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At least 217 records · Page 12

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

59 BASIC BIOLOGICAL SCIENCES↗

Fourier method for 3-dimensional data fusion of X-ray Computed Tomography and ultrasound

X-ray Computed Tomography (CT) is essential for nondestructive inspection of many manufactured components but is susceptible to various forms of artifacts and noise. In particular, multi-detector row cone-beam CT systems can suffer from so called “cone-beam” artifacts and partial volume effects, particularly on planar edges at the periphery of the field of view in the cone angle dimension. Uni-directional ultrasonic testing methods generally have extremely accurate in-plane depth resolution but poorer lateral resolution due to physical and geometric constraints. This paper presents a novel technique called Computed Tomographic Fusion (CT-F) which uses three-dimensional Fourier filtering to combine x-ray cone-beam CT reconstructions and ultrasound data in the frequency space. The result is a single image with improved accuracy and quality. CT-F mitigates artifacts while allowing for rapid, accurate characterization of large three-dimensional CT volumes. Finally, using simulations and experiments, we demonstrate artifact reduction and edge contrast improvement in volumetric reconstructions.

42 ENGINEERING↗

Elasto-viscoplastic fast Fourier transform modeling framework for assessing microstructural effects on stress intensity factors characterizing fracture toughness

A large-strain elasto-viscoplastic fast Fourier transform (LS-EVPFFT) model with non-periodic (NP) velocity-based boundary conditions is adapted to simulate the sensitivity of stress intensity factors on microstructure for 304L stainless steel. The material was characterized via electron backscattered diffraction (EBSD) serial-sectioning to obtain a measured 3-D microstructural cell to perform simulations. The NP-LS-EVPFFT model, including the simulation setup and boundary conditions, was verified using a crystal plasticity finite element (CPFE) model. To this end, the generation of meshes of notched specimens was developed, which involved creating Python scripts for mesh “cutting” in Abaqus, and Sculpt scripts in Cubit for meshing of the measured microstructural cell processed with DREAM.3D. The complexity of the mesh preparation highlighted the advantages of the FFT-based model, which circumvents the mesh generation process. Given the efficiency of the FFT-based model, statistical distribution of stress intensity factors in function of crystal orientation at the crack tip, grain structure, and crystallographic texture surrounding the crack tip were predicted. Further, the distributions reveal about 10% variation of stress intensity factors with microstructure with the most significant sensitivity found to be the crystal orientation at the crack tip. The methodology developed in this work is discussed as a practical simulation tool for predicting the sensitivity of stress intensity factors on microstructural variability in metallic materials.

36 MATERIALS SCIENCE↗

Narrow operator models of stellarator equilibria in Fourier Zernike basis

Numerical computation of the ideal magnetohydrodynamic (MHD) equilibrium magnetic field is at the base of stellarator optimisation and provides the starting point for solving more sophisticated partial differential equations like transport or turbulence models. Conventional approaches solve for a single stationary point of the ideal MHD equations, which is fully defined by three invariants and the numerical scheme employed by the solver. We present the first numerical approach that can solve for a continuous distribution of equilibria with fixed boundary and rotational transform, varying only the pressure invariant. This approach minimises the force residual by optimising parameters of multilayer perceptrons that map from a scalar pressure multiplier to the Fourier Zernike basis as implemented in the modern stellarator equilibrium solver DESC.

fusion plasma↗

Molecular Characterization of Organophosphorus Compounds in Wildfire Smoke Using 21-T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

Here, we present a detailed molecular characterization of organophosphorus compounds in ambient organic aerosol influenced by wildfire smoke. Biomass burning organic aerosol (BBOA) is an important source of phosphorus (P) to surface waters, where even a small imbalance in the P flux can lead to substantial effects on water quality, such as eutrophication, algal blooms, and oxygen depletion. We aimed to exploit the ultrahigh resolving power, mass accuracy, and sensitivity of Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) to explore the molecular composition of an ambient BBOA sample collected downwind of Pacific Northwest wildfires. The 21-T FT-ICR MS yielded 10533 distinct formulae, which included molecular species comprising C, H, O, and P with or without N, i.e., organophosphorus compounds that have long been quantified in wildfire smoke but have not yet been characterized at the molecular level. The lack of detailed molecular characterization of organophosphorus compounds in BBOA is primarily due to their inherently low concentrations in aerosols and poor ionization efficiency in complex mixtures. We demonstrate that the exceptional sensitivity of the 21-T FT-ICR MS allows qualitative analysis of a previously uncharacterized fraction of BBOA without its selective concentration from the organic matrix, exemplifying the need for ultrahigh-resolution tools for a more detailed and accurate molecular depiction of such complex mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Broadband Fourier-Transform Optical Photothermal Infrared Spectroscopy and Imaging

Infrared (IR) spectroscopy is a powerful method for mapping chemical heterogeneity on the microscale. Synchrotron IR radiation uniquely provides a high brightness and broad bandwidth to further extend the capabilities of IR spectroscopic imaging. However, the diffraction-limited spatial resolution of IR spectroscopy is insufficient for studies requiring submicrometer spatial differentiation. Optical photothermal IR (O-PTIR) microscopy is a powerful, emerging method that overcomes the IR diffraction limit in IR hyperspectral imaging by employing a modulated IR beam and a visible probe laser beam to detect local temperature-induced modulation at the visible diffraction limit. In this work, we extend the spectral range of photothermal infrared measurements by incorporating a synchrotron IR source, demonstrating a combined synchrotron-based O-PTIR modality that enables high spatial resolution far-field chemical imaging spanning the entire mid-IR range. Both optical- and fluorescence-detected photothermal modalities were performed using a step-scan interferometer, demonstrating improved spectral range (541-4000 cm-1) when compared to optical photothermal microscopy with commercial laser sources (800-1800 cm-1 for this particular source) and improved spatial resolution, when compared to synchrotron microspectroscopy measurements. Following these initial validation studies, synchrotron Fourier-transform fluorescence-detected photothermal IR spectroscopy in combination with synchrotron microspectroscopy measurements was used to differentiate cells in mouse brain tissue sections, which requires submicron spatial resolutions beyond those accessible by IR spectroscopy alone.

Razumtcev, Aleksandr↗

Poison or Promoter? Investigating the Dual-Role of Carbon Monoxide in Pincer-Iridium-Based Alkane Dehydrogenation Systems via Operando Diffuse Reflectance Infrared Fourier Transform Spectroscopy

Pincer-ligated iridium complexes of the form [( R 4 PCP)IrL] ( R 4 PCP = κ 3 -C 6 H 3 -2,6-(XPR 2 ) 2 ; X = CH 2 , O; R = tBu, iPr) have previously been shown competent for acceptorless alkane dehydrogenation when supported on silica. It was observed by postcatalysis solid-state NMR that silica-tethered [(≡SiO- tBu 4 POCOP)Ir(C 2 H 4 )] (3-C 2 H 4 ) was converted fully to [(≡SiO- tBu 4 POCOP)Ir(CO)] (3-CO) at 300 °C. In this work, the characterization of species under dehydrogenation reaction conditions far from equilibrium between butane and butenes (approach to equilibrium Q/K eq = 0.3 at 300 °C) is performed with operando Diffuse Reflectance Infrared Fourier–Transform Spectroscopy (DRIFTS) to show the kinetics of species conversion from 3-C 2 H 4 to 3-CO. It is further found that [(≡SiO- tBu 4 POCOP)IrHCl] (3-HCl), a species considered to be a precatalyst for alkane dehydrogenation, is also fully converted to 3-CO. Here, a mechanism of decomposition is proposed that implicates surface silanol groups, while carbon monoxide acts as a “stabilizer” for the catalyst by promoting their reductive elimination and maintaining the complex in the I oxidation state.

02 PETROLEUM↗

Deep Learning for Subsurface Flow: A Comparative Study of U‐Net, Fourier Neural Operators, and Transformers in Underground Hydrogen Storage

Subsurface flow research is essential for the sustainable management of natural resources and the environment. Deep learning (DL) has significantly advanced this field by developing efficient and accurate surrogate models to replace computationally expensive physics‐based simulations. These surrogate models are commonly used to predict the spatiotemporal evolution of state variables, such as gas saturation and reservoir pressure, in heterogeneous geological formations. Despite the various DL models applied to this task, there is a lack of studies systematically comparing their performance. This absence of comparative analysis leads to somewhat arbitrary DL model selection in subsurface flow research, resulting in suboptimal performance and potentially inaccurate predictions. To bridge this gap, we conduct a systematic comparison study of three popular DL architectures—U‐Net, Fourier Neural Operators (FNO), and Segmentation Transformer (SETR)—in surrogate modeling of underground hydrogen storage (UHS). We focus on UHS due to its promise of enhancing clean energy resilience and its cyclic operational conditions that represent common scenarios in various subsurface applications. We evaluate the models based on accuracy, training cost, and inference speed. The comparison shows that U‐Net achieves the highest accuracy, followed by SETR and FNO. Despite its lower accuracy, FNO has the highest inference speed. SETR offers competitive accuracy with the least training memory usage, demonstrating the potential of transformers in learning subsurface flow. Our results provide guidance for selecting DL models for surrogate modeling in a wide range of subsurface flow problems.

42 ENGINEERING↗

Double-pulse speckle contrast correlations with near Fourier transform limited free-electron laser light using hard X-ray split-and-delay

Abstract The ability to deliver two coherent X-ray pulses with precise time-delays ranging from a few femtoseconds to nanoseconds enables critical capabilities of probing ultra-fast phenomena in condensed matter systems at X-ray free electron laser (FEL) sources. Recent progress made in the hard X-ray split-and-delay optics developments now brings a very promising prospect for resolving atomic-scale motions that were not accessible by previous time-resolved techniques. Here, we report on characterizing the spatial and temporal coherence properties of the hard X-ray FEL beam after propagating through split-and-delay optics. Speckle contrast analysis of small-angle scattering measurements from nanoparticles reveals well-preserved transverse coherence of the beam. Measuring intensity fluctuations from successive X-ray pulses also reveals that only single or double temporal modes remain in the transmitted beam, corresponding to nearly Fourier transform limited pulses.

42 ENGINEERING↗

Probing the proton exchange kinetics of BaZr 0.1 Ce 0.7 Y 0.1 Yb 0.1 O 3− δ ceramic electrolyte by operando diffuse reflectance infrared Fourier transform spectroscopy

Proton exchange kinetics plays an important role in governing the performance of intermediate-temperature protonic ceramic electrolysis cells (PCECs) for hydrogen production. Our understanding of the nature of the surface hydration reaction at the single-cell level, however, remains very limited, hampering further efficiency improvements. Here, in this study, we developed a custom operando diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) platform that operates under high temperature and steam conditions with applied bias. Quantitative investigations of surface H 2 O/D 2 O isotope exchange in a BaZr 0.1 Ce 0.7 Y 0.1 Yb 0.1 O 3−δ (BZCYYb1711) protonic electrolyte-based single cell were conducted under different applied voltages using this DRIFTS platform, to gain molecular-level insight into hydration kinetics. The findings show that the application of an external voltage significantly enhances the surface proton exchange rate, decreasing the apparent activation energy from 29.1 kJ mol −1 at open-circuit voltage (OCV) to 6.8 kJ mol −1 at 1.3 V. In addition, distinct voltage-induced spectral shifts in O–D vibrations point to dynamic changes in surface hydration. These findings demonstrate a sensitive spectroscopic platform for probing interfacial proton processes and reveal strong electrochemical control over surface proton kinetics, offering new opportunities for probing electrolyte hydration behavior in PCECs.

36 - MATERIALS SCIENCE↗

Improved motional Stark effect signal processing using fast Fourier transform spectral analysis

A Fast Fourier Transform (FFT) based method has been developed, which improves the frequency response of the Motional Stark Effect (MSE) system by about a factor of 10 over the conventional analog lock-in method. The method uses fits to rigorously derived analytic expressions for the FFT spectral components of the MSE signal to accurately obtain the amplitudes and phases of the 2f1 and 2f2 photo-elastic modulator (PEM) frequencies that encode the polarization angle. Since no frequency filtering is used in the FFT method, the frequency response is limited by fundamental measurement properties: the frequency response of the detector, photon statistics, sample rate, and the ability to resolve the spectral components. In contrast, the frequency response of the analog lock-in is limited by a low pass filter with a cutoff of around 500 Hz. In the case of the DIII-D MSE system, the output of the photo-multiplier tube detector was sampled at 500 kHz and FFTs with as few as 100 points were used to obtain the amplitudes of the 2f1 and 2f2 PEM frequency components. This corresponds to a frequency response of 5 kHz, about ten times faster than the analog lock-in amplifier system. Details of the FFT method will be presented and compared to those of the analog lock-in system.

Makowski, M. A.↗

Modulation of intensity emerging from zero effort (MIEZE) with extended Fourier time at large scattering angle

Modulation of Intensity Emerging from Zero Effort (MIEZE) is a neutron resonant spin echo technique that allows one to measure time correlation scattering functions in materials by implementing radio-frequency (RF) intensity modulation at the sample and the detector. The technique avoids neutron spin manipulation between the sample and the detector and, thus, could find applications in cases where the sample depolarizes the neutron beam. However, the finite sample size creates a variance in the path length between the locations where scattering and detection happen, which limits the contrast in intensity modulation that one can detect, in particular, toward long correlation times or large scattering angles. We propose a modification to the MIEZE setup that will enable one to extend those detection limits to longer times and larger angles. Furthermore, we use Monte Carlo simulations of a neutron scattering beamline to show that by tilting the RF flippers in the primary spectrometer with respect to the beam direction, one can shape the wave front of the intensity modulation at the sample to compensate for the path variance from the sample and the detector. The simulation results indicate that this change enables one to operate a MIEZE instrument at much increased RF frequencies, thus improving the effective energy resolution of the technique. For the MIEZE instrument simulated, it shows that for an incident beam with the maximum divergence of 0.33°, the maximum Fourier time can be increased by a factor of 3.

47 OTHER INSTRUMENTATION↗

Sparsified time-dependent Fourier neural operators for fusion simulations

This paper presents a sparsified Fourier neural operator for coupled time-dependent partial differential equations (ST-FNO) as an efficient machine learning surrogate for fluid and particle-based fusion codes such as NIMROD (Non-Ideal Magnetohydrodynamics with Rotation - Open Discussion) and GTC (Gyrokinetic Toroidal Code). ST-FNO leverages the structures in the governing equations and utilizes neural operators to represent Green's function-like numerical operators in the corresponding numerical solvers. Once trained, ST-FNO can rapidly and accurately predict dynamics in fusion devices compared with first-principle numerical algorithms. In general, ST-FNO represents an efficient and accurate machine learning surrogate for numerical simulators for multi-variable nonlinear time-dependent partial differential equations, with the proposed architectures and loss functions. The efficacy of ST-FNO has been demonstrated using quiescent H-mode simulation data from NIMROD and kink-mode simulation data from GTC. The ST-FNO H-mode results show orders of magnitude reduction in memory and central processing unit usage in comparison with the numerical solvers in NIMROD when computing fields over a selected poloidal plane. The ST-FNO kink-mode results achieve a factor of 2 reduction in the number of parameters compared to baseline FNO models without accuracy loss.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Powers of magnetic graph matrix: Fourier spectrum, walk compression, and applications

Magnetic graphs, originally developed to model quantum systems under magnetic fields, have recently emerged as a powerful framework for analyzing complex directed networks. Existing research has primarily used the spectral properties of the magnetic graph matrix to study global and stationary network features. However, their capacity to model local, nonequilibrium behaviors, often described by matrix powers, remains largely unexplored. We present a combinatorial interpretation of the magnetic graph matrix powers through directed walk profiles—counts of graph walks indexed by the number of edge reversals. Crucially, we establish that walk profiles correspond to a Fourier transform of magnetic matrix powers. The connection allows exact reconstruction of walk profiles from magnetic matrix powers at multiple discrete potentials, and more importantly, an even smaller number of potentials often suffices for accurate approximate reconstruction in real networks. This shows the empirical compressibility of the information captured by the magnetic matrix. This fresh perspective suggests further applications; for example, we illustrate how powers of the magnetic matrix can identify frustrated directed cycles (e.g., feedforward loops) and can be effectively employed for link prediction by encoding local structural details in directed graphs.

complex networks↗

Windowed Fourier transform and cross-correlation algorithms for molecular tagging velocimetry

In this study, simulated and experimental molecular tagging velocimetry (MTV) images have been analyzed with a technique commonly used to process grid images on surfaces, the windowed Fourier transform with local spectrum analysis (WFT-LSA). A systematic synthetic image study of the modulation transfer function (MTF) and error tendencies of the WFT-LSA was performed and compared with a PIV-style cross-correlation algorithm to see if advanced strategies such as iterative image deformation can improve analysis of gridded images with high noise levels. Testing of single-pass algorithms showed that in typical MTV images, the WFT-LSA yields significantly lower bias errors than cross-correlation (CC) at displacements greater than 1 pixel but slightly higher random error at all displacements and image conditions. Analysis of the MTF shows that CC provided better resolution of spatial fluctuations than the WFT-LSA in many combinations of grid size and interrogation window. Tests of image deformation algorithms showed that the gap in performance between CC and WFT-LSA is maintained even as both methods improve. Additionally, WFT-LSA and CC methods are applied to real MTV experiments in high-speed gas jet flows. A preliminary analysis of phosphorescence lifetime provided by acetone vapor excited at 266 nm is used for assessing the required gas speeds for making MTV application feasible. The application of WFT-LSA to real MTV images demonstrates the ability of the algorithm to handle further real-world effects that could not be considered in the synthetic image analysis, like reduced signal-to-noise ratio and non-uniform intensity of the tagging grid across the image introduced by the actual laser beam energy distribution. With experimental images, CC is more accurate with shear flows but less robust to high noise levels than WFT-LSA, as predicted by the synthetic image analysis.

42 ENGINEERING↗

Moment-Fourier approach to ion parallel fluid closures and transport for a toroidally confined plasma

A general method of solving the drift kinetic equation is developed for an axisymmetric magnetic field. Expanding a distribution function in general moments, a set of ordinary differential equations is obtained. Successively expanding the moments and magnetic-field involved quantities in Fourier series, a set of linear algebraic equations is obtained. The set of full (Maxwellian and non-Maxwellian) moment equations is solved to express the first-order density, temperature, and flow velocity in terms of radial gradients of the zeroth-order pressure and temperature. Closure relations that connect parallel heat flux density and viscosity to the radial gradients and parallel gradients of temperature and flow velocity are also obtained by solving the non-Maxwellian moment equations. The closure relations combined with the linearized fluid equations reproduce the same solution obtained directly from the full moment equations. Furthermore, the method can be generalized to derive closures and transport for an electron-ion plasma and a multi-ion plasma in a general magnetic field.

neoclassical transport↗

DESI DR1 Ly α 1D power spectrum: the Fast Fourier Transform estimator measurement

Here, we present the one-dimensional Lyman-α forest power spectrum measurement derived from the data release 1 (DR1) of the Dark Energy Spectroscopic Instrument (DESI). The measurement of the Lyman-α forest power spectrum along the line of sight from high-redshift quasar spectra provides information on the shape of the linear matter power spectrum, neutrino masses, and the properties of dark matter. In this work, we use a Fast Fourier Transform (FFT)-based estimator, which is validated on synthetic data in a companion paper. Compared to the FFT measurement performed on the DESI early data release, we improve the noise characterization with a cross-exposure estimator and test the robustness of our measurement using various data splits. We also refine the estimation of the uncertainties and now present an estimator for the covariance matrix of the measurement. Furthermore, we compare our results to previous high-resolution and eBOSS measurements. In another companion paper, we present the same DR1 measurement using the Quadratic Maximum Likelihood Estimator (QMLE). These two measurements are consistent with each other and constitute the most precise one-dimensional power spectrum measurement to date, while being in good agreement with results from the DESI early data release.

Lyman alpha forest↗

Brighter-fatter Effect in Near-infrared Detectors—III. Fourier-domain Treatment of Flat Field Correlations and Application to WFIRST

Weak gravitational lensing has emerged as a leading probe of the growth of cosmic structure. However, the shear signal is very small and accurate measurement depends critically on our ability to understand how non-ideal instrumental effects affect astronomical images. The Wide-Field Infrared Survey Telescope (WFIRST) will fly a focal plane containing 18 Teledyne H4RG-10 near-infrared detector arrays, which present different instrument calibration challenges from previous weak lensing observations. Previous work [Paper I: Hirata & Choi, PASP, 132, 014501 (2020); and Paper II: Choi & Hirata, PASP, 132, 014502 (2020)] has shown that correlation functions of flat field images, including cross-correlations between different time slices that are enabled by the non-destructive read capability of the infrared detectors, are effective tools for disentangling linear and nonlinear inter-pixel capacitance (IPC) and the brighter-fatter effect (BFE). Here we present a Fourier-domain treatment of the flat field correlations, which allows us to expand the previous formalism to all orders in IPC, BFE, and classical nonlinearity. We show that biases in simulated flat field analyses in Paper I are greatly reduced through the use of this formalism. We then apply this updated formalism to flat field data from three WFIRST flight candidate detectors, and explore the robustness to variations in the analysis. We find that the BFE is present in all three detectors, and that its contribution to the flat field correlations dominates over the nonlinear IPC, in accordance with the results from Paper II on a development detector. The magnitude of the BFE is such that the effective area of a pixel is increased by (3.54 ± 0.03) × 10 -7 for every electron deposited in a neighboring pixel (sensor chip assembly [SCA] 20829, statistical error, not IPC-deconvolved). We compare IPC maps from flat field autocorrelation measurements to those obtained from the single pixel reset method and find a median difference of 0.113% for SCA 20829. After further diagnosis of this difference, we ascribe it largely to an additional source of cross-talk, the vertical trailing pixel effect, and recommend further work to develop a model for this effect. These results represent a significant step toward calibration of the non-ideal effects in WFIRST detectors.

79 ASTRONOMY AND ASTROPHYSICS↗