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At least 19 records

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS

3D small-gain formula allowing strong focusing and harmonic lasing for a ring-based x-ray free electron laser oscillator

We present a detailed derivation of a formula for the small-gain calculation for an x-ray free electron laser oscillator (XFELO) based on a medium-energy (3–4 GeV) storage ring. We found harmonic lasing and strong focusing are essential for this beam energy range. Taking the small-signal low-gain formula developed by Kim and his colleagues, we modified it in such a way that the gain can be calculated without the “no focusing approximation,” and a strong focusing can be applied, as well as harmonic lasing. In this formula, the gain is represented as a product of two factors with one of them depending only on the harmonic number, undulator period, and gap. Using this factor, we show that it is favorable to use harmonic lasing to achieve hard x-ray FEL working in the small-signal low-gain regime with the medium-energy electron beam. Our formula also allows FEL optimization by varying the vertical gradient of the undulator, the vertical dispersion, and the horizontal and vertical focusing, independently. As an example, we applied this formula to study the feasibility of an XFELO option for the National Synchrotron Light Source II (NSLS-II) upgrade. Since a quite high peak current is required for the FEL, collective effects of beam dynamics in medium-energy synchrotrons significantly affect the electron beam parameters. We carried out a multiparameter optimization taking collective effects into account. Note, even though our example is for a ring-based XFELO at 3 to 4 GeV, the formula and, in particular, the approach developed here may be applied to other types of FELs. Published by the American Physical Society 2024

36 MATERIALS SCIENCE

Leveraging 13C-Labeling to Assign Molecular Formulas to Unknown Yeast Metabolites

Mass spectrometry analyses have identified tens of thousands of unknown small molecule-associated peaks in different biological specimens. Notably, even the simplest and best studied organisms like Escherichia coli and Saccharomyces cerevisiae yield thousands of unknown peaks. A key question is how many of these reflect actual novel endogenous metabolites. To explore this, Mahieu and Patti used complete 13 C -labeling in E. coli to credential peaks as biological. This reduced the number of unknowns by more than 90%. Here, we carry out similar uniform 13 C-labeling in the Baker’s yeast S. cerevisiae and two less-studied bioenergy-relevant yeasts Rhodotorula toruloides (lipid producer) and Issatchenkia orientalis (organic acid producer). Identification of unknown metabolite peaks and their molecular formulas is facilitated through software tailored for 13 C labeling data and resulting knowledge of carbon atom count. A classification model evaluates the plausibility of each candidate formula, with peaks lacking plausible candidate formulas unlikely to reflect metabolite molecular ions. This approach prioritizes about one hundred candidate abundant unknown metabolites with logical molecular formulas. Most of these are species-specific rather than conserved across yeasts, and more are found in the nonmodel yeasts than S. cerevisiae. Thus, 13 C-labeling data on unknown metabolites highlights the potential for discovering new metabolites and pathways in nonmodel yeasts.

Carbon

Data Set Analysis to Reduce Uncertainty in Formula Assignments of Ultrahigh Resolution Mass Spectra

Environmental samples contain a vast array of organic compounds with diverse elemental compositions and heteroatom content. Molecular formula assignments of ultrahigh resolution mass spectra (HRMS) hold promise for elucidating the molecular composition of these compounds. However, the need to account for an assortment of heteroatoms increases the uncertainty associated with individual assignments – and ultimately the ecological, biological, and biogeochemical insights gleaned from the assignments. To address this challenge, we introduce a formula assignment strategy that leverages HRMS data sets to improve assignment confidence, filter false assignments, and mitigate bias in assignment routines. The strategy, implemented using CoreMS, first identifies the highest confidence assignment for a recurring ion in a data set by assessing the mass accuracy and isotopologue similarity of all assignments to the ion across the data set. The second component of the strategy examines the consistency of mass errors for an assigned ion throughout a data set and flags formulas with statistically unlikely deviations in mass error. Here, we illustrate the application and utility of the strategy by comparing its results against documented misassignment patterns within a set of oceanographic samples that were measured with 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Because the efficacy of our strategy improves with data set size, it is particularly useful for enhancing assignment confidence in large HRMS data sets common in studies of environmental systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Water Dielectric Function at Finite Wavelength and the Convergence of Its Large Wavelength Limit (Static Dielectric) by Fluctuation Formulas

Here we provide a general analysis of the longitudinal dielectric function ε l (k) via fluctuation formulas at finite wavelength k, including the static dielectric constant ε w = ε l (k → 0), and analyze the different sources of errors, deriving explicit formulas. Simulations with the SPC/E water model show that the convergence of fluctuation formulas to compute the static dielectric constant is slow and requires long simulations. The analysis of ε l (k) allows us to identify the long- and short-wavelength limits and provide a precise determination of the location of the poles as well as the zeros in the complex plane, which determine the short-distance form of the electrostatic (Coulomb) interaction among charged particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Spectral Bounds on Hyperbolic 3-Manifolds: Associativity and the Trace Formula

We constrain the low-energy spectra of Laplace operators on closed hyperbolic manifolds and orbifolds in three dimensions, including the standard Laplace--Beltrami operator on functions and the Laplacian on powers of the cotangent bundle. Our approach employs linear programming techniques to derive rigorous bounds by leveraging two types of spectral identities. The first type, inspired by the conformal bootstrap, arises from the consistency of the spectral decomposition of the product of Laplace eigensections, and involves the Laplacian spectra as well as integrals of triple products of eigensections. We formulate these conditions in the language of representation theory of PSL 2 (C) and use them to prove upper bounds on the first and second Laplacian eigenvalues. The second type of spectral identities follows from the Selberg trace formula. We use them to find upper bounds on the spectral gap of the Laplace--Beltrami operator on hyperbolic 3-orbifolds, as well as on the systole length of hyperbolic 3-manifolds, as a function of the volume. Further, we prove that the spectral gap λ 1 of the Laplace--Beltrami operator on all closed hyperbolic 3-manifolds satisfies λ 1 < 47.32. Along the way, we use the trace formula to estimate the low-energy spectra of a large set of example orbifolds and compare them with our general bounds, finding that the bounds are nearly sharp in several cases.

Bonifacio, James [University of Mississippi, MS (U

Analytic Chromaticity Formulas for the Muon g -2 experiment at fermilab

The Muon g-2 Experiment (E989) at Fermilab measured the muon anomalous magnetic moment aμ with unprecedented precision of 127 ppb using a storage ring. The experiment pushed the limits in terms of accuracy and systematic errors. Achieving the 78-ppb total systematic uncertainty required precise beam dynamics modeling and corrections for effects on the measured muon precession frequency. Here, we derived the first analytic aberration formulas up to the second order for the muon g-2 storage ring’s combined-function electrostatic quadrupoles (superimposed magnetic dipole and electric quadrupole fields) using an order-by-order perturbation method. From these, we obtained the exact chromaticity formulas for three ring models of different granularity and validated them against numerical calculations using COSY INFINITY, achieving analytic-numerical agreement to ⁠$\mathscr{O}(10^{-10})$. This work resolved discrepancies between previous approximate derivations and provided essential beam dynamics results for Runs 4-6 analyses. We also calculated nonlinear chromaticities up to ninth order. The experiment completed its final Run 6 in July 2023, collecting 21 times more data than the previous muon g-2 experiment at Brookhaven National Laboratory, with the final result announced in June 2025.

aberrations

Lorentzian OPE inversion formula: A geometric perspective

We give a new perspective on the Lorentzian operator product expansion inversion formula [S. Caron-Huot, Analyticity in spin in conformal theories, .; D. Simmons-Duffin, D. Stanford, and E. Witten, A spacetime derivation of the Lorentzian OPE inversion formula, .], building on [P. Agarwal , companion paper, Embedding space approach to Lorentzian CFT amplitudes and causal spherical functions, .]. We introduce an “auxiliary” fourpoint function that can be related to the traditionally defined ones via a Radon transform. The Mellin amplitudes associated with this auxiliary function can be shown to be equivalent to the conventional partial wave amplitudes. This has the intuitive geometrical meaning of a generalization of the projection-slice theorem. Published by the American Physical Society 2025

Agarwal, Pulkit (ORCID:0000000346581691)

Direct local parametrization of nuclear state densities using the back-shifted Bethe formula

Level densities are often parametrized using the back-shifted Bethe formula (BBF) for nuclei that possess experimental data for s-wave neutron resonance average spacings and a complete discrete level sequence at low excitation energies. However, these parametrizations require the additional modeling of the dependence of the spin-cutoff parameter on excitation energy. Here, in this work, we avoid the need to model the spin distribution of level densities by using the experimental data to parametrize directly the state densities, for which the BBF does not depend on the spin-cutoff parameter. This approach allows for a local parameterization of state densities that is independent of the spin-cutoff parameter. We provide these parameters in a tabulated form for applications in nuclear reaction calculations and for testing microscopic approaches to state densities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

National Electric Vehicle Infrastructure Formula Program (ANNUAL REPORT | PLAN YEAR 2023–2024)

The 2021 Infrastructure Investment and Jobs Act, also known as the Bipartisan Infrastructure Law (BIL), invests $\$$7.5 billion to build out a national electric vehicle (EV) charging network and created the Joint Office of Energy and Transportation (Joint Office) to “study, plan, coordinate, and implement issues of joint concern between the two agencies.” The BIL represents a historic effort to electrify the U.S. transportation system, which has significant potential to reduce U.S. greenhouse gas emissions and help tackle the climate crisis. The U.S. transportation sector accounts for one-third of the nation’s greenhouse gas emissions—the largest share of all primary sectors, including electricity production, industry, commercial and residential, and agriculture. The National Electric Vehicle Infrastructure (NEVI) Formula Program, one of the BIL funding programs, was launched in February 2022, providing nearly $\$$5 billion over 5 years to help states, the District of Columbia, and Puerto Rico (hereafter referred to as “states”) create a network of EV charging stations beginning with designated Federal Highway Administration (FHWA) Alternative Fuel Corridors (AFCs), with an emphasis on the Interstate Highway System. The funding is made available to the states in allocations each year pending FHWA certification of the state’s annual deployment plan. The NEVI program is in its third year, so there's a lot to celebrate. As of July 2024, 39 states have released solicitations for their NEVI programs and eight states have opened their first NEVI-funded stations (61 ports in total), which have already powered thousands of charging sessions for EV drivers across America. Additional stations are in the pipeline with more than 2,500 additional ports having been awarded or conditionally awarded by the states. All states released their Fiscal Year (FY) 2024 deployment plan updates to reflect the new minimum requirements and guidance, and several states added newly designated EV AFCs in their FY 2024 deployment plan updates, bringing the total AFC network of EV corridors to more than 81,000 miles.

33 ADVANCED PROPULSION SYSTEMS

MC Formula Protocol for H35HF Fueling (CRADA Final Report)

The National Renewable Energy Lab (NREL), Frontier Energy, and the industry partners worked together to help SAE J2601-5 develop an H35 high-flow (HF) medium-duty (MD) and heavy-duty (HD) fueling protocol. The team upgraded NREL's hydrogen filling simulations (H2FillS) model to accommodate an MC Formula fueling (t-final) table generation capability by leveraging NREL's high-performance computing system. Based on protocol boundary conditions (e.g., allowable maximum flow rate, range of storage system size) set by SAE J2601-5, the team generated the fueling tables and then validated the reliability of those tables by installing them on NREL's HD dispenser and ZBT's H35HF dispenser and then performing H35HF fueling experiments. Through the validation process, this team certified that the fueling tables generated were reliable to install in commercial H35HF dispensers and then performed H35HF fueling of commercial MD/HD vehicles.

08 HYDROGEN

Diabetes-specific formula with standard of care improves glycemic control, body composition, and cardiometabolic risk factors in overweight and obese adults with type 2 diabetes: results from a randomized controlled trial

Background and aims Medical nutrition therapy is important for diabetes management. This randomized controlled trial investigated the effects of a diabetes-specific formula (DSF) on glycemic control and cardiometabolic risk factors in adults with type 2 diabetes (T2D). Methods Participants ( n = 235) were randomized to either DSF with standard of care (SOC) (DSF group; n = 117) or SOC only (control group; n = 118). The DSF group consumed one or two DSF servings daily as meal replacement or partial meal replacement. The assessments were done at baseline, on day 45, and on day 90. Results There were significant reductions in glycated hemoglobin (−0.44% vs. –0.26%, p = 0.015, at day 45; −0.50% vs. −0.21%, p = 0.002, at day 90) and fasting blood glucose (−0.14 mmol/L vs. +0.32 mmol/L, p = 0.036, at day 90), as well as twofold greater weight loss (−1.30 kg vs. –0.61 kg, p < 0.001, at day 45; −1.74 kg vs. –0.76 kg, p < 0.001, at day 90) in the DSF group compared with the control group. The decrease in percent body fat and increase in percent fat-free mass at day 90 in the DSF group were almost twice that of the control group (1.44% vs. 0.79%, p = 0.047). In addition, the percent change in visceral adipose tissue at day 90 in the DSF group was several-fold lower than in the control group (−6.52% vs. –0.95%, p < 0.001). The DSF group also showed smaller waist and hip circumferences, and lower diastolic blood pressure than the control group (all overall p ≤ 0.045). Conclusion DSF with SOC yielded significantly greater improvements than only SOC in glycemic control, body composition, and cardiometabolic risk factors in adults with T2D.

Tey, Siew Ling

Towards a general subtraction formula for NNLO QCD corrections to processes at hadron colliders: final states with quarks and gluons

We describe the calculation of integrated subtraction terms in the nested soft-collinear subtraction scheme for hadron collider processes with quarks and gluons, thereby extending the results presented in ref. [1]. Although this extension eventually proves to be straightforward, it requires a more careful treatment of certain collinear limits to achieve a compact and physically-transparent final result. We also show that the cancellation of infrared divergences can be organized in such a way that, once soft contributions are removed, it occurs independently for each of the external partons. We consider these results to be important stepping stones on the way to deriving finite remainders of the integrated subtraction terms for fully-general hadron collider processes in the context of the nested soft-collinear subtraction scheme.

NNLO calculations

High-Order Wall-Modeled Large-Eddy Simulation of High-Lift Configuration

This paper presents the assessment of several recent enhancements for a high-order wall-modeled large-eddy simulation (WMLES) approach and demonstrates order independence with a fixed data exchange location in the wall model. The two enhancements include the use of isotropic tetrahedral elements to improve accuracy and an explicit subgrid-scale model, the Vreman model, to improve accuracy and robustness. The [Formula: see text] study focused on the high-lift Common Research Model (HL-CRM) at the angle of attack of 19.57 deg, a benchmark problem from the 4th AIAA High-Lift Prediction Workshop. Solution polynomial orders of [Formula: see text], and 5 were used in the study. The study demonstrated [Formula: see text] independence in integrated forces, pitch moment, velocity profile in the wall-normal direction, and surface flow topology. It also showed that a [Formula: see text] order of at least 3 ([Formula: see text]) was needed to correctly predict the external inviscid flow and the surface flow topology. Thereafter, [Formula: see text] simulations over several other angles of attack demonstrated that the high-order WMLES approach can correctly predict the maximum lift and flow separation regions for HL-CRM with about 40 million degrees of freedom (DOF) compared to at least 250 million DOF required by second-order methods.

Engineering

Exponentially Reduced Circuit Depths Using Trotter Error Mitigation

Product formulas are a popular class of digital quantum simulation algorithms due to their conceptual simplicity, low overhead, and performance, which often exceeds theoretical expectations. Recently, Richardson extrapolation and polynomial interpolation have been proposed to mitigate the Trotter error incurred by the use of these formulas. This work provides a rigorous, general analysis of these techniques for computing time-evolved observables, simplifying the interpolation algorithm in the process, and shows that extrapolation generically improves the performance of product formulas for this task. We demonstrate that, to achieve error 𝜖 in a simulation of time 𝑇 using a 𝑝 ⁢th-order product formula with extrapolation, circuit depths of 𝑂⁡(𝑇 1+1/𝑝 ⁢polylog (1/𝜖)) are sufficient—an exponential improvement in the precision over product formulas alone. Furthermore, we prove that these algorithms achieve commutator scaling, and improve the 𝑇 complexity for the interpolation algorithm. By relaxing the requirement of performing exact Chebyshev interpolation, our simplified algorithm eliminates the need for fractional implementations of Trotter steps, reducing computational overhead. Finally, we show these techniques can be combined with the classical shadows method to estimate many time-evolved local observables. Taken together, our findings provide the strongest evidence yet for the utility of Trotter error-mitigation techniques in algorithmic applications.

quantum algorithms & computation

Explicit Form for the Most General Lorentz Transformation Revisited

Explicit formulae for the 4×4 Lorentz transformation matrices corresponding to a pure boost and a pure three-dimensional rotation are very well known. Significantly less well known is the explicit formula for a general Lorentz transformation with arbitrary non-zero boost and rotation parameters. We revisit this more general formula by presenting two different derivations. The first derivation (which is somewhat simpler than previous ones appearing in the literature) evaluates the exponential of a 4×4 real matrix A, where A is a product of the diagonal matrix diag(+1,−1,−1,−1) and an arbitrary 4×4 real antisymmetric matrix. The formula for expA depends only on the eigenvalues of A and makes use of the Lagrange interpolating polynomial. The second derivation exploits the observation that the spinor product η†σ¯μχ transforms as a Lorentz four-vector, where χ and η are two-component spinors. The advantage of the latter derivation is that the corresponding formula for a general Lorentz transformation Λ reduces to the computation of the trace of a product of 2×2 matrices. Both computations are shown to yield equivalent expressions for Λ.

Science & Technology - Other Topics

Nonrenormalization theorem for $\mathcal{N}$ = (4, 4) interface entropy

We derive a formula for the half-BPS interface entropy between any pair of $\mathcal{N}$ = (4, 4) theories on the same conformal manifold. This generalizes the diastasis formula derived in [1] for $\mathcal{N}$ = (2, 2) theories, which is restricted to the conformal submanifolds generated by either chiral or twisted chiral multiples of $\mathcal{N}$ = (2, 2) supersymmetry. To derive the $\mathcal{N}$ = (4, 4) formula, we use the fact that the conformal manifold of $\mathcal{N}$ = (4, 4) theories is symmetric and quaternionic-Kähler and that its isotropy group contains the SU(2) ⊗ SU(2) external automorphism of the $\mathcal{N}$ = (4, 4) superconformal algebra. As an application of the formula, we prove a supersymmetric non-renormalization theorem, which explains the observation in [2] that the interface entropy for half-BPS Janus solutions in type IIB supergravity on AdS 3 × S 3 × T 4 coincides with the corresponding quantity in their free conformal field limits.

AdS-CFT correspondence