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At least 145 records · Page 8

Efficient Mixed-Precision Matrix Factorization of the Inverse Overlap Matrix in Electronic Structure Calculations with AI-Hardware and GPUs

In recent years, a new kind of accelerated hardware has gained popularity in the artificial intelligence (AI) community which enables extremely high-performance tensor contractions in reduced precision for deep neural network calculations. In this article, we exploit Nvidia Tensor cores, a prototypical example of such AI-hardware, to develop a mixed precision approach for computing a dense matrix factorization of the inverse overlap matrix in electronic structure theory, S –1 . This factorization of S –1 , written as ZZT = S –1 , is used to transform the general matrix eigenvalue problem into a standard matrix eigenvalue problem. Here we present a mixed precision iterative refinement algorithm where Z is given recursively using matrix–matrix multiplications and can be computed with high performance on Tensor cores. To understand the performance and accuracy of Tensor cores, comparisons are made to GPU-only implementations in single and double precision. Additionally, we propose a nonparametric stopping criteria which is robust in the face of lower precision floating point operations. The algorithm is particularly useful when we have a good initial guess to Z, for example, from previous time steps in quantum-mechanical molecular dynamics simulations or from a previous iteration in a geometry optimization.

36 MATERIALS SCIENCE

Laser-Induced Enhancement of Acoustic Mode Quality Factor Revealed by Correlated Single-Particle Optical and Electron Microscopy

Acoustic modes in plasmonic nanostructures provide fundamental insights into their optomechanical behavior at the nanoscale, enabling emerging applications in plasmon-enhanced optomechanics, ultrasensitive sensing, and nanoscale energy transduction. Here we explore the modulation of acoustic phonon dynamics in lithographically fabricated gold nanodisks via laser-induced photothermal annealing. Using a correlated approach that utilizes both single-particle transient extinction spectroscopy and advanced electron microscopy, we directly link nanoscale structural transformations to changes in mechanical properties as probed through the coherence of the excited acoustic modes. Specifically, ultrafast pump–probe microscopy reveals an enhancement in the acoustic mode quality factor of annealed gold nanodisks, indicative of reduced damping and improved vibrational coherence. Structural characterization via scanning electron microscopy and electron backscatter diffraction confirms that photoinduced annealing results in smoother surface morphology and overall enhanced crystallinity. The improved crystalline order reduces defect and crystal boundary scattering, which we suggest as the reason underlying the lower quality factor before annealing. Furthermore, these findings demonstrate that targeted structural engineering at the nanoscale offers a powerful strategy for optimizing the optomechanical performance of plasmonic nanostructures, with broad implications for the design of next-generation nanophotonic and optomechanical systems.

Annealing (metallurgy)

Environmental Factors Associated With Fall Phytoplankton Blooms in the Northern Bering and Chukchi Seas

This study investigates environmental drivers of fall phytoplankton blooms in the Arctic, focusing on the northern Bering and Chukchi seas. Random Forests models were used to analyze covariates of fall phytoplankton blooms from 2013 to 2018, incorporating shipboard, remote sensing, and modeled environmental properties. Four regional models and one comprehensive all-station model considered fall as well as midsummer conditions. Midsummer properties included suspended particulate matter, chlorophyll-a, and the proportion of degraded pheophytin to chlorophyll-a used as a proxy for bloom stage. Open water duration was one of the highest ranked factors in predicting fall blooms. Open water duration also influences the stage of midsummer (July) blooms as indicated by pheophytin proportions, which in turn were the highest-ranked factor for predicting fall bloom events in the Chirikov Basin (northern Bering Sea between St. Lawrence Island and the Bering Strait) and the Chukchi Sea. Wind direction, specifically easterly winds, was an important predictor in the northern Bering Sea. Maximum wind speed ranked highly at stations located within the nutrient-poor Alaska Coastal Current in the Chukchi Sea. However, stormy days, average and maximum wind speeds generally ranked low in importance as a predictor of fall bloom events. Other parameters, including photosynthetic active radiation, modeled nutrient concentrations, mixed layer depth, and time since sea ice breakup date showed strong but regionally varying relationships with fall blooms. Altogether, results from these Random Forests models suggest that high wind events and storms in the absence of sea ice provide an incomplete narrative for initiating fall bloom events.

Gaffey, C. B. [Clark University, Worcester, MA (Un

Spatial variability in Arctic–boreal fire regimes influenced by environmental and human factors

Abstract Wildfire activity in Arctic and boreal regions is rapidly increasing, with severe consequences for climate and human health. Regional long-term variations in fire frequency and intensity characterize fire regimes. The spatial variability in Arctic–boreal fire regimes and their environmental and anthropogenic drivers, however, remain poorly understood. Here we present a fire tracking system to map the sub-daily evolution of all circumpolar Arctic–boreal fires between 2012 and 2023 using 375 m Visible Infrared Imaging Radiometer Suite active fire detections and the resulting dataset of the ignition time, location, size, duration, spread and intensity of individual fires. We use this dataset to classify the Arctic–boreal biomes into seven distinct ‘pyroregions’ with unique climatic and geographic environments. We find that these pyroregions exhibit varying responses to environmental drivers, with boreal North America, eastern Siberia and northern tundra regions showing the highest sensitivity to climate and lightning density. In addition, anthropogenic factors play an important role in influencing fire number and size, interacting with other factors. Understanding the spatial variability of fire regimes and its interconnected drivers in the Arctic–boreal domain is important for improving future predictions of fire activity and identifying areas at risk for extreme events.

Geology

Evaluating the factors influencing accuracy, interpretability, and reproducibility in the use of machine learning classifiers in biology to enable standardization

The complexity and variability of biological data has promoted the increased use of machine learning methods to understand processes and predict outcomes. These same features complicate reliable, reproducible, interpretable, and responsible use of such methods, resulting in questionable relevance of the derived. outcomes. Here we systematically explore challenges associated with applying machine learning to predict and understand biological processes using a well- characterized in vitro experimental system. We evaluated factors that vary while applying machine learning classifers: (1) type of biochemical signature (transcripts vs. proteins), (2) data curation methods (pre- and post-processing), and (3) choice of machine learning classifier. Using accuracy, generalizability, interpretability, and reproducibility as metrics, we found that the above factors significantly mod- ulate outcomes even within a simple model system. Our results caution against the unregulated use of machine learning methods in the biological sciences, and strongly advocate the need for data standards and validation tool-kits for such studies.

59 BASIC BIOLOGICAL SCIENCES

Targeting transcription factors through an IMiD independent zinc finger domain

Abstract Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in three clusters, including an IMiD degron in zinc finger cluster one (ZFC1). Surprisingly, IMiDs do not inhibit the growth of SALL4-expressing cancer cells. To overcome this limit, we focused on a non-IMiD domain, SALL4 zinc finger cluster four (ZFC4). By combining ZFC4-DNA crystal structure and an in silico docking algorithm, in conjunction with cell viability assays, we screened several chemical libraries against a potentially druggable binding pocket, leading to the discovery of SH6, a compound that selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 treatment led to a significant 87% tumor growth inhibition of SALL4+ patient-derived xenografts and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors such as SALL4 in cancer.

Liu, Bee Hui

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING

SHP2 genetic variants in NSML-associated RASopathies disrupt the PZR–IRX transcription factor signaling axis

Noonan syndrome with multiple lentigines (NSML) is a rare autosomal dominant disorder caused by mutations inPTPN11(protein tyrosine phosphatase nonreceptor type 11) which encodes for the protein tyrosine phosphatase, SHP2. Approximately 85% of NSML patients develop hypertrophic cardiomyopathy (HCM). Here, we show that SHP2 is recruited to tyrosyl phosphorylated protein-zero related (PZR) in NSML mice. This recruitment is required for the Iroquois homeobox (IRX) transcription factors 3 and 5 to suppress BMP10 which negatively regulates postnatal cardiac growth. The protein expression of IRX3 and IRX5 was elevated in hypertrophied NSML hearts. IRX3 and IRX5 upregulation was rescued in NSML mice harboring a knock-in mutation of PZR that fails to become tyrosyl phosphorylated and recruit SHP2. NSML mice treated with low-dose dasatinib also exhibited normalized IRX3 and IRX5 expression levels. Consistent with this, BMP10 expression levels were reduced in NSML mice and rescued in PZR tyrosyl phosphorylation-deficient and low-dose dasatinib-treated NSML mice. A crystal structure of the tandem SH2 domains of SHP2 bound to tyrosyl phosphorylated PZR reveals that recruitment constrains the open SHP2 conformation to facilitate cellular-Src (c-Src) binding. Disruption of c-Src binding to SHP2 abolished IRX activation and failure to suppress BMP10. Hence, NSML-associated SHP2 genetic variants disrupt IRX transcription factor signaling to BMP10, implicating this axis as a target for RASopathy-associated HCM.

Science & Technology - Other Topics

High-throughput small-angle X-ray scattering reveals effective structure factor transitions linked to high-concentration antibody viscosity

High-concentration monoclonal antibody (mAb) formulations are often constrained by elevated viscosity, largely driven by protein–protein interactions, which complicates manufacturing and limits subcutaneous delivery. Early viscosity risk assessment is essential during discovery, yet traditional measurements require large sample volumes, and lack high-throughput capability. Here, we develop a high-throughput small-angle X-ray scattering (SAXS) protocol to detect mAb self-association at dilute concentrations, enabling early predictive insights into high-concentration viscosity. Synchrotron SAXS measurements were conducted for 21 mAbs formulated in a histidine buffer at pH 6.0. An initial subset of 10 mAbs analyzed across 1–150 mg/mL revealed that effective structure factor transitions in the low-q region, indicative of interparticle interactions, consistently emerged below 25 mg/mL. Subsequently, 11 additional mAbs were analyzed at 1–25 mg/mL using automated liquid handling and flow cells to enable high-throughput screening. High-viscosity mAbs exhibited detectable low-q upturns at concentrations ≤10 mg/mL, whereas low-viscosity mAbs showed downturns. A classification criterion based on effective structure factor transitions accurately classified all high- and low-viscosity mAbs at 150 mg/mL, offering a scalable, sample-efficient alternative to conventional methods. These results extend recent findings on the concentration-dependent sensitivity of SAXS to short-range attractions, demonstrating that they can emerge at lower concentrations than previously reported. This study presents the most comprehensive and diverse SAXS dataset for mAbs reported to date within a single formulation, providing a valuable resource for developing and validating coarse-grained models that can more accurately capture intermolecular interactions governing high-concentration solution behavior, thereby enabling rational antibody engineering and improved developability.

36 MATERIALS SCIENCE

Simultaneous control of the electron temperature and safety factor profiles in DIII-D using model-based optimal control techniques

Future tokamak power plants will likely operate using a single, well-defined plasma scenario, either in steady state or for very long pulse lengths. In order to enhance the robustness of the scenario, feedback controllers for a variety of plasma properties will be necessary to counteract any disturbances and ensure safe operation. However, only a limited set of actuators will be available to control many different quantities. Because of this, it is necessary to develop controllers that are able to regulate multiple plasma properties using a limited set of actuators. To this end, a controller has been developed for the simultaneous regulation of both the electron temperature and safety factor profiles in DIII-D. This algorithm uses a linear quadratic integral control synthesis approach based on a linearized model of the dynamics of the two profiles. Two neural network surrogate models, NubeamNet and MMMnet, are included to improve the fidelity of the model. Furthermore, the controller has been tested in simulation using COTSIM, and has demonstrated the ability to simultaneously track changes in both the electron temperature and safety factor targets, including changes in both the magnitude and the shape of the profiles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Hybrid model predictive control techniques for safety factor profile and stored energy regulation while incorporating NBI constraints

Abstract A novel hybrid Model Predictive Control (MPC) algorithm has been designed for simultaneous safety factor ( q ) profile and stored energy ( w ) control while incorporating the pulse-width-modulation constraints associated with the neutral beam injection (NBI) system. Regulation of the q -profile has been extensively shown to be a key factor for improved confinement as well as non-inductive sustainment of the plasma current. Simultaneous control of w is necessary to prevent the triggering of pressure-driven magnetohydrodynamic instabilities as the controller shapes the q profile. Conventional MPC schemes proposed for q -profile control have considered the NBI powers as continuous-time signals, ignoring the discrete-time nature of these actuators and leading in some cases to performance loss. The hybrid MPC scheme in this work has the capability of incorporating the discrete-time actuator dynamics as additional constraints. In nonlinear simulations, the proposed hybrid MPC scheme demonstrates improved q -profile+ w control performance for NSTX-U operating scenarios.

Physics

On infinite tensor networks, complementary recovery and type II factors

We initiate a study of local operator algebras at the boundary of infinite tensor networks, using the mathematical theory of inductive limits. In particular, we consider tensor networks in which each layer acts as a quantum code with complementary recovery, a property that features prominently in the bulk-to-boundary maps intrinsic to holographic quantum error-correcting codes. In this case, we decompose the limiting Hilbert space and the algebras of observables in a way that keeps track of the entanglement in the network. As a specific example, we describe this inductive limit for the holographic Harlow-Pastawski-Preskill-Yoshida code model and relate its algebraic and error-correction features. We find that the local algebras in this model are given by the hyperfinite type II$_\infty$ factor. Next, we discuss other networks that build upon this framework and comment on a connection between type II factors and stabilizer circuits. We conclude with a discussion of multiscale entanglement renormalization ansatz networks in which complementary recovery is broken. We argue that this breaking possibly permits a limiting type III von Neumann algebra, making them more suitable ansätze for approximating subregions of quantum field theories.

holographic dualities

ϕ → 3 π and ϕ π 0 transition form factor from Khuri-Treiman equations

This work studies the ϕ → 3 π decay and the ϕ → π 0 γ * transition form factor, utilizing the Khuri-Treiman formalism to account for analyticity, crossing, and unitarity. Using once-subtracted dispersion relations, we perform a simultaneous fit to the ϕ → 3 π Dalitz plot distribution and the ϕ → π 0 γ * measurements from the KLOE collaboration, finding good agreement with these experimental data. These results reaffirm the applicability of the Khuri-Treiman approach in the analysis of three-body decays. An interesting result is that the subtraction constant appearing in the equations is similar to a sum rule expectation, in contrast to analogous studies of ω → 3 π decays and ω → π 0 γ * , which shows significant deviations. Our results also provide a reasonable description of the trend of the transition form factor data from in the e + e − → ϕ π 0 scattering region. These intriguing theoretical differences between the decays of ϕ and ω could encourage further experimental measurements to assess the discrepancies and refine the theoretical predictions.

Lorenzo, A. G. [Instituto de Física Corpuscular; U

Rosenbluth-like separation of the $J/ψ$ near-threshold photoproduction: An access to the gluon gravitational form factors at high t

Here, we perform analysis of the near-threshold $J/\psi $ photoproduction data off the proton based on two theoretical approaches, GPD \cite{Guo3} and holographic \cite{Zahed2}, that represent the differential cross sections as powers of the skewness parameter with coefficients that depend only on the momentum transfer $t$. This allows to separate kinematically the corresponding coefficient functions, in much the same way as this is done for the electric and magnetic form factors using the Rosenbluth separation. We examine the independence of the extracted functions with the photon beam energy. These functions, under additional assumptions, are related to the proton's gluon Gravitational Form Factors (gGFFs). We compare the extracted functions with lattice calculations of the gGFFs in the region of $0.5<|t|<2$~GeV$^{2}$, where they overlap. Such analysis demonstrates the possibility of extracting some combinations of the gGFFs from the data at high $t$, complementary to the lattice calculations available in the low $t$ region. However, higher statistics are needed to more accurately check the predicted scaling behavior of the data and compare with the lattice results, thus testing and comparing the theoretical assumptions used in the GPD and holographic models.

Pentchev, Lubomir [Thomas Jefferson National Accel

Transverse-momentum-dependent pion structures from lattice QCD: Collins-Soper kernel, soft factor, TMDWF, and TMDPDF

We present the first lattice quantum chromodynamics (QCD) calculation of the pion valence-quark transverse-momentum-dependent parton distribution function (TMDPDF) within the framework of large-momentum effective theory (LaMET). Using correlators fixed in the Coulomb gauge (CG), we computed the quasi-TMD beam function for a pion with a mass of 300 MeV, a fine lattice spacing of 𝑎 =0.06 fm, and multiple large momenta up to 3 GeV. The intrinsic soft functions in the CG approach are extracted from form factors with large momentum transfer, and as a byproduct, we also obtain the corresponding Collins-Soper (CS) kernel. Our determinations of both the soft function and the CS kernel agree with perturbation theory at small transverse separations (𝑏 ⊥ ) between the quarks. At larger 𝑏 ⊥ , the CS kernel remains consistent with recent results obtained using both CG and gauge-invariant TMD correlators in the literature. By combining next-to-leading logarithmic factorization of the quasi-TMD beam function and the soft function, we obtain an 𝑥-dependent pion valence-quark TMDPDF for transverse separations 𝑏 ⊥ ≳1 fm. Interestingly, we find that the 𝑏 ⊥ dependence of the phenomenological parametrizations of TMDPDF for moderate values of 𝑥 are in reasonable agreement with our QCD determinations. In addition, we present results for the transverse-momentum-dependent wave function for a heavier pion with 670 MeV mass.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Fast and accurate calculation of EXAFS Debye-Waller factors in U⁢O2 using the dynamical matrix method

Theoretical modeling of bonding dynamics in metal oxides is required for predicting their thermal conductivity, catalytic activity, and mechanical properties. A primary challenge is the scarcity of experimental methods for validating theoretical predictions of these atomic-scale dynamics. This work presents a workflow that uses experimental extended x-ray absorption fine structure (EXAFS) data collected at high temperatures to validate an interatomic force field for uranium dioxide (UO2), an important model material. The validated force field is then used to drive computationally intensive molecular dynamics (MD) simulations and as input for the much faster dynamical matrix Debye-Waller (DMDW) method. The predicted values of the Debye-Waller factors from the DMDW calculations are in good agreement with those obtained from the MD simulations, with residual pair-specific differences attributable to quantum zero-point motion at low temperatures and lattice anharmonicity at high temperatures. We further show that theoretical EXAFS spectra constructed directly from DMDW-derived Debye-Waller factors reproduce the experimental data (at relatively low temperatures) with accuracy comparable to full MD-EXAFS, providing an additional validation of the choice of the potential. This study establishes a validated, rapid computational pathway for modeling bond dynamics, naturally incorporating quantum nuclear\\\\r\\\\nstatistics absent in classical simulations, which are essential for the mechanistic understanding of complex oxide materials.

58 GEOSCIENCES

Electromagnetic and two-photon transition form factors of the pseudoscalar mesons: An algebraic model computation

We compute electromagnetic and two-photon transition form factors of ground-state pseudoscalar mesons: π , K , η c , η b . To this end, we employ an algebraic model based upon the coupled formalism of Schwinger-Dyson and Bethe-Salpeter equations. Within this approach, the dressed quark propagator and the relevant Bethe-Salpeter amplitude encode the internal structure of the corresponding meson. Electromagnetic properties of the meson are probed via the quark-photon interaction. The algebraic model employed by us unifies the treatment of all ground-state pseudoscalar mesons. Its parameters are carefully fitted performing a global analysis of existing experimental data including the knowledge of the charge radii of the mesons studied. We then compute and predict electromagnetic and two-photon transition form factors for a wide range of probing photon momentum-squared which is of direct relevance to the experimental observations carried out thus far or planned at different hadron physics facilities such as the Thomas Jefferson National Accelerator Facility (JLab) and the forthcoming Electron-Ion Collider. We also present comparisons with other theoretical models and approaches and lattice quantum chromodynamics. Published by the American Physical Society 2024

Higuera-Angulo, I. M. (ORCID:0000000256008875)

Gravitational form factors and mechanical properties of quarks in protons: A basis light-front quantization approach

We compute the gravitational form factors (GFFs) and study their applications for the description of the mechanical properties such as the pressure, shear force distributions, and the mechanical radius of the proton from its light-front wave functions (LFWFs) based on basis light-front quantization (BLFQ). The LFWFs of the proton are given by the lowest eigenvector of a light-front effective Hamiltonian that incorporates a three-dimensional confining potential and a one-gluon exchange interaction with fixed coupling between the constituent quarks solved in the valence Fock sector. We find acceptable agreement between our BLFQ computations and the lattice QCD for the GFFs. Our D -term form factor also agrees well with the extracted data from the deeply virtual Compton scattering experiments at Jefferson Lab, and the results of different phenomenological models. The distributions of pressures and shear forces are similar to those from different models. Published by the American Physical Society 2024

Astronomy & Astrophysics