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DOE OSTI2024

A taxonomy of automatic differentiation pitfalls

Automatic differentiation is a popular technique for computing derivatives of computer programs. While automatic differentiation has been successfully used in countless engineering, science, and machine learning applications, it can sometimes nevertheless produce surprising results. In this paper, we categorize problematic usages of automatic differentiation, and illustrate each category with examples such as chaos, time-averages, discretizations, fixed-point loops, lookup tables, linear solvers, and probabilistic programs, in the hope that readers may more easily avoid or detect such pitfalls. We also review debugging techniques and their effectiveness in these situations.

Autodiff↗

DOE OSTI2024

Collocation methods for nonlinear differential equations on low-rank manifolds

We introduce new methods for integrating nonlinear differential equations on low-rank manifolds. These methods rely on interpolatory projections onto the tangent space, enabling low-rank time integration of vector fields that can be evaluated entry-wise. A key advantage of our approach is that it does not require the vector field to exhibit low-rank structure, thereby overcoming significant limitations of traditional dynamical low-rank methods based on orthogonal projection. To construct the interpolatory projectors, we develop a sparse tensor sampling algorithm based on the discrete empirical interpolation method (DEIM) that parameterizes tensor train manifolds and their tangent spaces with cross interpolation. Using these projectors, we propose two time integration schemes on low-rank tensor train manifolds. The first scheme integrates the solution at selected interpolation indices and constructs the solution with cross interpolation. The second scheme generalizes the well-known orthogonal projector-splitting integrator to interpolatory projectors. We demonstrate the proposed methods with applications to several tensor differential equations arising from the discretization of partial differential equations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

SUNDIALS time integrators for exascale applications with many independent systems of ordinary differential equations

Many complex systems can be accurately modeled as a set of coupled time-dependent partial differential equations (PDEs). However, solving such equations can be prohibitively expensive, easily taxing the world’s largest supercomputers. One pragmatic strategy for attacking such problems is to split the PDEs into components that can more easily be solved in isolation. This operator splitting approach is used ubiquitously across scientific domains, and in many cases leads to a set of ordinary differential equations (ODEs) that need to be solved as part of a larger “outer-loop” time-stepping approach. The SUNDIALS library provides a plethora of robust time integration algorithms for solving ODEs, and the U.S. Department of Energy Exascale Computing Project (ECP) has supported its extension to applications on exascale-capable computing hardware. In this paper, we highlight some SUNDIALS capabilities and its deployment in combustion and cosmology application codes (Pele and Nyx, respectively) where operator splitting gives rise to numerous, small ODE systems that must be solved concurrently.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Measurement of inclusive and differential cross sections of single top quark production in association with a W boson in proton-proton collisions at $\sqrt{s}$ = 13.6 TeV

The first measurement of the inclusive and normalised differential cross sections of single top quark production in association with a W boson in proton-proton collisions at a centre-of-mass energy of 13.6 TeV is presented. The data were recorded with the CMS detector at the LHC in 2022, and correspond to an integrated luminosity of 34.7 fb −1 . The analysed events contain one muon and one electron in the final state. For the inclusive measurement, multivariate discriminants exploiting the kinematic properties of the events are used to separate the signal from the dominant top quark-antiquark production background. A cross section of $82.3\pm 2.1{\left(\textrm{stat}\right)}_{-9.7}^{+9.9}\left(\textrm{syst}\right)\pm 3.3\left(\textrm{lumi}\right)$ pb is obtained, consistent with the predictions of the standard model. A fiducial region is defined according to the detector acceptance to perform the differential measurements. The resulting differential distributions are unfolded to particle level and show good agreement with the predictions at next-to-leading order in perturbative quantum chromodynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Differential cross section measurements for the production of top quark pairs and of additional jets using dilepton events from pp collisions at $\sqrt{s}$ = 13 TeV

Differential cross sections for top quark pair ($\textrm{t}\overline{\textrm{t}}$) production are measured in proton-proton collisions at a center-of-mass energy of 13 TeV using a sample of events containing two oppositely charged leptons. The data were recorded with the CMS detector at the CERN Large Hadron Collider and correspond to an integrated luminosity of 138 fb −1 . The differential cross sections are measured as functions of kinematic observables of the $\textrm{t}\overline{\textrm{t}}$ system, the top quark and antiquark and their decay products, as well as of the number of additional jets in the event. The results are presented as functions of up to three variables and are corrected to the parton and particle levels. When compared to standard model predictions based on quantum chromodynamics at different levels of accuracy, it is found that the calculations do not always describe the observed data. The deviations are found to be largest for the multi-differential cross sections.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Inclusive and differential measurements of the $\textrm{t}\overline{\textrm{t}}\mathcal{γ}$ cross section and the $\textrm{t}\overline{\textrm{t}}\mathcal{γ}/\textrm{t}\overline{\textrm{t}}$ cross section ratio in proton-proton collisions at $\sqrt{s}=13$ TeV

Inclusive and differential cross section measurements of top quark pair $(\textrm{t}\overline{\textrm{t}})$ production in association with a photon (γ) are performed as a function of lepton, photon, top quark, and $\textrm{t}\overline{\textrm{t}}$ kinematic observables, using data from proton-proton collisions at $\sqrt{s}=13$ TeV, corresponding to an integrated luminosity of 138 fb −1 , collected at the CERN LHC with the CMS detector. Events containing two leptons (electrons or muons) and a photon in the final state are considered. The fiducial cross section of $\textrm{t}\overline{\textrm{t}}$γ is measured to be 137 ± 8 fb, in a phase space including events with a high momentum, isolated photon. The fiducial cross section of $\textrm{t}\overline{\textrm{t}}$γ is also measured to be 56 ± 5 fb when considering only events where the photon is emitted in the production part of the process. Both measurements are in agreement with the theoretical predictions, of 126 ± 19 fb and 57 ± 5 fb, respectively. Differential measurements are performed at the particle and parton levels. Additionally, inclusive and differential ratios between the cross sections of $\textrm{t}\overline{\textrm{t}}$γ and $\textrm{t}\overline{\textrm{t}}$ production are measured. The inclusive ratio is found to be 0.0133 ± 0.0005, in agreement with the standard model prediction of 0.0127 ± 0.0008. The top quark charge asymmetry in $\textrm{t}\overline{\textrm{t}}$γ production is also measured to be −0.012 ± 0.042, compatible with both the standard model prediction and with no asymmetry.

Hadron-Hadron Scattering↗

DOE OSTI2024

Inclusive and differential cross-section measurements of $ t\overline{t}Z$ production in pp collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector, including EFT and spin-correlation interpretations

Measurements of both the inclusive and differential production cross sections of a top-quark-top-antiquark pair in association with a Z boson ($t\overline{t}Z$) are presented. Final states with two, three or four isolated leptons (electrons or muons) are targeted. The measurements use the data recorded by the ATLAS detector in pp collisions at $\sqrt{s}$ = 13 TeV at the Large Hadron Collider during the years 2015–2018, corresponding to an integrated luminosity of 140 fb -1 . The inclusive cross section is measured to be ${\sigma}_{t\overline{t}Z}$ = 0.86 ± 0.04 (stat.) ± 0.04 (syst.) pb and found to be in agreement with the most advanced Standard Model predictions. The differential measurements are presented as a function of a number of observables that probe the kinematics of the $t\overline{t}Z$ system. Both the absolute and normalised differential cross-section measurements are performed at particle level and parton level for specific fiducial volumes, and are compared with NLO+NNLL theoretical predictions. The results are interpreted in the framework of Standard Model effective field theory and used to set limits on a large number of dimension-6 operators involving the top quark. The first measurement of spin correlations in $t\overline{t}Z$ events is presented: the results are in agreement with the Standard Model expectations, and the null hypothesis of no spin correlations is disfavoured with a significance of 1.8 standard deviations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Measurement of double-differential charged-current Drell-Yan cross-sections at high transverse masses in $pp$ collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

This paper presents a first measurement of the cross-section for the charged-current Drell-Yan process pp → W ± → ℓ ± ν above the resonance region, where ℓ is an electron or muon. The measurement is performed for transverse masses, $m$$^{W}_{T}$, between 200 GeV and 5000 GeV, using a sample of 140 fb −1 of pp collision data at a centre-of-mass energy of = 13 TeV collected by the ATLAS detector at the LHC during 2015–2018. The data are presented single differentially in transverse mass and double differentially in transverse mass and absolute lepton pseudorapidity. A test of lepton flavour universality shows no significant deviations from the Standard Model. The electron and muon channel measurements are combined to achieve a total experimental precision of 3% at low $m$$^{W}_{T}$. The single- and double differential W-boson charge asymmetries are evaluated from the measurements. A comparison to next-to-next-to-leading-order perturbative QCD predictions using several recent parton distribution functions and including next-to-leading-order electroweak effects indicates the potential of the data to constrain parton distribution functions. The data are also used to constrain four fermion operators in the Standard Model Effective Field Theory formalism, in particular the lepton-quark operator Wilson coefficient $c$$^{(c)}_{ℓq}$.

Hadron-Hadron Scattering↗

DOE OSTI2025

Measurements of inclusive and differential Higgs boson production cross sections at $\sqrt{\text{s}} = 13.6$ TeV in the H → γγ decay channel

Inclusive and differential cross sections for Higgs boson production in proton-proton collisions at a centre-of-mass energy of 13.6 TeV are measured using data collected with the CMS detector at the LHC in 2022, corresponding to an integrated luminosity of 34.7 fb −1 . Events with the diphoton final state are selected, and the measured inclusive fiducial cross section is ${\sigma }_{\text{fid}}={74}\pm {11}{\left({\text{stat}}\right)}_{-4}^{+5}\left({\text{syst}}\right)$ fb, in agreement with the standard model prediction of 67.8 ± 3.8 fb. Differential cross sections are measured as functions of several observables: the Higgs boson transverse momentum and rapidity, the number of associated jets, and the transverse momentum of the leading jet in the event. Within the uncertainties, the differential cross sections agree with the standard model predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Measurements of inclusive and differential cross-sections of $t\overline{t}\gamma$ production in pp collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

Inclusive and differential cross-sections are measured at particle level for the associated production of a top quark pair and a photon ($t\overline{t}\gamma$). The analysis is performed using an integrated luminosity of 140 fb -1 of proton-proton collisions at a centre-of-mass energy of 13 TeV collected by the ATLAS detector. The measurements are performed in the single-lepton and dilepton top quark pair decay channels focusing on ($t\overline{t}\gamma$) topologies where the photon is radiated from an initial-state parton or one of the top quarks. The absolute and normalised differential cross-sections are measured for several variables characterising the photon, lepton and jet kinematics as well as the angular separation between those objects. The observables are found to be in good agreement with the Monte Carlo predictions. The photon transverse momentum differential distribution is used to set limits on effective field theory parameters related to the electroweak dipole moments of the top quark. The combined limits using the photon and the Z boson transverse momentum measured in $t\overline{t}$ production in associations with a Z boson are also set.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Measurement of differential ZZ + jets production cross sections in pp collisions at $ \sqrt{s} $ = 13 TeV

Diboson production in association with jets is studied in the fully leptonic final states, pp → (Z/γ$^{*}$)(Z/γ$^{*}$) + jets → 2ℓ2ℓ′ + jets, (ℓ, ℓ′ = e or μ) in proton-proton collisions at a center-of-mass energy of 13 TeV. The data sample corresponds to an integrated luminosity of 138 fb$^{−1}$ collected with the CMS detector at the LHC. Differential distributions and normalized differential cross sections are measured as a function of jet multiplicity, transverse momentum p$_{T}$, pseudorapidity η, invariant mass and ∆η of the highest-p$_{T}$ and second-highest-p$_{T}$ jets, and as a function of invariant mass of the four-lepton system for events with various jet multiplicities. These differential cross sections are compared with theoretical predictions that mostly agree with the experimental data. However, in a few regions we observe discrepancies between the predicted and measured values. Further improvement of the predictions is required to describe the ZZ+jets production in the whole phase space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Spectrally accurate, reverse-mode differentiable bounce-averaging algorithm and its applications

We present a fast, spectrally (exponentially) accurate, automatically differentiable bounce-averaging algorithm that is used to simplify kinetic models. Using this algorithm, implemented in the DESC stellarator optimisation suite, we can perform efficient optimisation of many objectives to improve stellarator performance, such as the effective ripple 𝜖 eff metric for the neoclassical transport coefficient in the low collisionality regime and proxies for energetic particle confinement. For the first time, we optimise a finite-beta stellarator to directly reduce neoclassical ripple transport using reverse-mode differentiation. This ensures the computational cost of differentiation is independent of the number of controllable parameters.

fusion plasma↗

DOE OSTI2025

Deciphering metabolic differentiation during Bacillus subtilis sporulation

Abstract The bacteriumBacillus subtilisundergoes asymmetric cell division during sporulation, producing a mother cell and a smaller forespore connected by the SpoIIQ-SpoIIIA (or Q-A) channel. The two cells differentiate metabolically, and the forespore becomes dependent on the mother cell for essential building blocks. Here, we investigate the metabolic interactions between mother cell and forespore using genome-scale metabolic and expression models as well as experiments. Our results indicate that nucleotides are synthesized in the mother cell and transported in the form of nucleoside di- or tri-phosphates to the forespore via the Q-A channel. However, if the Q-A channel is inactivated later in sporulation, then glycolytic enzymes can form an ATP and NADH shuttle, providing the forespore with energy and reducing power. Our integrated in silico and in vivo approach sheds light into the intricate metabolic interactions underlying cell differentiation inB. subtilis, and provides a foundation for future studies of metabolic differentiation.

Science & Technology - Other Topics↗

DOE OSTI2025

Importance of hydrogen oxidation reaction current in quantifying hydrogen crossover in PEM water electrolyzers at high differential pressure

Understanding hydrogen permeation in proton exchange membrane water electrolyzers (PEMWEs) operating at high differential pressures (>25 bar) is critical towards developing effective gas recombination strategies that enable safe operation and high efficiency. Developing this understanding relies on accurate quantification of hydrogen crossover rates in water electrolyzers operating under such conditions. In this work, we show that PEMWEs operating at high differential pressures exhibit noticeable hydrogen oxidation reaction (HOR) currents. As the HOR consumes part of the permeated hydrogen at the anode, neglecting HOR currents leads to severe underestimation of the hydrogen crossover rate. We implemented a new method combining hydrogen oxidation current with online gas chromatography measurements to accurately quantify hydrogen crossover rates as a function of operating current density in PEMWEs operating at high differential pressures (10–30 bar g ).

25 ENERGY STORAGE↗

DOE OSTI2026

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

GEAR-MC and Differential-Operator Methods Applied to Electron-Photon Transport in the Integrated TIGER Series

The sensitivity analysis algorithms that have been developed by the radiation transport community in multiple neutron transport codes, such as MCNP and SCALE, are extensively used by fields such as the nuclear criticality community. However, these techniques have seldom been considered for electron transport applications. In the past, the differential-operator method with the single scatter capability has been implemented in Sandia National Laboratories’ Integrated TIGER Series (ITS) coupled electron-photon transport code. This work is meant to extend the available sensitivity estimation techniques in ITS by implementing an adjoint-based sensitivity method, GEAR-MC, to strengthen its sensitivity analysis capabilities. To ensure the accuracy of this method being extended to coupled electron-photon transport, it is compared against the central-difference and differential-operator methodologies to estimate sensitivity coefficients for an experiment performed by McLaughlin and Hussman. Energy deposition sensitivities were calculated using all three methods, and the comparison between them has provided confidence in the accuracy of the newly implemented method. Unlike the current implementation of the differential-operator method in ITS, the GEAR-MC method was implemented with the option to calculate the energy-dependent energy deposition sensitivities, which are the sensitivity coefficients for energy deposition tallies to energy-dependent cross sections. The energy-dependent cross sections could be the cross sections for the material, elements in the material, or reactions of interest for the element. Further, these sensitivities were compared to the energy-integrated sensitivity coefficients and exhibited a maximum percentage difference of 2.15%.

42 ENGINEERING↗

DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗

DOE OSTI2026

SODAs: sparse optimization for the discovery of differential and algebraic equations

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by time-scale separation, conservation laws and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods for DAE systems with unknown constraints and time scales. We introduce sparse optimization for differential-algebraic systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems. It has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves since SODAs is singular numerical stability when handling high correlations between library terms, caused by near-perfect algebraic relationships, by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.

DAE↗