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Mass Spectrometry Adduct Calculator

We describe the Mass Spectrometry Adduct Calculator (MSAC), an automated Python tool to calculate the adduct ion masses of a parent molecule. Here, adduct refers to a version of a parent molecule [M] that is charged due to addition or loss of atoms and electrons resulting in a charged ion, e.g. [M+H] + . MSAC includes a database of 2,341 potential ions and their mass-to-charge ratios (m/z) as extracted from the NIST/EPA/NIH Mass Spectral Library (NIST17), the Global Natural Products Social Molecular Networking Public Spectral Libraries (GNPS), and MassBank of North America (MoNA). The calculator relies on user-selected subsets of the combined database to calculate expected m/z for adducts of molecules supplied as formulas This tool is intended to help researchers create identification libraries to collect evidence for the presence of molecules in mass spectrometry data. While the included adduct database focuses on adducts typically detected during liquid chromatography-mass spectrometry analyses, users may supply their own lists of adducts and charge states for calculating expected m/z. We also analyzed statistics on adducts from spectra contained in the three selected mass spectral libraries. MSAC is freely available at https://github.com/pnnl/MSAC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stochastic Real-Time Second-Order Green’s Function Theory for Neutral Excitations in Molecules and Nanostructures

We present a real-time second-order Green’s function (GF) method for computing excited states in molecules and nanostructures, with a computational scaling of O(N e 3 ), where N e is the number of electrons. The cubic scaling is achieved by adopting the stochastic resolution of the identity to decouple the 4-index electron repulsion integrals. To improve the time propagation and the spectral resolution, we adopt the dynamic mode decomposition technique and assess the accuracy and efficiency of the combined approach for a chain of hydrogen dimer molecules of different lengths. We find that the stochastic implementation accurately reproduces the deterministic results for the electronic dynamics and excitation energies. Furthermore, we provide a detailed analysis of the statistical errors, bias, and long-time extrapolation. Overall, the approach offers an efficient route to investigate excited states in extended systems with open or closed boundary conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tracking atomic structure evolution during directed electron beam induced Si-atom motion in graphene via deep machine learning

Using electron beam manipulation, we enable deterministic motion of individual Si atoms in graphene along predefined trajectories. Structural evolution during the dopant motion was explored, providing information on changes of the Si atom neighborhood during atomic motion and providing statistical information of possible defect configurations. The combination of a Gaussian mixture model and principal component analysis applied to the deep learning-processed experimental data allowed disentangling of the atomic distortions for two different graphene sublattices. This approach demonstrates the potential of e-beam manipulation to create defect libraries of multiple realizations of the same defect and explore the potential of symmetry breaking physics. The rapid image analytics enabled via a deep learning network further empowers instrumentation for e-beam controlled atom-by-atom fabrication. Here, the analysis described in the paper can be reproduced via an interactive Jupyter notebook at https://git.io/JJ3Bx.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Physical-mass calculation of ρ ( 770 ) and K * ( 892 ) resonance parameters via π π and K π scattering amplitudes from lattice QCD

We present our study of the ρ ( 770 ) and K * ( 892 ) resonances from lattice quantum chromodynamics (QCD) employing domain-wall fermions at physical quark masses. We determine the finite-volume energy spectrum in various momentum frames and obtain phase-shift parametrizations via the Lüscher formalism and as a final step the complex resonance poles of the π π and K π elastic scattering amplitudes via an analytical continuation of the models. By sampling a large number of representative sets of underlying energy-level fits, we also assign a systematic uncertainty to our final results. This is a significant extension to data-driven analysis methods that have been used in lattice QCD to date, due to the two-step nature of the formalism. Our final pole positions, M + i Γ / 2 , with all statistical and systematic errors exposed, are M K * = 893 ( 2 ) ( 8 ) ( 54 ) ( 2 ) MeV and Γ K * = 51 ( 2 ) ( 11 ) ( 3 ) ( 0 ) MeV for the K * ( 892 ) resonance and M ρ = 796 ( 5 ) ( 15 ) ( 48 ) ( 2 ) MeV and Γ ρ = 192 ( 10 ) ( 28 ) ( 12 ) ( 0 ) MeV for the ρ ( 770 ) resonance. The four differently grouped sources of uncertainties are, in the order of occurrence: statistical, data-driven systematic, an estimation of systematic effects beyond our computation (dominated by the fact that we employ a single lattice spacing), and the error from the scale-setting uncertainty on our ensemble. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Broadband Noise Predictions Based on a New Aeroacoustic Formulation

A new analytic result in acoustics called 'Formulation 1B,' proposed by Farassat, is used to compute the loading noise from an unsteady surface pressure distribution on a thin airfoil in the time domain. This formulation is a new solution of the Ffowcs Williams-Hawkings equation with the loading source term. The formulation contains a far-field surface integral that depends on the time derivative and the surface gradient of the pressure on the airfoil, as well as a contour integral on the boundary of the airfoil surface. As a first test case, the new formulation is used to compute the noise radiated from a flat plate, moving through a sinusoidal gust of constant frequency. The unsteady surface pressure for this test case is specified analytically from a result that is based on linear airfoil theory. This test case is used to examine the velocity scaling properties of Formulation 1B, and to demonstrate its equivalence to Formulation 1A, of Farassat. The new acoustic formulation, again with an analytic surface pressure, is then used to predict broadband noise radiated from an airfoil immersed in homogeneous turbulence. The results are compared with experimental data previously reported by Paterson and Amiet. Good agreement between predictions and measurements is obtained. The predicted results also agree very well with those of Paterson and Amiet, who used a frequency-domain approach. Finally, an alternative form of Formulation 1B is described for statistical analysis of broadband noise.

Casper, J.↗

Reevaluating Contour Visualizations for Power Systems Data

Effective visual analytics tools are needed now more than ever as emerging energy systems data and models are rapidly growing in scale and complexity. Here we examined the suitability of colored contour maps to visually represent bus values in two different power system models: a dense 24k-bus distribution system and a 240-bus transmission system. In a quantitative analysis, we found that contour maps misrepresent power systems data, changing the statistical dispersion of the bus values, including the loss of extreme values. In a controlled empirical study with thirty professional power system research engineers, we found that these distortions significantly impact excursion identification tasks. Additionally, the engineers were less confident in their assessments using contour-based visualizations than glyph-based visualizations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Evaluating Retention Index Score Assumptions to Refine GC–MS Metabolite Identification

As metabolomics grows into a high-throughput and high demand research field, current metrics for the identification of small molecules in gas chromatography–mass spectrometry (GC–MS) still require manual verification. Though steps have been taken to improve scoring metrics by combining spectral similarity (SS) and retention index (RI), the problem persists. A large body of literature has analyzed and refined SS scores, but few studies have explicitly studied improvements to RI scores. Here, in this study, we examined whether uninvestigated assumptions of the RI score are valid and propose ways to improve them. Query RIs were matched to library RI with a generous window of ±35 to avoid unintentional removal of valid compound identifications. Each match was manually verified as a true positive (TP), true negative, or unknown. Metabolites with at least 30 TP identifications were included in downstream analyses, resulting in a total of 87 metabolites from samples of varying complexity and type (e.g., amino acid mixtures, human urine, fungal species, and so on.). Our results showed that the RI score assumptions of normality, consistent variance across metabolites, and a mean error centered at 0 are often violated. We demonstrated through a cross-validation analysis that modifying these underlying assumptions according to empirical metabolite-specific distributions improved the TP and negative rankings. Further, we statistically determined the minimum number of samples required to estimate distributional parameters for scoring metrics. Overall, this work proposes a robust statistical pipeline to reduce the time bottleneck of metabolite identification by improving RI scores and thus minimize the effort to complete manual verification.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Delineating the Effects of Counterions on the Structural and Vibrational Properties of U(IV) Lindqvist Polyoxometalate Complexes

Herein we conducted a full investigation into the fundamental structural and vibrational properties of uranium(IV) Peacock−Weakley-type lacunary Lindqvist (W 10 ) polyoxometalate (POM) complexes. We recently demonstrated the importance of the secondary lattice elements in tuning the distortion of the D 4d symmetry in W 10 POM complexes, and here, we synthesized eight UW 10 complexes with different alkali metal counterions and evaluated how the composition and packing of counterion species affected complex structural and vibrational properties. Single-crystal X-ray diffraction analysis on complexes 1−8 revealed changes in structural distortion parameters as a function of differences in counterion configurations, while far-infrared and Raman spectra for 1−8 also demonstrated that vibrational mode frequencies were sensitive to changes in counterion composition and packing. To more effectively compare different counterion configurations, we developed counterion effective ionic radius (eIR) as a new structural parameter, and comparisons between structural distortion parameters and eIR values strongly suggested that modulation by the secondary lattice elements can affect structural and vibrational manifolds within POM complexes. Partial least squares (PLS) analysis was used to quantitatively evaluate correlations observed within this investigation, and PLS statistical models showed a strong correlation between counterion eIR and both structural distortion parameters and vibrational mode frequencies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polishing the Gold Standard: The Role of Orbital Choice in CCSD(T) Vibrational Frequency Prediction

While CCSD(T) with spin-restricted Hartree-Fock (RHF) orbitals has long been lauded for its ability to accurately describe closed-shell interactions, the performance of CCSD(T) on open-shell species is much more erratic, especially when using a spin-unrestricted HF (UHF) reference. Previous studies have shown improved treatment of open-shell systems when a non-HF set of molecular orbitals, like Brueckner or Kohn-Sham density functional theory (DFT) orbitals, is used as a reference. Inspired by the success of regularized orbital-optimized second-order Møller-Plesset perturbation theory (κ-OOMP2) orbitals as reference orbitals for MP3, we investigate the use of κ-OOMP2 orbitals and various DFT orbitals as reference orbitals for CCSD(T) calculations of the corrected ground-state harmonic vibrational frequencies of a set of 36 closed-shell (29 neutrals, 6 cations, 1 anion) and 59 open-shell diatomic species (38 neutrals, 15 cations, 6 anions). The aug-cc-pwCVTZ basis set is used for all calculations. The use of κ-OOMP2 orbitals in this context alleviates difficult cases observed for both UHF orbitals and OOMP2 orbitals. Removing two multireference systems and 12 systems with ambiguous experimental data leaves a pruned data set. Overall performance on the pruned data set highlights CCSD(T) with a B97 orbital reference (CCSD(T):B97), CCSD(T) with a κ-OOMP2 orbital reference (CCSD(T):κ-OOMP2), and CCSD(T) with a B97M-rV orbital reference (CCSD(T):B97M-rV) with RMSDs of 8.48 cm -1 , and 8.50 cm -1 , and 8.75 cm -1 respectively, outperforming CCSD(T):UHF by nearly a factor of 5. Moreover, the performance on the closed- and open-shell subsets shows these methods are able to treat open-shell and closed-shell systems with comparable accuracy and robustness. CCSD(T) with RHF orbitals is seen to improve upon UHF for the closed-shell species, while spatial symmetry breaking in a number of restricted open-shell HF (ROHF) references leads CCSD(T) with ROHF reference orbitals to exhibit the poorest statistical performance of all methods surveyed for open-shell species. The use of κ-OOMP2 orbitals has also proven useful in diagnosing multireference character that can hinder the reliability of CCSD(T).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Decadal predictability of North Atlantic blocking and the NAO

Can multi-annual variations in the frequency of North Atlantic atmospheric blocking and mid-latitude circulation regimes be skilfully predicted? Recent advances in seasonal forecasting have shown that mid-latitude climate variability does exhibit significant predictability. However, atmospheric predictability has generally been found to be quite limited on multi-annual timescales. New decadal prediction experiments from NCAR are found to exhibit remarkable skill in reproducing the observed multi-annual variations of wintertime blocking frequency over the North Atlantic and of the North Atlantic Oscillation (NAO) itself. This is partly due to the large ensemble size that allows the predictable component of the atmospheric variability to emerge from the background chaotic component. The predictable atmospheric anomalies represent a forced response to oceanic low-frequency variability that strongly resembles the Atlantic Multi-decadal Variability (AMV), correctly reproduced in the decadal hindcasts thanks to realistic ocean initialization and ocean dynamics. The occurrence of blocking in certain areas of the Euro-Atlantic domain determines the concurrent circulation regime and the phase of known teleconnections, such as the NAO, consequently affecting the stormtrack and the frequency and intensity of extreme weather events. Therefore, skilfully predicting the decadal fluctuations of blocking frequency and the NAO may be used in statistical predictions of near-term climate anomalies, and it provides a strong indication that impactful climate anomalies may also be predictable with improved dynamical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analytical methods for performance evaluation of nonlinear filters.

In the investigation, the filtering problem is considered in the continuous time domain. The postulated simple suboptimal nonlinear filter structure closely parallels the structure of the Kalman-Bucy optimal linear filter algorithm. Two filter performance evaluation methods are developed based on the Kolmogorov equations for the transition density of Markov processes. The expansions in the approximations for the nonlinear system and observation functions are in effect carried out up to second-order terms in both methods. The description of the filter's performance is sought in terms of second-order statistics in both methods.

Bejczy, A. K.↗

Distributions in CFT. Part II. Minkowski space

CFTs in Euclidean signature satisfy well-accepted rules, such as the convergent Euclidean OPE. It is nowadays common to assume that CFT correlators exist and have various properties also in Lorentzian signature. Some of these properties may represent extra assumptions, and it is an open question if they hold for familiar statistical-physics CFTs such as the critical 3d Ising model. Here we consider Wightman 4-point functions of scalar primaries in Lorentzian signature. We derive a minimal set of their properties solely from the Euclidean unitary CFT axioms, without using extra assumptions. We establish all Wightman axioms (temperedness, spectral property, local commutativity, clustering), Lorentzian conformal invariance, and distributional convergence of the s-channel Lorentzian OPE. This is done constructively, by analytically continuing the 4-point functions using the s-channel OPE expansion in the radial cross-ratios ρ, ρ¯. We prove a key fact that |ρ|, |ρ¯| < 1 inside the forward tube, and set bounds on how fast |ρ|, |ρ¯| may tend to 1 when approaching the Minkowski space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measuring the giant radio galaxy length distribution with the LoTSS

Many massive galaxies launch jets from the accretion disk of their central black hole, but only ~10 3 instances are known in which the associated outflows form giant radio galaxies (GRGs, or giants): luminous structures of megaparsec extent that consist of atomic nuclei, relativistic electrons, and magnetic fields. Large samples are imperative to understanding the enigmatic growth of giants, and recent systematic searches in homogeneous surveys constitute a promising development. For the first time, it is possible to perform meaningful precision statistics with GRG lengths, but a framework to do so is missing. We measured the intrinsic GRG length distribution by combining a novel statistical framework with a LOFAR Two-metre Sky Survey (LoTSS) sample of freshly discovered giants. In turn, this allowed us to answer an array of questions on giants. For example, we can now assess how rare a 5 Mpc giant is compared with one of 1 Mpc, and how much larger – given a projected length – the corresponding intrinsic length is expected to be. Notably, we can now also infer the GRG number density in the Local Universe. We assumed the intrinsic GRG length distribution to be Paretian (i.e. of power-law form) with tail index ξ, and predicted the observed distribution by modelling projection and selection effects. To infer ξ, we also systematically searched the LoTSS for hitherto unknown giants and compiled the largest catalogue of giants to date. We show that if intrinsic GRG lengths are Pareto distributed with index ξ, then projected GRG lengths are also Pareto distributed with index ξ. Selection effects induce curvature in the observed projected GRG length distribution: angular length selection flattens it towards the lower end, while surface brightness selection steepens it towards the higher end. We explicitly derived a GRG’s posterior over intrinsic lengths given its projected length, laying bare the ξ dependence. We also discovered 2060 giants within LoTSS DR2 pipeline products; our sample more than doubles the known population. Spectacular discoveries include the largest, second-largest, and fourth-largest GRG known (l p = 5.1 Mpc, l p = 5.0 Mpc, and l p = 4.8 Mpc), the largest GRG known hosted by a spiral galaxy (l p = 2.5 Mpc), and the largest secure GRG known beyond redshift 1 (l p = 3.9 Mpc). We increase the number of known giants whose angular length exceeds that of the Moon from 10 to 23; among the discoveries is the angularly largest known radio galaxy in the Northern Sky, which is also the angularly largest known GRG ($\phi$ = 2°). Combining theory and data, we determined that intrinsic GRG lengths are well described by a Pareto distribution, and measured the index ξ = –3.5 ± 0.5. This implies that, given its projected length, a GRG’s intrinsic length is expected to be just 15% larger. Finally, we determined the comoving number density of giants in the Local Universe to be n GRG = 5 ± 2(100 Mpc) –3 . We developed a practical mathematical framework that elucidates the statistics of giant radio galaxy lengths. Through a LoTSS search, we also discovered 2060 new giants. By combining both advances, we determined that intrinsic GRG lengths are well described by a Pareto distribution with index ξ = –3.5 ± 0.5, and that giants are truly rare in a cosmological sense: most clusters and filaments of the Cosmic Web are not currently home to a giant. Thus, our work yields new observational constraints for analytical models and simulations featuring radio galaxy growth.

79 ASTRONOMY AND ASTROPHYSICS↗

Johnson Space Center's Risk and Reliability Analysis Group 2008 Annual Report

The Johnson Space Center (JSC) Safety & Mission Assurance (S&MA) Directorate s Risk and Reliability Analysis Group provides both mathematical and engineering analysis expertise in the areas of Probabilistic Risk Assessment (PRA), Reliability and Maintainability (R&M) analysis, and data collection and analysis. The fundamental goal of this group is to provide National Aeronautics and Space Administration (NASA) decisionmakers with the necessary information to make informed decisions when evaluating personnel, flight hardware, and public safety concerns associated with current operating systems as well as with any future systems. The Analysis Group includes a staff of statistical and reliability experts with valuable backgrounds in the statistical, reliability, and engineering fields. This group includes JSC S&MA Analysis Branch personnel as well as S&MA support services contractors, such as Science Applications International Corporation (SAIC) and SoHaR. The Analysis Group s experience base includes nuclear power (both commercial and navy), manufacturing, Department of Defense, chemical, and shipping industries, as well as significant aerospace experience specifically in the Shuttle, International Space Station (ISS), and Constellation Programs. The Analysis Group partners with project and program offices, other NASA centers, NASA contractors, and universities to provide additional resources or information to the group when performing various analysis tasks. The JSC S&MA Analysis Group is recognized as a leader in risk and reliability analysis within the NASA community. Therefore, the Analysis Group is in high demand to help the Space Shuttle Program (SSP) continue to fly safely, assist in designing the next generation spacecraft for the Constellation Program (CxP), and promote advanced analytical techniques. The Analysis Section s tasks include teaching classes and instituting personnel qualification processes to enhance the professional abilities of our analysts as well as performing major probabilistic assessments used to support flight rationale and help establish program requirements. During 2008, the Analysis Group performed more than 70 assessments. Although all these assessments were important, some were instrumental in the decisionmaking processes for the Shuttle and Constellation Programs. Two of the more significant tasks were the Space Transportation System (STS)-122 Low Level Cutoff PRA for the SSP and the Orion Pad Abort One (PA-1) PRA for the CxP. These two activities, along with the numerous other tasks the Analysis Group performed in 2008, are summarized in this report. This report also highlights several ongoing and upcoming efforts to provide crucial statistical and probabilistic assessments, such as the Extravehicular Activity (EVA) PRA for the Hubble Space Telescope service mission and the first fully integrated PRAs for the CxP's Lunar Sortie and ISS missions.

Valentine, Mark↗

Effect of secondary gas-phase reactions (SGR) in pyrolysis of carbon feedstocks for anisotropic carbon materials production – 2: Effects of SGR on tars produced from varying ranks of coal

Herein, this work explores the extent to which secondary gas-phase reactions (SGR) in pyrolysis can be used to modify coal tar chemistries from coals of different ranks in favor of improved anisotropy formation in their respective pitches. Pyrolysis was performed on four different coals of varying bituminous rank (Utah Sufco, Wyoming PRB Black Thunder, Illinois #6, and West Virginia Flying Eagle), with SGR temperatures ranging from 800 to 900° C and nominal SGR gas-phase residence times from 1 to 2.5 s. The oxygen content, aliphatic content, and molecular weight distributions of the coal tar samples were measured to indicate the changes with increasing levels of SGR, and microscopy was also used to measure changes in anisotropy formation in the resulting pitch samples. Generally, for all coals tested, increased levels of pyrolysis SGR led to decreased oxygen and aliphatic content, increased molecular weight sizes, and improved anisotropy formation. However, it was clear that the extent of these property changes depended on the chemistry and rank of the starting coal feedstock. Despite the relatively high rank of the Illinois #6 coal, its respective pitch samples performed poorly in improving anisotropy formation, due to its high sulfur content. The PRB, Sufco, and Flying Eagle coals performed better in their anisotropy formation than Illinois #6, depending on their respective coal ranks. Statistical analysis (analysis of variance, ANOVA) performed on the sample characterization data also suggests that SGR temperature is consistently the most dominant and significant effect on the resulting coal products.

01 COAL, LIGNITE, AND PEAT↗

Exploration of lattice Hamiltonians for functional and structural discovery via Gaussian process-based exploration–exploitation

Statistical physics models ranging from simple lattice to complex quantum Hamiltonians are one of the mainstays of modern physics that have allowed both decades of scientific discovery and provided a universal framework to understand a broad range of phenomena from alloying to frustrated and phase separated materials to quantum systems. Traditionally, exploration of the phase diagrams corresponding to multidimensional parameter spaces of Hamiltonians was performed using a combination of basic physical principles, analytical approximations, and extensive numerical modeling. However, exploration of complex multidimensional parameter spaces is subject to the classic dimensionality problem, and the behaviors of interest concentrated on low dimensional manifolds remain undiscovered. Here, we demonstrate that a combination of exploration and exploration–exploitation with Gaussian process modeling and Bayesian optimization allows effective exploration of the parameter space for lattice Hamiltonians and effectively maps the regions at which specific macroscopic functionalities or local structures are maximized. We argue that this approach is general and can be further extended well beyond the lattice Hamiltonians to effectively explore the parameter space of more complex off-lattice and dynamic models.

42 ENGINEERING↗