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At least 145 records · Page 8

Mechanistic within-host mathematical model of inhalational anthrax

We present a mathematical model of the dynamics of Bacillus anthracis bacteria within the lymph nodes and blood of a host, following inhalation of an initial dose of spores. We also incorporate the dynamics of protective antigen, which is the binding component of the anthrax toxin produced by the bacteria. The model offers a mechanistic description of the early infection dynamics of inhalational anthrax, while its stochastic nature allows us to study the probabilities of different outcomes (for example, how likely it is that the infection will be cleared for a given inhaled dose of spores) in order to explain dose-response data for inhalational anthrax. The model is calibrated via a Bayesian approach, using in vivo data from New Zealand white rabbit and guinea pig infection studies, enabling within-host parameters to be estimated. We also leverage incubation-period data from the Sverdlovsk 1979 anthrax outbreak to show that the model can accurately describe human time-to-symptoms data under reasonable parameter regimes. Finally, we derive a simple approximate formula for the probability of symptom onset before time t, assuming that the number of inhaled spores has a Poisson distribution.

59 BASIC BIOLOGICAL SCIENCES↗

Vidyut3d: A Gpu Accelerated Fluid Solver for Non-Equilibrium Plasmas on Adaptive Grids

We present the numerical methods, programming methodology, verification, and performance assessment of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit (CPU+GPU) architectures, in this work. Our plasma fluid model solves the coupled conservation equations for species transport, electrostatic Poisson and electron temperature on adaptive Cartesian grids. Our solver is written using performance portable adaptive-grid/particle management library, AMReX, and is portable over widely available vendor specific GPU architectures. We present verification of our solver using method of manufactured solutions that indicate formal second order accuracy with central diffusion and fifth-order weighted-essentially-non-oscillatory (WENO) advection scheme. We also verify our solver with published literature on capacitive discharges and atmospheric pressure streamer propagation. We demonstrate the use of our solver on two 3D simulation cases: an atmospheric streamer propagation in Ar-H2 mixtures and a low pressure twin electrode radio frequency reactor. Our performance studies on three different CPU+GPU architectures indicate approximately 150-400X speed-up using AMD and NVIDIA GPUs per time step compared to a single CPU core for a 4 million cell simulation with 15 species.

Sitaraman, Hariswaran↗

Achieving Higher Order Accuracy in Space in Hydrodynamic Simulations of Self-Gravitating Gas

Modern astrophysical simulation codes employ a variety of numerical algorithms capable of achieving higher-order accuracy in both space and time. Albeit they succeed in achieving an effective higher spatial resolution and in suppressing the numerical damping of waves, to our knowledge, all current astrophysical simulations invoking self-gravity are limited to second-order accuracy in space. If we can devise an algorithm to evaluate self-gravity with a higher-order spatial accuracy, we can better the evaluation of the gravitational acceleration and gravitational energy release which dictate the evolution of many astrophysical systems. Herein, we present a numerical algorithm for self-gravitating hydrodynamics capable of achieving fourth order accuracy for a given density distribution on a Cartesian uniform grid. First, we derive the cell-averaged gravitational potential at fourth-order accuracy from the cell-averaged density by solving the Poisson equation. Next, we obtain the cell average of the product of the density and gravitational acceleration, which differs from the cell-averaged density multiplied by the cell-averaged gravitational acceleration. We then show the verification of the algorithm by applying it to critical test problems: (1) maintaining equilibria of self-gravitating slabs, even upon advection, (2) evolving a polytropic sphere with a massive power-law envelope, and (3) conservation of specific entropy during the propagation of a sound wave.

79 ASTRONOMY AND ASTROPHYSICS↗

Understanding Twinning and Deformation in High Entropy Alloys

On the one hand, multi-principal element alloys (MPEAs) have created a paradigm shift in alloy design due to large compositional space, whereas on the other, they have presented enormous computational challenges for theory-based materials design, especially density functional theory (DFT), which is inherently computationally expensive even for traditional dilute alloys. In this project, we developed a machine learning framework, namely PREDICT ( PR edict properties from E xisting D atabase I n C omplex alloys T erritory), that opens a pathway to predict elastic constants in large compositional space with little computational expense. The framework only relies on the DFT database of binary alloys and predicts Voigt–Reuss–Hill Young’s modulus, shear modulus, bulk modulus, elastic constants, and Poisson’s ratio in MPEAs. We show that the key descriptors of elastic constants are the A–B bond length and cohesive energy. The framework can predict elastic constants in hypothetical compositions as long as the constituent elements are present in the database, thereby enabling property exploration in multi-compositional systems. We illustrate predictions in a FCC Ni-Cu-Au-Pd-Pt system.

36 MATERIALS SCIENCE↗

ASCR Workshop Position Paper: Challenges and Opportunities in High Energy Physics

High energy particle physics and cosmology concern themselves with estimating fundamental parameters of nature, such as the masses and interactions of fundamental particles like the Higgs boson and the rate of expansion of the universe. In doing so, they analyze exabyte-scale datasets, some of the largest in all of science, and face many challenges in subsequent data analysis. These challenges are shared between the two disciplines, but we focus on particle physics to highlight one specific domain. In particle physics, the standard method for estimating parameters involves performing Monte Carlo (MC) integration as a function of both parameters of interest and nuisance parameters using an expensive simulator, counting the number of observed collision events (i.i.d. samples) from an experiment in the corresponding integration domains, and forming a Poisson likelihood function. This likelihood function is then used in a Frequentist manner to construct a maximum likelihood point estimate (MLE) and confidence set for the parameters. To sufficiently populate the high-dimensional integration domains, simulators consume billions of CPU-hours annually and produce hundreds of petabytes of intermediate output data. Several techniques have been developed to: optimize definitions of the integration domains so as to be maximally sensitive to a particular subset of parameters, efficiently estimate the integrals, and build robust surrogate models by interpolating between integral evaluations at different parameter points. One can view this whole endeavor as classical Simulation-Based Inference (SBI).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Spectrally Stabilized Interface Capturing Formulation and Implementation in Nek5000/NekRS

This report documents the formulation of a novel level-set method for incompressible two-phase flows in the continuous Galerkin (CG) high order spectral element framework. The overall method hinges on a novel implementation of the spectral vanishing viscosity (SVV) operator for the stabilization of linear/non-linear hyperbolic problems. The multidimensional SVV convolution kernels, which in essence, have a similar effect as a high pass filter applied to the derivatives, are formulated by exploiting the tensor product form, analogous to the construction of the usual stiffness matrix system. The resulting kernels are directionally decoupled and ensure a linear, symmetric positive definite, elliptic matrix operator. The SVV formulation is demonstrated to provide a robust stabilizing mechanism through challenging linear and non-linear hyperbolic problems, including problems pertinent to the level-set formulation. The two-phase framework conceptualized herein is based on the conservative level-set (CLS) method which represents the interface between the fluids by the 0.5 iso-contour of the smoothed Heaviside function. The CLS method is augmented with a preconditioning procedure for interface normals using the signed distance function which precludes the manifestation of spurious oscillations in the vicinty of the interface. Further, the existing mixed explicit-implicit approach for the solution of Navier-Stokes equations in Nek5000, as described in Tomboulides et al, is augmented with a pressure coefficient splitting approach for the Poisson equation, which greatly accelerated the convergence of pressure solver for two-phase systems with large density ratio. The robustness and accuracy of the overall two-phase method is demonstrated through canonical challenging problems involving high density and viscosity ratios, with and without surface tension. The two-phase formulation is wholly implemented in Nek5000 and the SVV stabilization method is implemented in NekRS, which is the essential precursor to the two-phase framework, undergoing active development.

97 MATHEMATICS AND COMPUTING↗

Near-Efficient and Non-Asymptotic Multiway Inference

We establish non-asymptotic efficiency guarantees for tensor decomposition–based inference in count data models. Under a Poisson framework, we consider two related goals: (i) parametric inference , the estimation of the full distributional parameter tensor, and (ii) multiway analysis , the recovery of its canonical polyadic (CP) decomposition factors. Our main result shows that in the rank-one setting, a rank-constrained maximum-likelihood estimator achieves multiway analysis with variance matching the Cramér–Rao Lower Bound (CRLB) up to absolute constants and logarithmic factors. This provides a general framework for studying “near-efficient” multiway estimators in finite-sample settings. For higher ranks, we illustrate that our multiway estimator may not attain the CRLB; nevertheless, CP-based parametric inference remains nearly minimax optimal, with error bounds that improve on prior work by offering more favorable dependence on the CP rank. Numerical experiments corroborate near-efficiency in the rank-one case and highlight the efficiency gap in higher-rank scenarios.

97 MATHEMATICS AND COMPUTING↗

PISCES two-detector covariance matrix fit for the NOvA Experiment

NOvA is a long-baseline neutrino oscillation experiment with two functionally identical detectors: a Near Detector (ND) at Fermilab, placed 1 km from the neutrino source, and a Far Detector (FD) located 810 km away from the ND in Minnesota. NOvA's primary physics goals are the precise measurements of neutrino oscillation parameters $\theta_{23}$ and $\Delta m^2_{32}$ , determine the neutrino mass ordering, and constrain the value of $\delta_{CP}$, via the study of muon neutrino to electron neutrino oscillation. In the standard NOvA three-flavor analysis, oscillation parameters are extracted using an extrapolation technique in which the ND data constrain the FD prediction through a ratio method. While this allows for systematic uncertainties sharing the same effects in both detectors to cancel, it remains an FD-only fit and does not fully leverage the constraining power of the high-statistics ND. This analysis proposes a simultaneous ND+FD fit using the PISCES method. PISCES (Parameter Inference with Systematic Covariance and Exact Statistics) is a framework designed to support complex configurations such as a joint ND+FD fit. This allows PISCES to take full advantage of the ND data to directly constrain systematic uncertainties across all samples. In PISCES, systematic uncertainties are encoded in a fractional covariance matrix, and statistical uncertainties are handled with a Poisson likelihood, making the approach well suited for low-statistics samples. For interpretability, we further use a Newton–Raphson + PCA method to recover per-systematic pulls from the covariance formulation. This poster presents the full PISCES joint ND+FD fit for the NOvA three-flavor analysis, describes its implementation and evaluates its performance through extensive robustness tests and fake data studies. It also provides a comparison between the PISCES joint ND+FD results and the standard NOvA extrapolation method.

Rajaoalisoa, Miriama [Cincinnati U.] (ORCID:000000↗

Non-conformal interface-cohesive modeling with the shifted boundary method

The accurate simulation of boundary- and interface-dominated problems on complex geometries remains challenging when boundary- or interface-fitted meshes are difficult to generate, particularly for curved boundaries, polycrystalline microstructures, and dense interface networks. The Shifted Boundary Method (SBM) alleviates this meshing burden by shifting the enforcement of boundary conditions from the true boundary to a nearby surrogate boundary and recovering the effect of the true boundary through geometric correction terms, thereby enabling standard finite element spaces on non-boundary-fitted meshes. In this report, we develop a general shiftedboundary and shifted-interface framework within the open-source MOOSE framework. We first present a general SBM implementation for complex geometries on non-boundary-fitted meshes. We then adopt the Shifted Interface Method (SIM) for internal interfaces and develop a unified shifted-interface treatment in which the interface law is enforced on a surrogate interface and the effect of the true interface is recovered through shifted jumps, fluxes, and tractions. This perspective brings scalar thermal-contact and vector-valued cohesive-zone mechanics into a single framework, the latter realized as the Shifted Cohesive Zone Method (SCZM) and coupled with history-dependent constitutive models from NEML2. We further extend the MOOSE mesh infrastructure to support cohesive-zone calculations on distributed meshes. The framework is verified and demonstrated through three progressive studies: Poisson’s equation on a smoothed starshaped domain, a manufactured thermal-contact problem on a non-interface-fitted mesh, and a two-dimensional polycrystalline representative volume element combining crystal plasticity with cohesive grain-boundary interfaces. Across these studies, the shifted formulations reproduce boundary- and interface-fitted reference solutions with high fidelity, indicating that the proposed framework provides an accurate and efficient route to boundary- and interface-dominated simulations on arbitrary geometries without requiring fitted meshes.

Yang, Cheng-Hau↗

Assessment of Weld Microstructure Through Sound Velocity Measurements for Power Plant Applications

Here, this research study employed an immersion-based micro-resolution ultrasonic velocity measurement technique (MUVT) to evaluate Grade 91 (9Cr-1Mo-V) steel welds. This process utilized a 20 MHz focused ultrasonic beam with a spot size of 250 µm, a 6 µm laser vibrometer spot size for detection, and an automated 3-axis raster scanner to accurately collect ultrasonic velocity data from two Grade 91 steel welds fabricated using cold metal transfer (CMT) and flux-cored arc welding (FCAW) processes. By analyzing the MUVT data, the Poisson’s ratio (υ) and modulus of elasticity (E), which are important mechanical properties for weldments, were calculated. The correlation between mechanical properties and ultrasonic velocity was examined. The results indicated that longitudinal ultrasonic velocity could effectively identify base metal, heat-affected zone (HAZ), and weld metal areas, showing a strong correlation with hardness. In particular, the distinctive V-shaped dip in velocity and hardness data across the HAZ areas of both samples highlighted changes in the microstructure of creep strength–enhanced ferritic steel welds. Importantly, the immersion-based MUVT demonstrated high accuracy in small sections of the weld, surpassing the conventional contact ultrasonic testing method in spatial resolution detection.

arc welding↗

Mechanical Properties of a Solvated Biomolecule: RGD (1FUV) Peptide

The mechanical properties of proteins/peptides play an essential role in their functionalities and implications, as well as their structure and dynamic properties. Understanding mechanical properties is pivotal to our knowledge of protein folding and the molecular basis of diverse cellular processes. Herein, we present a computational approach using ab initio quantum mechanical calculations to determine the mechanical properties—such as bulk modulus, shear modulus, Young’s modulus, and Poisson’s ratio—of a solvated Arg-Gly-Asp (RGD) peptide model. Since this peptide serves as the RGD-directed integrin recognition site and may participate in cellular adhesion, it is considered a promising small peptide for medicinal applications. This successful approach paves the way for investigating larger and more complex biomolecules.

Biochemistry & Molecular Biology↗

Mesoscale Linear Elastic Modeling and Homogenization of Marine Energy Composites

The design of fiber-reinforced composite (FRC)-based components for marine energy applications necessitates a fundamental understanding of material properties and the resulting geometry to predict long-term performance. In this work, we present a modeling workflow to predict linear elastic and diffusive bulk properties at the mesoscale for an idealized geometry based on knowledge of fiber and resin properties. A parametric study was performed to identify the key model input parameters that influence bulk properties. Furthermore, we demonstrate how bulk properties can be leveraged in high-fidelity image-based simulations, where imperfections in tow geometry and voids captured during X-ray computed tomography imaging are explicitly represented within the simulation. Bulk properties of interest include moduli, Poisson’s ratios, hygroscopic swelling, diffusivity, and moisture uptake, which are key parameters for characterizing FRC performance within marine environments. Modeling predictions agreed well with experimental data, except for estimating swelling coefficients, likely due to crack accumulation as a function of moisture uptake. The mesoscale modeling workflow ultimately highlights a versatile framework for understanding the influence of material and geometric properties, which can be leveraged to rapidly assess new FRC-based components.

computational mechanics↗

Sound Velocities in Vanadium Reveal Complex Elastic Behavior at High Pressures

Compressional (VP) and shear (VS) wave velocities of polycrystalline vanadium were measured simultaneously up to 11.5 GPa at room temperature using ultrasonic interferometry in a multi-anvil press. Complex softening behavior in VS and resulting shear moduli are discovered, possibly revealing a precursor to the reported phase transition within 30–60 GPa. The current data enables a comprehensive assessment of the elastic and mechanical properties of vanadium at high pressures, including bulk and shear moduli, Young’s modulus, Poisson’s ratio, and Pugh’s ratio. Through fitting to the 3rd-order finite strain equations, the elastic moduli and their pressure derivatives were determined to be K S0 = 151 (2) GPa, G 0 = 46.9 (8) GPa, K$^{’}_{S0}$ = 3.47 (5), and G$^{’}_{0}$ = 0.62 (1). These experimental results allow us to compare with and benchmark the existing Steinberg–Guinan models for extrapolations to extreme pressure and temperature conditions.

36 MATERIALS SCIENCE↗

How Do Uncertainties in Galaxy Formation Physics Impact Field-level Galaxy Bias?

Our ability to extract cosmological information from galaxy surveys is limited by uncertainties in the galaxy–dark matter halo relationship for a given galaxy population, which are governed by the intricacies of galaxy formation. To quantify these uncertainties, we examine quenched and star-forming galaxies using two distinct approaches to modeling galaxy formation: U$\scriptsize{NIVERSE}$M$\scriptsize{ACHINE}$, an empirical semianalytic model, and the I$\scriptsize{llustris}$TNG hydrodynamical simulation. We apply a second-order hybrid N-body perturbative bias expansion to each galaxy sample, enabling direct comparison of modeling approaches and revealing how uncertainties in the galaxy–halo connection affect bias parameters and non-Poisson noise across number densities and redshifts. Notably, we find that quenched and star-forming galaxies occupy distinct parts of the bias parameter space, and that the scatter induced from these different galaxy formation models is small when conditioned on similar selections of galaxies. We also detect the signature of assembly bias in our samples; this leads to small but significant deviations from analytic bias predictions, while assembly bias-removed samples match these predictions well. This work indicates that galaxy samples from a spectrum of reasonable, physically motivated models for galaxy formation give a relatively small range of field-level galaxy bias parameters. We estimate a set of priors from these models that should be useful in extracting cosmological constraints from luminous red galaxy– and emission line galaxy–like samples. Looking forward, careful estimates of the range of impacts of galaxy formation, for a given sample and cosmological analysis, will be an essential ingredient for extracting the most precise cosmological information from current and future large galaxy surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Surrogate Modeling of Landau Damping with Deep Operator Networks

Kinetic simulations excel at capturing microscale plasma physics phenomena with high accuracy, but their computational demands make them impractical for modeling large-scale space and astrophysical systems. In this context, we build a surrogate model, using Deep Operator Networks (DeepONets), based upon the Vlasov–Poisson simulation data to model the dynamical evolution of plasmas, focusing on the Landau damping process—a fundamental kinetic phenomenon in space and astrophysical plasmas. The trained DeepONets are able to capture the evolution of electric field energy in both linear and nonlinear regimes under various conditions. Extensive validation highlights DeepONets’ robust performance in reproducing complex plasma behaviors with high accuracy, paving the way for large-scale modeling of space and astrophysical plasmas.

plasma astrophysics↗

Forecasting the Cross Correlation of Terahertz Intensity Mapper [C ii] Line Intensity Maps with Euclid Galaxies

We forecast that the Terahertz Intensity Mapper (TIM) cross-correlated with Euclid’s Deep Field Fornax (EDF-F), TIM × EDF-F, will detect the [C ii]-galaxy cross-power spectrum at a median redshift of 1.1 with ≳7σ confidence. The Poisson component of the cross-power spectrum at 0.1 ≤ k ≤ 10 h Mpc$^{−1}$ (i.e., cross-shot noise) will be detected at ≳3σ in four bins spanning 0.5 < z < 1.7. This measurement will constrain the mean [C ii] specific intensity over half of cosmic history and assess the degree to which Euclid-selected galaxies account for the [C ii] intensity observed by TIM. We find that TIM can detect the cross-power spectrum across a wide range of [C ii] intensity models.

Bracks, Justin S. [UCLA; Caltech; UPenn, Philadelp↗

Toward Higher-order Accuracy in Self-gravitating Hydrodynamics

High-order algorithms have emerged in numerical astrophysics as a promising avenue to reduce truncation error (proportional to a power of the linear resolution Δ x ) with only a moderate increase to computational expense. Significant effort has been placed in the development of finite-volume algorithms for (magneto)hydrodynamics; however, state-of-the-art astrophysical simulations tightly couple a plenitude of physics, additionally including gravity, photon transport, cosmic-ray transport, chemistry, and/or diffusion, to name a few. Algorithms frequently operator-split this additional physics (often a first-order error in time) and/or adopt a model wherein their evaluation is limited to second-order accuracy in space. In this work, we present a fourth-order-accurate finite-volume scheme for self-gravitating hydrodynamics on a uniform Cartesian grid. The method supplies source terms for the gravitational acceleration ( ρ g ) and gravitational energy release ( ρ v · g ) associated with fourth-order-accurate solutions to the Poisson equation. Our scheme (1) guarantees the conservation of total linear momentum while (2) decreasing (in proportion to Δ x 4 ) the effects of spurious heating and/or cooling associated with truncation error in the gravity. We demonstrate expected convergence rates for the algorithm by measuring errors in test problems evolving self-gravity modified linear waves and 3D polytropic equilibria. We test robustness of the algorithm by integrating an induced “inside-out” adiabatic collapse. We also discuss a method to smoothly downgrade the solution to second-order spatial accuracy to avoid spurious overshoots near steep density and/or pressure gradients.

79 ASTRONOMY AND ASTROPHYSICS↗

pCubit

SAND2025-01894O pCubit is a software tool that can easily place particles or pores into a given geometry using desired statistics and the Poisson point process. It reduces the need for users to manually create complex geometry creation and placement. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Buche, Michael↗