during storage hinder their mass production and commercialization. Here, in this study, a validated chemical method is employed to deconvolute and quantify the evolution of each residual lithium compound in four representative cathodes during ambient-air storage, viz., LiNiO 2 (LNO), LiNi 0.95 Co 0.05 O 2 (NC), LiNi 0.95 Mn 0.05 O 2 (NM), and LiNi 0.95 Al 0.05 O 2 (NA). Furthermore, the activation energy of the reaction between water and the cathode is determined by measuring the leached LiOH concentration at various temperatures. While residual lithium and time-of-flight secondary-ion mass spectrometry measurements collectively reveal that the air stability overall follows the trend of NM > NA ≈ NC > LNO, the aged NM exhibits the highest charge-transfer resistance and the worst electrochemical performance among the cathodes. In situ, X-ray diffraction and scanning transmission electron microscopy unveil that the aged NM is plagued by a large area of resistive spinel-like M 3–x Li x O 4 phases, leading to aggravated particle reaction heterogeneity. Finally, a one-step recalcination method is demonstrated effective in fully restoring the degraded cathodes. This work provides insights into overcoming air sensitivity issues of high-Ni cathodes.
Kinetically Dormant Ni‐Rich Layered Cathode During High‐Voltage Operation
Abstract The degradation of Ni‐rich cathodes during long‐term operation at high voltage has garnered significant attention from both academia and industry. Despite many post‐mortem qualitative structural analyses, precise quantification of their individual and coupling contributions to the overall capacity degradation remains challenging. Here, by leveraging multiscale synchrotron X‐ray probes, electron microscopy, and post‐galvanostatic intermittent titration technique, the thermodynamically irreversible and kinetically reversible capacity loss is successfully deconvoluted in a polycrystalline LiNi 0.83 Mn 0.1 Co 0.07 O 2 cathode during long‐term charge/discharge cycling in full cell configuration. Contradicting the dramatic capacity loss, the layered structure remains highly alive even after 1000 cycles at 4.6 V while undergoing a three‐order of magnitude reduction in the mass transfer kinetics, leading to almost fully recoverable capacity under kinetic‐free conditions. Such kinetic dormant behavior after cycling is not simply ascribed to poor chemical diffusion by reconstructed cathode surface but highly synchronizes with the lattice strain evolution stemming from the structural heterogeneity between deeply delithiated layered and degraded rock‐salt phases at high voltage. These findings deepen the degradation mechanism of high‐voltage cathodes to achieve long‐cycling and fast‐charging performance.
Propane Activation on Pt Electrodes at Room Temperature: Quantification of Adsorbate Identity and Coverage
Abstract C−H bond activation is the first step in manufacturing chemical products from readily available light alkane feedstock and typically proceeds via carbon‐intensive thermal processes. The ongoing emphasis on decarbonization via electrification motivates low‐temperature electrochemical alternatives that could lead to sustainable chemicals production. Platinum (Pt) electrocatalysts have shown activity towards reacting alkanes; however, little is known about propane electrocatalytic activation and conditions suitable for enabling selective oxidation to valuable products. Herein, we utilize a combination of electrochemical mass spectrometry (ECMS) and density functional theory (DFT) calculations to elucidate the potential dependence of propane activation on Pt electrocatalysts. Results show a strong dependence of adsorption on the applied potential in room‐temperature aqueous acidic electrolyte, with a maximum coverage of propane‐derived adsorbates at 0.30 V vs RHE. Using charge deconvolution and deuterated experiments, the mechanism of adsorption was elucidated, and C 3 H 2 * was determined as the average dehydrogenated propane‐derived adsorbate species. DFT calculations further corroborate these results, showing that the formation of deeply dehydrogenated species is energetically accessible at room temperature. The combined theoretical and experimental findings yield insights for selective activation of paraffinic C−H bonds at room temperature, aqueous conditions—a critical step towards decarbonized chemical manufacturing.
Accessing Transient Isomers in the Photoreaction of Metastable‐State Photoacid
The photoreaction of a metastable‐state photoacid (mPAH) generally involves multiple isomers with various connected pathways of photoinduced structural changes during a single reaction cycle. However, only a limited number of isomers have been identified experimentally so far owing to the inherent complexity in combination with the presence of various competing electronic and vibrational processes, as well as the constantly varying interactions between mPAH isomers and solvent molecules. Here, in this work, an optical spectroscopic study on a benzimidazole‐based mPAH, a novel photoacid using benzimidazole as the structural moiety with the active proton, is reported. Through measurements of linear absorption and steady‐state fluorescence in neat solvents and binary mixtures, a pronounced effect of neat water and its binary mixture with glycerol is discovered on the photoreaction of this benzimidazole‐mPAH, manifested by the remarkably distinct spectral responses to irradiation from that observed for an organic solution under identical conditions. Measurements of time‐ and frequency‐resolved fluorescence emission further enable to access transient isomers and the associated spectral characteristics from other competing electronic excited‐state relaxation processes. Spectral deconvolution analysis and time‐dependent density functional theory calculations are applied to separate distinct spectral components and access their potential origin.
Investigation of Uranyl Perchlorate Anion Complexes in the Gas Phase via Infrared Multiphoton Dissociation and Collision‐Induced Dissociation
The infrared multiphoton dissociation spectrum of the gas-phase uranyl perchlorate anion ([UO 2 (ClO 4 ) 3 ] − ) was measured. Here, the asymmetric uranyl stretch lies somewhere between 930 and 1030 cm −1 , though it could not be deconvoluted from a closely located perchlorate stretching mode. The experimentally measured spectrum was in good agreement with spectra calculated using density functional theory with the B3LYP and TPSSh functionals and Grimme's D3 dispersion corrections with Becke–Johnson damping. The calculations suggest that the asymmetric uranyl stretch lies in the range of 970–980 cm −1 , about 20–30 cm −1 higher than for the analogous uranyl trinitrato complex and consistent with perchlorate as a weaker ligand than nitrate. Like the uranyl trinitrato anion, fragmentation of [UO 2 (ClO 4 ) 3 ] − by collision-induced dissociation resulted in loss of a ClO 3 • radical to form [UO 3 (ClO 4 ) 2 ] − . Infrared multiphoton dissociation measurements of [UO 3 (ClO 4 ) 2 ] − indicate that the structure of the product ion has an O − ligand bound to the uranyl in a T-arrangement and two perchlorate ligands, matching the findings from uranyl nitrato complexes. The uranyl stretch in this complex was slightly separated from the perchlorate modes and was measured at 906 cm −1 , slightly higher than for the analogous nitrate complex, again consistent with perchlorate as a weaker ligand than nitrate in the gas phase.
In Situ Characterization of Interface Evolution in Argyrodite‐Based All‐Solid‐State Li Batteries
Interfacial stability is one of the critical challenges in all-solid-state Li metal batteries. Multiple processes such as solid electrolyte (SE) decomposition and lithium dendrite growth take place at the solid interfaces during cycling, leading to the overall cell failure. To deconvolute these complex processes, in situ characterization is of paramount importance to elucidate the interfacial evolution on the SE upon Li plating/stripping. Herein, an all-solid-state asymmetric in situ cell is developed that allows the direct visualization of the highly localized Li plating/stripping processes under the optical microscope. Moreover, this cell configuration enables reliable post-mortem chemical and morphological analysis of the intact SE/Li interface. Using combined scanning electron microscopy and energy-dispersive X-ray spectroscopy, the study reveals that the evolution of the Li argyrodite interface is strongly influenced by the current density, particularly in terms of chemical distribution and Li plating morphology. More specifically, the solid interface is LiCl-rich with the formation of Li cubes at low current densities, while high currents result in more uniform elemental distribution and filament morphology. These findings elucidate the dynamic evolution mechanism at solid interfaces and offer valuable guidance for developing stable solid interfaces in all-solid-state Li metal batteries.
Decoding α-MoC 1− x Nanoparticle Formation in Continuous Flow via Machine Learning
Molybdenum carbide nanoparticles (α-MoC 1−x NPs) are promising catalysts that offer noble-metal-like performance at lower cost. We report a mild continuous-flow synthesis of α-MoC 1−x NPs from Mo(CO) 6 , coupled with in-line spectroscopic monitoring and machine learning (ML)-based analysis to quantify precursor conversion and product formation in real time. A multilayer perceptron ML model was found to accurately deconvolute complex, nonlinear spectral patterns, enabling identification of a two-step reaction pathway, involving precursor conversion to an amorphous intermediate followed by intraparticle crystallization to α-MoC 1−x NPs, with the first step being rate limiting. Ex situ small angle X-ray scattering (SAXS) and X-ray diffraction (XRD) validation confirm the predicted concentration profiles and crystallization behavior. This integrated approach showcases how ML can empower insights into NP nucleation and growth, paving the way for self-driving, flow-based platforms for NP synthesis.