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At least 181 records · Page 10

SpectraCodec: A Hilbert curve-based method for encoding metadata in mass spectra for machine learning applications (SpectraCodec) v1

Machine learning approaches to mass spectrometry (MS) data analysis require structured metadata for optimal performance. However, current MS file formats necessitate external metadata sources, creating integration challenges that impede analytical workflows. Here, we present a novel approach for encoding metadata directly within mzML files using one-hot encoding of ASCII characters mapped via Hilbert space-filling curves. This strategy embeds metadata in the first spectrum's m/z-intensity space, ensuring persistence with the primary data, eliminating the need for external metadata files, and maintaining compatibility with existing MS software. We demonstrate that the Hilbert curve mapping efficiently utilizes the two-dimensional spectral space while maintaining robust data recovery. This method offers a practical solution for machine learning applications in mass spectrometry by ensuring metadata and spectral data remain unified through all stages of analysis.

Bowen, Benjamin [Lawrence Berkeley National Labora↗

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate in varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of bending propensities of BMC hexamers (BMC-H), the most abundant shell constituents. Published data show that some BMC-H, like β -carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted us to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the arrangement adopted in crystals by BMC-H that experimentally form curved objects, leading to very similar arrangements to those found in structures of recomposed BMC shells. Simulations on triplets of planar-behaving hexamers, which were previously reconfigured to comply with such organization, confirmed that bending propensity is mostly defined by the precise lateral positioning of hexamers, rather than by BMC-H identity. Finally, an interfacial lysine was pinpointed as the most decisive residue in controlling PduA spontaneous curvature. Globally, results presented herein should contribute to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.

59 BASIC BIOLOGICAL SCIENCES↗

Annular Core Research Reactor (ACRR) Pulse Curve Characterization

Reactor pulse characterization at the Annular Core Research Reactor (ACRR) at Sandia Technical Area V (TA-V) is commonly done through photo conductive detection (PCD) and calorimeter detectors. Each of these offer a mode of analyzing a digital signal with different advantages/methods for determination of integrated dose or temporal based metrology. This report outlines a method and code that takes the millions of data points from such detectors and delivers a characteristic pulse trendline through two main methods: digital signal filtration and machine learning, in particular, Support Vector Machines (SVMs). Each method's endpoint is to deliver a characteristic curve for the many bucket environments of ACRR while considering other points of interest including delayed gamma removal for prompt dose metrics. This work draws and adds on previous work detailing the delayed gamma fraction contributions from CINDER simulations of the ACRR. Results from this project show a method to determine characteristic curves in a way that has previously been limited by data set size.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Guidelines for IAEA Small Specimen Test Techniques Master Curve Fracture Toughness Testing

Under the auspices of International Atomic Energy Agency (IAEA), a coordinated research project (CRP) entitled “Towards the Standardization of Small Specimen Test Techniques for Fusion Applications” has started since 2017. The overall objective of the project is to provide a set of guidelines for small specimen test techniques (SSTT) based on commonly agreed best practices on main test techniques including tensile, creep, low cycle fatigue, fracture toughness, and fatigue crack growth rate. This will act as the first step of a full standardization of the SSTT. Fusion structural materials, i.e., reduced activation ferritic/martensitic (RAFM) steels, are used for testing. In addition, the project will create a comprehensive mechanical property database of RAFM steels tested by SSTT. For the fracture toughness task of the CRP, three testing methods including Master Curve, local approach for ductile crack growth and cleavage fracture, and ductile approach at room temperature will be evaluated. This report focuses on developing guidelines for the round-robin Master Curve testing based on the ASTM standard E1921-19b “Standard Test Method for Determination of Reference Temperature, T 0 , for Ferritic Steels in the Transition Range” and commonly agreed best practice from researchers at Oak Ridge National Laboratory (ORNL), Centre for Energy, Environment and Technology (CIEMAT), and UK Atomic Energy Authority (UKAEA).

36 MATERIALS SCIENCE↗

Machine-Learning of Nonlocal Kernels for Anomalous Subsurface Transport from Breakthrough Curves

Anomalous behavior is ubiquitous in subsurface solute transport due to the presence of high degrees of heterogeneity at different scales in the media. Although fractional models have been extensively used to describe the anomalous transport in various subsurface applications, their application is hindered by computational challenges. Simpler nonlocal models characterized by integrable kernels and finite interaction length represent a computationally feasible alternative to fractional models; yet, the informed choice of their kernel functions still remains an open problem. We propose a general data-driven framework for the discovery of optimal kernels on the basis of very small and sparse data sets in the context of anomalous subsurface transport. Using spatially sparse breakthrough curves recovered from fine-scale particle-density simulations, we learn the best coarse-scale nonlocal model using a nonlocal operator regression technique. Predictions of the breakthrough curves obtained using the optimal nonlocal model show good agreement with fine-scale simulation results even at locations and time intervals different from the ones used to train the kernel, confirming the excellent generalization properties of the proposed algorithm. A comparison with trained classical models and with black-box deep neural networks confirms the superiority of the predictive capability of the proposed model.

97 MATHEMATICS AND COMPUTING↗

Dynamics and Instabilities of a Plasma Blob in Curved Magnetic Geometries [Slides]

Blobs are filament-like structures within a bulk plasma. They move radially outward in curved magnetic fields, across magnetic field lines. They account for significant amount of transport at plasma edge in tokamaks and are found in tokamaks, solar coronal filaments, planetary magnetospheres, and high altitude nuclear explosions. MHD offers some analytical descriptions of blob dynamics. In a curved geometry such as our cases of interest charged particles are subject to curvature drift, grad B drift, and E x B drifts.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Preserving Superconvergence of Spectral Elements for Curved Domains

Spectral element methods (SEM), extensions of finite element methods (FEM), have emerged as significant techniques for solving partial differential equations in physics and engineering. SEM can potentially deliver superior accuracy due to the potential superconvergence in nodal solutions for well-shaped tensor-product elements. However, the accuracy of SEM often degrades in complex geometries due to geometric inaccuracies near curved boundaries and the loss of superconvergence with simplicial or non-tensor-product elements. To overcome the first issue, we propose using geometric refinement, which both refines the mesh near high-curvature regions and increases the degree of geometric basis functions. We show that when using mixed-element meshes with tensor-product elements in the interior of the domain, curvature-based geometric refinement near boundaries can improve the accuracy of the interior elements by reducing pollution errors and preserving the superconvergence in nodal solutions. To address the second issue, we introduce ApSEM, a post-processing technique using the adaptive extended stencil finite element method (AES-FEM) to recover the accuracy near the curved boundaries. The combination of curvature-based geometric refinement and accurate post-processing offers an effective and easier-to-implement alternative to methods reliant on exact geometries. We demonstrate our techniques by solving the convection-diffusion equation in 2D and 3D and show up to two orders of magnitude of improvement in the solution accuracy, even when the elements are poorly shaped near boundaries. We also show the efficiency of ApSEM as it can recover superconvergence in nodal solutions without drastically increasing the computational cost.

97 MATHEMATICS AND COMPUTING↗

Matching Curved Lattices to Anisotropic Tangent Planes

Radial quantization would be the ideal formalism for studying strongly-coupled near-conformal quantum field theories but it requires the ability to perform lattice calculations on static, curved manifolds, specifically a very long cylinder whose cross section is a sphere. Smoothly discretizing the surface of a sphere requires a graph with unequal edge lengths. The geometry of such graphs is well understood since 1961 using Regge Calculus. But, lattice quantum field theories are defined in terms of couplings which appear in the action rather than edge lengths and so the relationship between couplings and lengths must be determined dynamically. A simple example is computing the ratio of spatial to temporal lattice spacings in anisotropic lattice QCD. I will discuss our conjecture that computing anisotropic lattice spacing ratios on affine transformations of regular flat lattices is sufficient to determine coupling assignments on curved lattices.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Shallow Strain Tensor Type-Curve Analysis to Characterizing Reservoir Boundaries

Pressure data measured in monitoring wells during well tests are typically used to estimate subsurface boundaries, but the resolution of this technique is often limited. We have shown that the strain tensor at shallow depth can be measured with optical strainmeters, and this signal responds to pressure changes in an underlying aquifer or reservoir. Moreover, these data can be inverted to estimate reservoir properties using analyses similar to classical type-curve analyses. The objective of this investigation is to evaluate the feasibility of extending the type-curve analysis of strain tensor data to include the characterization of aquifer boundaries.

Roudini, Soheil↗

Noise-resistant Landau-Zener sweeps from geometrical curves

Landau-Zener physics is often exploited to generate quantum logic gates and to perform state initialization and readout. The quality of these operations can be degraded by noise fluctuations in the energy gap at the avoided crossing. We leverage a recently discovered correspondence between qubit evolution and space curves in three dimensions to design noise-robust Landau-Zener sweeps through an avoided crossing. In the case where the avoided crossing is purely noise-induced, we prove that operations based on monotonic sweeps cannot be robust to noise. Hence, we design families of phase gates based on non-monotonic drives that are error-robust up to second order. In the general case where there is an avoided crossing even in the absence of noise, we present a general technique for designing robust driving protocols that takes advantage of a relationship between the Landau-Zener problem and space curves of constant torsion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Page curves and typical entanglement in linear optics

Bosonic Gaussian states are a special class of quantum states in an infinite dimensional Hilbert space that are relevant to universal continuous-variable quantum computation as well as to near-term quantum sampling tasks such as Gaussian Boson Sampling. In this work, we study entanglement within a set of squeezed modes that have been evolved by a random linear optical unitary. We first derive formulas that are asymptotically exact in the number of modes for the Rényi-2 Page curve (the average Rényi-2 entropy of a subsystem of a pure bosonic Gaussian state) and the corresponding Page correction (the average information of the subsystem) in certain squeezing regimes. We then prove various results on the typicality of entanglement as measured by the Rényi-2 entropy by studying its variance. Using the aforementioned results for the Rényi-2 entropy, we upper and lower bound the von Neumann entropy Page curve and prove certain regimes of entanglement typicality as measured by the von Neumann entropy. Our main proofs make use of a symmetry property obeyed by the average and the variance of the entropy that dramatically simplifies the averaging over unitaries. In this light, we propose future research directions where this symmetry might also be exploited. We conclude by discussing potential applications of our results and their generalizations to Gaussian Boson Sampling and to illuminating the relationship between entanglement and computational complexity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Measurement Uncertainty of Highly Asymmetrically Curved Elliptical Mirrors Using Multi-Pitch Slope Stitching Technique

Soft X-ray off-axis elliptical mirrors bring new challenges for X-ray mirror metrology. These highly asymmetrically curved elliptical cylindrical mirrors with a total slope range >10 mrad are extremely challenging to measure. Their total slope range exceeds the measuring range of most angular sensors used for X-ray mirror inspection. To overcome this problem, it is possible to stitch partial slope data by measuring the mirror at different pitch angles (multi-pitch angles). By revisiting the theory of the multi-pitch Nano-accuracy Surface Profiler (NSP), we derive the sampling position error on the mirror surface as a function of the mirror height profile and the measurement error of the pitch rotation center. When measuring “extreme”, highly asymmetrically curved, elliptical mirrors, the calculation of the mirror height profile with iterative reconstruction outperforms the classical “flat assumption” (i.e., assuming that the mirror sag is negligible). As demonstrated by our simulations, a proper tolerance evaluation on the measurement of pitch rotation center is needed to assess the measurement accuracy (systematic error) for these strongly aspherical mirrors using the multi-pitch NSP technique. Taking a real design of an “extreme” elliptical mirror as a case study, we conduct a Monte Carlo simulation to mimic the measurement and characterization process to analyze the impact of several error sources. With the measurement uncertainty of the pitch rotation center, the multi-pitch NSP measurement can estimate the grazing angle θ and the chief ray location x o with their uncertainties, as well as the slope residuals.

36 MATERIALS SCIENCE↗

TESS Observations of the WASP-121 b Phase Curve

We study the red-optical photometry of the ultrahot Jupiter WASP-121 b as observed by the Transiting Exoplanet Survey Satellite (TESS) and model its atmosphere through a radiative transfer simulation. Given its short orbital period of ∼1.275 days, inflated state, and bright host star, WASP-121 b is exceptionally favorable for detailed atmospheric characterization. Toward this purpose, we use allesfitter to characterize its full red-optical phase curve, including the planetary phase modulation and secondary eclipse. We measure the day- and nightside brightness temperatures in the TESS passband as 3012{sub −42}{sup +40} and 2022{sub −602}{sup +254} K, respectively, and do not find a statistically significant phase shift between the brightest and substellar points. This is consistent with inefficient heat recirculation on the planet. We then perform an atmospheric retrieval analysis to infer the dayside atmospheric properties of WASP-121 b, such as its bulk composition, albedo, and heat recirculation. We confirm the temperature inversion in the atmosphere and suggest H{sup −}, TiO, and VO as potential causes of the inversion, absorbing heat at optical wavelengths at low pressures. Future Hubble Space Telescope and James Webb Space Telescope observations of WASP-121 b will benefit from its first full phase curve measured by TESS.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quasi-periodic Oscillations in the TESS Light Curve of TX Col, a Diskless Intermediate Polar on the Precipice of Forming an Accretion Disk

One of the fundamental properties of an intermediate polar is the dynamical nature of the accretion flow as it encounters the white dwarf’s (WD’s) magnetosphere. Many works have presumed a dichotomy between disk-fed accretion, in which the WD accretes from a Keplerian disk, and stream-fed accretion, in which the matter stream from the donor star directly impacts the WD’s magnetosphere without forming a disk. However, there is also a third, poorly understood regime in which the accretion flow consists of a torus of diamagnetic blobs that encircles the WD. This mode of accretion is expected to exist at mass-transfer rates below those observed during disk-fed accretion, but above those observed during pure stream-fed accretion. We invoke the diamagnetic-blob regime to explain the exceptional Transiting Exoplanet Survey Satellite light curve of the intermediate polar TX Col, which transitioned into and out of states of enhanced accretion during Cycles 1 and 3. Power-spectral analysis reveals that the accretion was principally stream fed. However, when the mass-transfer rate spiked, large-amplitude quasi-periodic oscillations (QPOs) abruptly appeared and dominated the light curve for weeks. The QPOs have two striking properties: they appear in a stream-fed geometry at elevated accretion rates, and they occur preferentially within a well-defined range of frequencies (∼10–25 cycle day{sup −1}). We propose that during episodes of enhanced accretion, a torus of diamagnetic blobs forms near the binary’s circularization radius and that the QPOs are beats between the white dwarf’s spin frequency and unstable blob orbits within the WD’s magnetosphere. We discuss how such a torus could be a critical step in producing an accretion disk in a formerly diskless system.

79 ASTRONOMY AND ASTROPHYSICS↗

On the Use of Field RR Lyrae as Galactic Probes. V. Optical and Radial Velocity Curve Templates

We collected the largest spectroscopic catalog of RR Lyrae (RRLs) including ≈20,000 high-, medium-, and low-resolution spectra for ≈10,000 RRLs. We provide the analytical forms of radial velocity curve (RVC) templates. These were built using 36 RRLs (31 fundamental—split into three period bins—and five first-overtone pulsators) with well-sampled RVCs based on three groups of metallic lines (Fe, Mg, Na) and four Balmer lines (H$α$, H$β$, H$γ$, H$δ$). We tackled the long-standing problem of the reference epoch to anchor light-curve and RVC templates. For the V-band, we found that the residuals of the templates anchored to the phase of the mean magnitude along the rising branch are ~35% to ~45% smaller than those anchored to the phase of maximum light. For the RVC, we used two independent reference epochs for metallic and Balmer lines and we verified that the residuals of the RVC templates anchored to the phase of mean RV are from 30% (metallic lines) up to 45% (Balmer lines) smaller than those anchored to the phase of minimum RV. We validated our RVC templates by using both the single-point and the three phase point approaches. We found that barycentric velocities based on our RVC templates are two to three times more accurate than those available in the literature. We applied the current RVC templates to Balmer lines RVs of RRLs in the globular NGC 3201 collected with MUSE at VLT. We found the cluster barycentric RV of $V$$γ$ = 496.89 ± 8.37(error) ± 3.43 (standard deviation) km s -1 , which agrees well with literature estimates.

79 ASTRONOMY AND ASTROPHYSICS↗

Gravitational Lensing Formalism in a Curved Arc Basis: A Continuous Description of Observables and Degeneracies from the Weak to the Strong Lensing Regime

Gravitationally lensed curved arcs provide a wealth of information about the underlying lensing distortions. Extracting precise lensing information from extended sources is a key component in many studies aiming to answer fundamental questions about the universe. To maintain accuracy with increased precision, it is of vital importance to characterize and understand the impact of degeneracies inherent in lensing observables. In this work, we present a formalism to describe the gravitational lensing distortion effects resulting in curved extended arcs based on the eigenvectors and eigenvalues of the local lensing Jacobian and their directional differentials. We identify a nonlocal and nonlinear extended deflector basis that inherits these local properties. Our parameterization is tightly linked to observable features in extended sources and allows one to accurately extract the lensing information of extended images without imposing an explicit global deflector model. We quantify what degeneracies can be broken based on specific assumptions about the local lensing nature and assumed intrinsic source shape. Our formalism is applicable from the weak linear regime to the semi-linear regime and all the way up to the highly nonlinear regime of highly magnified arcs of multiple images. Furthermore, the methodology and implementation presented in this work provides a framework to assessing systematics, to guide inference efforts in the right choices in complexity based on the data at hand, and to quantify the lensing information extracted in a model-independent way

79 ASTRONOMY AND ASTROPHYSICS↗

Hubble Space Telescope Observations of GW170817: Complete Light Curves and the Properties of the Galaxy Merger of NGC 4993

We present the complete set of Hubble Space Telescope imaging of the binary neutron star merger GW170817 and its optical counterpart AT 2017gfo. Including deep template imaging in F814W, F110W, F140W, and F160W at 3.4 yr post-merger, we reanalyze the full light curve of AT 2017gfo across 12 bands from 5 to 1273 rest-frame days after merger. We obtain four new detections of the short γ-ray burst 170817A afterglow from 109 to 170 rest-frame days post-merger. These detections are consistent with the previously observed β = -0.6 spectral index in the afterglow light curve with no evidence for spectral evolution. We also analyze our limits in the context of kilonova afterglow or IR dust echo emission but find that our limits are not constraining for these models. We use the new data to construct deep optical and IR stacks, reaching limits of M = -6.3 to -4.6 mag, to analyze the local environment around AT 2017gfo and low surface brightness features in its host galaxy NGC 4993. We rule out the presence of any globular cluster at the position of AT 2017gfo to 2.3 × 10$^{4}$L$_{⊙}$, including those with the reddest V - H colors. Finally, we analyze the substructure of NGC 4993 in deep residual imaging and find shell features that extend up to 71."8 (14.2 kpc) from NGC 4993. The shells have a cumulative stellar mass of 6.3 × 10$^{8}$M$_{⊙}$, roughly 2% of NGC 4993, and mass-weighted ages of >3 Gyr. We conclude that it was unlikely that the GW170817 progenitor system formed in the galaxy merger.

79 ASTRONOMY AND ASTROPHYSICS↗

Connecting the Light Curves of Type IIP Supernovae to the Properties of Their Progenitors

Abstract Observations of core-collapse supernovae (CCSNe) reveal a wealth of information about the dynamics of the supernova ejecta and its composition but very little direct information about the progenitor. Constraining properties of the progenitor and the explosion requires coupling the observations with a theoretical model of the explosion. Here we begin with the CCSN simulations of Couch et al., which use a nonparametric treatment of the neutrino transport while also accounting for turbulence and convection. In this work we use the SuperNova Explosion Code to evolve the CCSN hydrodynamics to later times and compute bolometric light curves. Focusing on Type IIP SNe (SNe IIP), we then (1) directly compare the theoretical STIR explosions to observations and (2) assess how properties of the progenitor’s core can be estimated from optical photometry in the plateau phase alone. First, the distribution of plateau luminosities ( L 50 ) and ejecta velocities achieved by our simulations is similar to the observed distributions. Second, we fit our models to the light curves and velocity evolution of some well-observed SNe. Third, we recover well-known correlations, as well as the difficulty of connecting any one SN property to zero-age main-sequence mass. Finally, we show that there is a usable, linear correlation between iron core mass and L 50 such that optical photometry alone of SNe IIP can give us insights into the cores of massive stars. Illustrating this by application to a few SNe, we find iron core masses of 1.3–1.5 M ⊙ with typical errors of 0.05 M ⊙ . Data are publicly available online on Zenodo: doi: 10.5281/zenodo.6631964 .

79 ASTRONOMY AND ASTROPHYSICS↗