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DOE OSTI2025

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

DOE OSTI2025

Evaluation of Flow Routing on the Unstructured Voronoi Meshes in Earth System Modeling

Flow routing is a fundamental process of Earth System Models' (ESMs) river component. Traditional flow routing models rely on Cartesian rectangular meshes, which exhibit limitations, particularly when coupled with unstructured mesh-based ocean components. They also lack the support for regionally refined models. While previous studies have highlighted the potential benefits of unstructured meshes for flow routing, their widespread application and comprehensive evaluation within ESMs remain limited. This study extends the river component of the Energy Exascale Earth System Model to unstructured Voronoi meshes. We evaluated the model's performance in simulating river discharge and water depth across three watersheds spanning the Arctic, temperate, and tropical regions. The results show that while providing several benefits, unstructured mesh-based flow routing can achieve comparable performance to structured mesh-based routing, and their difference is often less than 10%. Although the unstructured mesh-based method could address several existing limitations, this research also shows that additional improvements in the numerical method are needed to fully exploit the advantages of unstructured mesh for hydrologic and ESMs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

An Optimized Parameterization of Sub‐Grid Scale Advection for Convection Permitting Models

Convection‐permitting models (CPMs) explicitly resolve deep convection yet under‐resolve the organized lateral exchanges among drafts and their environment that control entrainment/detrainment, precipitation efficiency, and mesoscale structure. In this work, we introduce the Optimized Advection Scheme (OAS), which introduces a small rotation of the Cartesian frame of reference for the horizontal winds relative to other variables used in advection that induces cross‐gradient transport to mimic under‐resolved convective mixing. The rotation angle is selected to minimize the Kullback–Leibler divergence between the simulated and satellite observed precipitation intensity distributions, yielding a physically consistent perturbation that is computationally inexpensive and portable. Optimized Advection Scheme is implemented in WRF and evaluated over Amazon (April 2014). It shifts precipitation–precipitable‐water joint distributions toward lighter rain, reduces overly intense rates, and improves mesoscale convective system (MCS) lifetime and propagation. Mechanistically, the added cross‐gradient transport promotes convective detrainment and environmental mixing, which cools and moistens the mid‐troposphere, weakens downward momentum transport, alleviates excessive downwelling shortwave biases, and warms the surface temperature. The optimized rotation angle yields comparable improvements at 4‐km and 1‐km grid spacing, demonstrating resolution‐independent benefits across the CPM gray zone. By targeting the dynamical root of under‐mixed convective circulations, rather than tuning model microphysics or closures, OAS delivers robust, scale‐aware improvements in precipitation statistics, cloud vertical structure, and characteristics of MCS (MCSs), offering a practical pathway to more reliable CPM simulations for weather and climate applications.

CPM↗

DOE OSTI2024

MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Nonlocal, diamagnetic electromagnetic effects in magnetically insulated transmission lines

We identify the time-dependent physics responsible for the critical reduction of current losses in magnetically insulated transmission lines (MITLs) due to uninsulated space charge-limited currents of electrons emitted by field stress. A drive current of sufficiently short pulse length introduces a strong enough time dependence that steady-state results alone become inadequate for the complete understanding of current losses. The time-dependent physics can be described as a nonlocal, diamagnetic electromagnetic response of space charge limited currents. As the pulse length is increased or equivalently, the MITL length reduced, these time-dependent effects diminish and current losses converge to those predicted by the well-known Child–Langmuir law in the external (vacuum) fields. We present a simple one-dimensional (1D) model that encapsulates the essence of this physics. We find excellent agreement with 2D particle-in-cell simulations for two MITL geometries, Cartesian parallel plate and azimuthally symmetric straight coaxial. Based on the 1D model, we explore various scaling dependencies of MITL losses with relevant parameters, e.g., peak current, pulse length, geometrical dimensions, etc. We propose an improved physics model of magnetic insulation in the form of a Hull curve, which could also help improve predictions of current losses by common circuit element codes, such as BERTHA. Finally, we describe how to calculate the temperature rise due to electron impact within the 1D model.

Computer simulation↗

DOE OSTI2025

PIAFS: A 2D nonlinear hydrodynamics code to model gaseous optics

The survivability of final optics is expected to be a major challenge for all future inertial fusion energy concepts. Due to their higher damage threshold, gaseous optics have been identified as a promising solution to this problem. Gaseous optics can be created through the photoabsorption of spatially modulated UV light, which induces various chemical processes that heat the gas. This heating leads to a pressure perturbation, which in turn launches a density perturbation that can imprint a refractive index modulation such as a grating. In this article, we introduce a parallel C/C++ code to simulate gaseous optics. PIAFS2D is a high-order conservative finite-difference code to solve the compressible Navier–Stokes equations along with the photochemical heating sources on Cartesian grids. The simulations are validated by the linear theory derived in a previous paper [Michel et al., Phys. Rev. Appl. 22, 024014 (2024)]. For larger perturbations, the behavior of the system—particularly the evolution of the generated acoustic wave—demonstrates strong nonlinearity. PIAFS2D allows the study of nonlinear behaviors and can be used for the design of high-efficiency gaseous optics elements in realistic experimental conditions.

Oudin, A. [Lawrence Livermore National Laboratory ↗

DOE OSTI2025

Extending the Mott–Gurney law to one-dimensional nonplanar diodes using point transformations

Recent studies have applied variational calculus, conformal mapping, and point transformations to generalize the one-dimensional (1D) space-charge limited current density (SCLCD) and electron emission mechanisms to nonplanar geometries; however, these assessments have focused on extending the Child–Langmuir law (CLL) for SCLCD in vacuum. Since the charge in the diode is independent of the coordinate system (i.e., covariant), we apply bijective point transformations to extend the Mott–Gurney law (MGL) for the SCLCD in a collisional or semiconductor gap to nonplanar 1D geometries. This yields a modified MGL that replaces the Cartesian gap distance with a canonical gap distance that may be written generally in terms of geometric scale factors that are known for multiple geometries. We tabulate results for common geometries. Such an approach may be applied to any current density, including non-space-charge limited gaps and SCLCD that may fall between the CLL and MGL.

Garner, Allen L. [Purdue Univ., West Lafayette, IN↗

DOE OSTI2026

SHarmonic: A fast and accurate implementation of spherical harmonics for electronic-structure calculations

The authors present SHarmonic, a new implementation of the spherical harmonics targeted for electronic-structure calculations. Their approach is to use explicit formulas for the harmonics written in terms of normalized Cartesian coordinates. This approach results in a code that is as precise as other implementations while being at least one order of magnitude more computationally efficient. The library can run on graphics processing units as well, achieving an additional order of magnitude in execution speed. This new implementation is simple to use and is provided under an open-source license; it can be readily used by other codes to avoid the error-prone and cumbersome implementation of the spherical harmonics.

Mathematics and Computing↗

DOE OSTI2025

Selection of Sampling and Surrogate Modeling Methods for State-Point Evaluations of an AGN-201M Reactor

Nuclear reactor digital twins (DTs) have been proposed for use as a safeguards technology to efficiently monitor new and novel reactors as they come online. A safeguards DT needs to be capable of detecting misuse and diversion as they occur, requiring physics models to be accurate and efficient. Mathematical surrogate models are capable of achieving the necessary efficiency and can largely maintain the accuracy of higher-order models given a quality training sample. The Multiphysics Object-Oriented Simulation Environment (MOOSE) code framework is specifically equipped to generate training samples and create surrogate models using full-order reactor physics models. Utilizing an operational AGN-201M reactor’s specifications, two surrogate types were trained on samples of variable size, and using Cartesian products, Latin hypercube sampling, and quadrature sampling, each was compared and evaluated on accuracy when compared to a full-order Monte Carlo model. Both surrogate types were able to capture reactivity changes within 0.05 $ of the Monte Carlo model while reducing the computation costs by eight orders of magnitude.

MOOSE↗

DOE OSTI2026

The Physics Imposed on a Streaming Operator by Spherical Transport Problems

The streaming operator, which generates a displacement of a particle on a straight line at a constant speed in transport theory, is derived algebraically from a spherical coordinate formulation of Newton’s second law. This derivation leads to an operator that has more partial derivatives than a Cartesian coordinate formulation of the operator. The additional partial derivatives, which are with respect to the normalized velocity variables of a particle, take into account the intrinsic curvature of a ball. Moreover, these partial derivatives mitigate ray effects, which arise when a finite number of normalized velocities (also called directions or discrete ordinates) are used to simulate a continuous S 2 sphere of directions, by rotating the polar axis of the S 2 sphere into the radial direction of the coordinate system. As a consequence of this rotation, the number of actual discrete ordinates is greatly amplified to an enormous number of effective discrete ordinates by a multiplier that is equal to the number of patches that partitions a spherical surface. In addition to the derivation of the streaming operator, we provide in closed form a solution to the system of characteristic equations that is equivalent to the streaming operator. Furthermore, the solution to the system of characteristic equations enables the construction of an integral operator that is the inverse to the streaming operator. Examples in which ray effects are immensely mitigated by spherical coordinates are presented.

integral operator↗

DOE OSTI2025

Modeling of convective cells, turbulence, and transport induced by a radio-frequency antenna in the tokamak boundary plasma

The edge turbulence model Hermes (Dudson et al 2017 Plasma Phys. Control. Fusion 59 05401) is set up for plasma boundary simulations with an radiofrequency (RF) antenna, using parameters characteristic of a tokamak edge. Cartesian slab geometry is used with thin plate limiters representing the ion cyclotron range of frequency (ICRF) antenna side-wall limiters. Ad-hoc DC electric biasing of the limiters, motivated by calculations with VSim (Nieter et al 2004 J. Comput. Phys. 196 448), represents an induced RF sheath rectified potential in the plasma turbulence model. Flux-driven turbulence simulations demonstrate a realistic distribution of plasma profiles and fluctuations. There is a clear effect of the antenna sheath voltage leading to formation of convective cells; bias-induced convective transport flattens the scrape-off layer density profile and fluctuations penetrate into the shadow region of the limiters as the bias voltage increases. Turbulent transport for impurity ions is inferred by following ion trajectories in the simulated plasma turbulence fields, showing Bohm-like effective diffusion rates. All in all, the model elucidates the key physical phenomena governing the effects of ICRF-induced antenna biasing on the tokamak boundary plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Algorithmic Advancements for High-Order Self-Gravitating Hydrodynamics

Self-gravity plays a key role in the formation and evolution of many astronomical objects. Though gravity is often dominant at large scales, other forces (e.g., gas pressure gradients, radiation, and/or magnetic fields) often compete. It is therefore essential for numerical simulations to evaluate their interplay accurately and robustly. Hanawa & Mullen derived a 4th-order accurate finite volume scheme to solve the equations of self-gravitating hydrodynamics on a uniform Cartesian grid. In this work, we supply improvements to the algorithm that (1) mitigate spurious gravitational circulation and (2) greatly simplify the evaluation of the high order corrections. The proposed algorithm provides the gravitational acceleration (ρg) and the gravitational energy release (ρv · g) as source terms for the hydrodynamic equations, all while preserving conservation of linear momentum. Spurious heating and/or cooling associated with truncation error in the numerical evaluation of the gravitational energy release decreases in proportion to the fourth power of the cell width. We demonstrate fourth order convergence on smooth problems (e.g., 3D inclined sound wave propagation and 3D equilibria). An application test tracks the spherical collapse of a polytrope by an imposed, sudden decrease of the central gas pressure; a bounce and second collapse (associated with a spherical accretion shock) are robustly captured by the high order algorithm.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Muon-induced fission as a probe of the underlying dynamics in nuclear fission

Muon-induced fission could be utilized as a probe to study the underlying dynamics of nuclear fission. Here, the probability of muon attachment to the light asymmetric fission fragment is sensitive to fission dynamics, such as the timescale and friction of the fission event, charge asymmetry, and possibly the shape of the fission fragments. We focus on muonic atoms that are formed with actinide nuclei. A relativistic approach is employed, solving the Dirac equation for the muonic wave function in the presence of a time-dependent electromagnetic field generated by the fissioning nucleus. Computations are carried out on a three-dimensional Cartesian lattice with no symmetry assumptions. The results show a strong dependence of the attachment probability on the fission charge asymmetry and a more modest dependence on friction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Particle-in-cell simulation of laser wakefield accelerators with oblique lasers in quasicylindrical geometry

In the studies of optical injections in laser or beam-driven wakefield accelerators, there is a frequent demand for using obliquely propagating assistant lasers in particle-in-cell simulations. In conventional methods, this is only possible in either two- or three-dimensional Cartesian geometries, which have the drawbacks of either lack of fidelity for the actual situation or requiring a huge amount of computational resources. In this work, we develop a new method that uses an expression-defined oblique laser field to simulate such situations in quasicylindrical geometry particle-in-cell simulations, having the advantages of both maintaining good fidelity and saving computational resources. As an example, we use this method in the scissor-cross ionization injection scheme for the optimization of the injected beam quality. This method is widely applicable to particle injections with assistant lasers in wakefield accelerators, as long as the assistant lasers only influence the injected particles during the injection process. Published by the American Physical Society 2025

Ma, Minghao (ORCID:0009000602317775)↗

DOE OSTI2024

Theoretical Assessment of the Transition Between Electron Emission Mechanisms for Nonplanar Diodes

Theoretically and computationally describing the operation of nanodiodes requires characterizing the transitions between multiple electron emission mechanisms for nanodiodes with complicated geometries. This motivates our development of techniques to determine when simplified theories for individual mechanisms suffice compared to more complete, but more computationally expensive, models. Leveraging recent theories that define a canonical gap distance to translate planar theory to nonplanar diodes, we derive the conditions for the transitions among thermal emission, field emission, and space-charge-limited current density (SCLCD) in vacuum and with collisions for non-Cartesian coordinate systems, including spherical, cylindrical, and prolate spheroidal coordinate systems. Particle-in-cell (PIC) simulations of the current density as a function of applied voltage for a tip-to-plate geometry in vacuum agreed qualitatively with the asymptotes for thermal emission at low voltage and SCLCD at higher voltage using the canonical gap distance. As a result, this demonstrates the utility of this approach for guiding system design and suggests future extensions to save simulation time for more realistic geometries that are more computationally expensive.

Conformal mapping↗

DOE OSTI2025

Analog In-Memory Computing for the Synthetic Aperture Radar Polar Format Algorithm

As the utility of synthetic aperture radar (SAR) systems increases in autonomous vehicles, satellites, and other power- and space-constrained edge applications, there is a growing need for processors that can form SAR images at low power. In recent years, analog in-memory compute (AIMC) has shown immense promise for accelerating neural networks and other matrix-vector multiplication (MVM) heavy workloads at the edge. Here, in this work, we examine how the polar format algorithm (PFA), a popular SAR image formation algorithm, can be mapped to these AIMC systems. The PFA maps readily onto analog MVMs because it primarily consists of two linear operations: interpolation of frequency-domain data to a Cartesian grid, followed by a 2-D Fourier transform. This work presents two approaches to map the interpolation operation onto MVMs in analog hardware: a chirp transform and a modified form of sinc interpolation. These mappings introduce algorithmic errors, and their effect on the quality of SAR image formation is examined, both quantitatively and qualitatively. In addition, the impact of errors introduced by the analog hardware is explored to determine which approach is optimal under varying assumptions about the underlying analog memory devices and circuits.

Analog computing↗

DOE OSTI2024

EchemAMR (electro-chemical microsctructure scale models with adaptive meshing) [SWR-23-111]

A 3D microstructure resolving electrochemical transport and interfacial chemistry solver. Electrode microstructure plays an important role in determining the performance of an electrochemical system, e.g. lithium ion battery. EchemAMR is a microstructure scale model that solves the governing equations for ion transport, electrical current continuity, interfacial chemistry and structural mechanics. Complex microstructure geometries from imaging can be directly imported into EchemAMR. A volume fraction based description of the geometry on Cartesian grid with an immersed interface formulation enables simplified meshing and large-scale simulations with millions of degrees of freedom. EchemAMR has been tested against systems with analytic solutions for numerical convergence and highly resolved lithium ion battery microstructures. EchemAMR demonstrates excellent mass conversation and efficient scaling on heterogenous High-Performance Computing (HPC) with central and graphics processing units.

Sitaraman, Hariswaran↗

DOE OSTI2025

athenapk

The LANL fork of the AthenaPK project, which contains curvlinear coordinates The Code is a set of modifications to AthenaPK, an existing open source 3D hydrodynamics and magnetohydrodynamics simulation software for astrophysics, which enable simulation with uniform curvilinear geometries. Specifically it extends the existing Cartesian coordinates to uniform spherical coordinate and uniform cylindrical coordinate systems

Miller, Jonah [@LANL]↗