A high order cut-cell method for solving the shallow-shelf equations
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97 MATHEMATICS AND COMPUTING↗
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A Block-Structured Adaptive Mesh Framework to Solve Radiation Transfer Equation in Irregular Embedded Geometries
Radiation transport arises in various scientific, industrial, and medical fields, and understanding its effect in applications is needed to make accurate predictions, safety assessments and performance optimizations. Solving the Radiation Transport Equation (RTE) is challenging due to its integro-differential nature, which involves both differential and integral terms. The differential term describes the change in radiation intensity due to absorption and emission, while the integral term accounts for scattering. The accurate modeling of radiation is further complicated in many applications due to the complex, irregular geometries. Various methods exist for solving the RTE, including the zonal, Monte Carlo, spherical harmonics, discrete ordinates, and finite volume methods. Traditional mesh-based approaches, which rely on structured or unstructured meshes, struggle with irregular geometries due to: a) the difficulty of conforming structured grids to irregular domains, b) challenges in enforcing boundary conditions correctly, and c) the additional computational cost of unstructured mesh methods. This work presents a second-order accurate method for solving the RTE in irregular geometries. The radiation intensity is discretized using the finite-volume method in both spatial and angular directions on regular Cartesian grid blocks. Leveraging the block-structured adaptive mesh refinement (AMR) framework provided by AMReX, our method refines the grid locally to reduce spatial discretization error, ensuring a converged numerical solution while minimizing computational costs elsewhere. A two-stage deferred correction approach is employed: First, a first-order discretization on grid blocks is solved using an algebraic multigrid method in HYPRE. Second, a correction term is applied explicitly to achieve second-order accuracy. The correction term is calculated by approximating the radiation flux on cell faces using a Total Variation Diminishing (TVD) scheme. This approach ensures quick convergence of the multigrid method while preserving higher-order accuracy of the numerical solution. Irregular geometries are resolved as embedded boundaries (EB), resulting in both cut cells and regular cells. In cut cells, we modify the fluxes using face fractions and incorporate additional contributions from EB boundary conditions. To ensure higher-order convergence near the EB interface, the correction term is modified by interpolating the radiation intensity to fictitious ghost points. The implementation takes advantage of modern supercomputers by leveraging AMReX’sMPI/X parallelization strategy where X can be MPI or a GPU accelerator including CUDA, HIP and DPC++. We validate our solver using classical test cases, both with and without EB, demonstrating accuracy and efficiency. Additionally, we analyze the impact of adaptive mesh refinement on solution accuracy and computational cost, highlighting the advantages of our approach for high-resolution radiation transport simulations.
computational fluid dynamics (CFD)↗
Analysis of the weighted shifted boundary method for the Poisson and Stokes problems
The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods, and relies on reformulating the original boundary value problem over a surrogate (approximate) computational domain. Accuracy is maintained by properly shifting the location and values of the boundary conditions. This avoids integration over cut cells and the associated implementation issues. Recently, the Weighted SBM (WSBM) was proposed for the Navier-Stokes equations with free surfaces and the Stokes flow with moving boundaries. The attribute “weighted” in the name WSBM stems from the fact that its variational form is weighted with the elemental volume fraction of active fluid. The motivation for the development of the WSBM was the preservation of the volume of active fluid to a higher degree of accuracy, which in turn resulted in improved stability and robustness characteristics in moving-boundary, time-dependent simulations. In this article, we present the numerical analysis of the WSBM formulations for the Poisson and Stokes problems. We give mathematical conditions under which the bilinear forms defining the discrete variational formulations are uniformly coercive (Poisson problem) or inf-sup stable (Stokes problem). By these results, stability and optimal convergence is proven in the natural norm; L2-error estimates can also be derived.
Approximate domain boundaries↗
A constrained-transport embedded boundary method for compressible resistive magnetohydrodynamics
Motivated by the increased interest in pulsed-power magneto-inertial fusion devices in recent years, we present a method for implementing an arbitrarily shaped embedded boundary on a Cartesian mesh while solving the equations of compressible resistive magnetohydrodynamics. The method is built around a finite volume formulation of the equations in which a Riemann solver is used to compute fluxes on the faces between grid cells, and a face-centered constrained transport formulation of the induction equation. The small time step problem associated with the cut cells is avoided by always computing fluxes on the faces and edges of the Cartesian mesh. We extend the method to model a moving interface between two materials with different properties using a ghost-fluid approach, and show some preliminary results including shock-wave-driven and magnetically-driven dynamical compressions of magnetohydrostatic equilibria. In conclusion, we present a thorough verification of the method and show that it converges at second order in the absence of discontinuities, and at first order with a discontinuity in material properties.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis
Copper (Cu) is essential for respiration, neurotransmitter synthesis, oxidative stress response, and transcription regulation, with imbalances leading to neurological, cognitive, and muscular disorders. Here we show the role of a novel Cu-binding protein (Cu-BP) in mammalian transcriptional regulation, specifically on skeletal muscle differentiation using murine primary myoblasts. Utilizing synchrotron X-ray fluorescence-mass spectrometry, we identified murine cysteine-rich intestinal protein 2 (mCrip2) as a key Cu-BP abundant in both nuclear and cytosolic fractions. mCrip2 binds two to four Cu + ions with high affinity and presents limited redox potential. CRISPR/Cas9-mediated deletion of mCrip2 impaired myogenesis, likely due to Cu accumulation in cells. CUT&RUN and transcriptome analyses revealed its association with gene promoters, including MyoD1 and metallothioneins, suggesting a novel Cu-responsive regulatory role for mCrip2. Our work describes the significance of mCrip2 in skeletal muscle differentiation and metal homeostasis, expanding understanding of the Cu-network in myoblasts. Copper (Cu) is essential for various cellular processes, including respiration and stress response, but imbalances can cause serious health issues. This study reveals a new Cu-binding protein (Cu-BP) involved in muscle development in primary myoblasts. Using unbiased metalloproteomic techniques and high throughput sequencing, we identified mCrip2 as a key Cu-BP found in cell nuclei and cytoplasm. mCrip2 binds up to four Cu + ions and has a limited redox potential. Deleting mCrip2 using CRISPR/Cas9 disrupted muscle formation due to Cu accumulation. Further analyses showed that mCrip2 regulates the expression of genes like MyoD1, essential for muscle differentiation, and metallothioneins in response to copper supplementation. This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.
59 BASIC BIOLOGICAL SCIENCES↗
A weighted shifted boundary method for immersed moving boundary simulations of Stokes' flow
The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods, and relies on reformulating the original boundary value problem over a surrogate (approximate) computational domain. The surrogate domain is constructed so as to avoid cut cells and the associated problematic implementation and numerical integration issues. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions: hence the name of the method, that shifts the location and values of the boundary conditions. Here, in this article, we extend the SBM to the simulation of incompressible Stokes flow, by appropriately weighting its variational form with the elemental volume fraction of active fluid. This approach allows to drastically reduce spurious pressure oscillations in time, which are produced if the total volume of active fluid were to change abruptly over a time step. The proposed Weighted SBM (W-SBM) exactly preserves states of hydrostatic equilibrium, and induces small mass and momentum conservation errors, which converge as the grid is refined. This is in analogy to cutFEMs and related unfitted approaches, which rely on an affine representation of cut boundaries. We demonstrate the robustness and accuracy of the proposed method with an extensive suite of two-dimensional tests.
97 MATHEMATICS AND COMPUTING↗
A high-order Shifted Interface Method for Lagrangian shock hydrodynamics
Here, we present a new method for two-material Lagrangian hydrodynamics, which combines the Shifted Interface Method (SIM) with a high-order Finite Element Method. Our approach relies on an exact (or sharp) material interface representation, that is, it uses the precise location of the material interface. The interface is represented by the zero level-set of a continuous high-order finite element function that moves with the material velocity. This strategy allows to evolve curved material interfaces inside curved elements. By reformulating the original interface problem over a surrogate (approximate) interface, located in proximity of the true interface, the SIM avoids cut cells and the associated problematic issues regarding implementation, numerical stability, and matrix conditioning. Accuracy is maintained by modifying the original interface conditions using Taylor expansions. We demonstrate the performance of the proposed algorithms on established numerical benchmarks in one, two and three dimensions.
97 MATHEMATICS AND COMPUTING↗
The chromatin remodeler ADNP regulates neurodevelopmental disorder risk genes and neocortical neurogenesis
Although chromatin remodelers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), the roles of these complexes during brain development are in many cases unclear. Here, we focused on the recently discovered ChAHP chromatin remodeling complex. The zinc finger and homeodomain transcription factor ADNP is a core subunit of this complex, and de novoADNPmutations lead to intellectual disability and autism spectrum disorder. However, germlineAdnpknockout mice were previously shown to exhibit early embryonic lethality, obscuring subsequent roles for the ChAHP complex in neurogenesis. To circumvent this early developmental arrest, we generated a conditionalAdnpmutant allele. Using single-cell transcriptomics, cut&run-seq, and histological approaches, we show that during neocortical development, Adnp orchestrates the production of late-born, upper-layer neurons through a two-step process. First, Adnp is required to sustain progenitor proliferation specifically during the developmental window for upper-layer cortical neurogenesis. Accordingly, we found that Adnp recruits the ChAHP subunit Chd4 to genes associated with progenitor proliferation. Second, in postmitotic differentiated neurons, we define a network of risk genes linked to NDDs that are regulated by Adnp and Chd4. Taken together, these data demonstrate that ChAHP is critical for driving the expansion of upper-layer cortical neurons and for regulating neuronal gene expression programs, suggesting that these processes may potentially contribute to NDD etiology.
Science & Technology - Other Topics↗
Nanoporous Wood Chips Based Sizable, Robust, and Low-Cost Honeycomb Vacuum Insulation Panels (DOE BENEFIT Final Research Performance Progress Report (RPPR))
Conventional vacuum insulation panels (VIPs) suffer from severe limitations including high cost, vulnerability to perforation, and significant performance degradation over time due to vacuum loss. InventWood Inc. (IW) and partnering teams completely re-engineered the VIP structure by constructing arrays of isolated vacuum-cells to enable limited cutting at designated areas (in between vacuum cells) and reduced consequential vacuum loss due to puncture. The teams also replaced the expensive vacuum insulation core materials with a low-cost commercial wood pulp and recycled long fiber. The wood pulp derived VIP can deliver an overall panel insulation of R15 (<0.01W/m·K) with over 90% thermal resistance retention after cutting (R13.5 overall, R5 along the cut edges). In addition, the vacuum-cell-array design minimizes edge losses, resulting in more durable performance, longer service life (>50 years), and higher R-value per dollar towards a cost target of <$1/ft 2 ·in. It is anticipated that the Nanochip-VIP will attract strong market interest and become an affordable insulation solution for energy efficient buildings and retrofits, leading to significant reductions in energy usage.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
SITCOMTN-162: Testing the implementation of Metadetection and Cell-Based Coadds on Abell 360 LSSTComCam data
The purpose of this technote is to test the technical quality of LSSTComCam commissioning data, specifically the Rubin_SV_38_7 field, by utilizing cell-based coadds and Metadetection by measuring the tangential and cross weak lensing shear profiles of the massive cluster Abell 360 (called A360 throughout the technote). The process entails generating the cell-based coadds for Metadetection to run on, identifying and removing cluster member galaxies, applying quality cuts, calibrating the shear measurements, and validation. Cell-based coadds and Metadetection are both currently in the process of being implemented within the LSST Science Pipelines at the time of this technote. There is substantial technical value in attempting a difficult measurement prior to full implementation. Measuring the tangential shear around A360 will showcase the current abilities of these algorithms, as well as highlight where work is still needed. As seen from the resulting shear profile of A360, the cell-based coadds and Metadetection are able to work in tandem to produce a shear catalog and resulting reduced shear profile. This technote is one part of a series studying A360 in order to both stress test the commissioning camera and demonstrate the technical capabilities of the Vera Rubin Observatory. We study the quality of the PSF modeling and impact it can have on cluster WL in [Combet et al., 2025], implementation of cell-based coadds and subsequent use for Metadetect [Sheldon et al., 2023] in this technote, photometric calibration in (in prep), source selection and photometric redshifts in [Adari et al., 2025], use of Anacal [Li et al., 2024] to produce a cluster shear profile in [Li et al., 2025], and background subtraction in this field and Fornax in [Zhou et al., 2025].
79 ASTRONOMY AND ASTROPHYSICS↗
Abrasive Waterjet Machining
The abrasive waterjet machining process was introduced in the 1980s as a new cutting tool; the process has the ability to cut almost any material. Currently, the AWJ process is used in many world-class factories, producing parts for use in daily life. A description of this process and its influencing parameters are first presented in this paper, along with process models for the AWJ tool itself and also for the jet–material interaction. The AWJ material removal process occurs through the high-velocity impact of abrasive particles, whose tips micromachine the material at the microscopic scale, with no thermal or mechanical adverse effects. The macro-characteristics of the cut surface, such as its taper, trailback, and waviness, are discussed, along with methods of improving the geometrical accuracy of the cut parts using these attributes. For example, dynamic angular compensation is used to correct for the taper and undercut in shape cutting. The surface finish is controlled by the cutting speed, hydraulic, and abrasive parameters using software and process models built into the controllers of CNC machines. In addition to shape cutting, edge trimming is presented, with a focus on the carbon fiber composites used in aircraft and automotive structures, where special AWJ tools and manipulators are used. Examples of the precision cutting of microelectronic and solar cell parts are discussed to describe the special techniques that are used, such as machine vision and vacuum-assist, which have been found to be essential to the integrity and accuracy of cut parts. The use of the AWJ machining process was extended to other applications, such as drilling, boring, milling, turning, and surface modification, which are presented in this paper as actual industrial applications. To demonstrate the versatility of the AWJ machining process, the data in this paper were selected to cover a wide range of materials, such as metal, glass, composites, and ceramics, and also a wide range of thicknesses, from 1 mm to 600 mm. The trends of Industry 4.0 and 5.0, AI, and IoT are also presented.
36 MATERIALS SCIENCE↗
An epitaxial surface heterostructure anchoring approach for high-performance Ni-rich layered cathodes
Nickel-rich (Ni≥90%) layered oxides materials have emerged as a promising candidate for next-generation high-energy-density lithium-ion batteries (LIBs). However, their widespread application is hindered by structural fatigue and lattice oxygen loss. In this work, an epitaxial surface rock-salt nanolayer is successfully developed on the LiNi 0.9 Co 0.1 O 2 sub-surface via heteroatom anchoring utilizing high-valence element molybdenum modification. This in-situ formed conformal buffer phase with a thickness of 1.2nm effectively suppresses the continuous interphase side-reactions, and thus maintains the excellent structure integrity at high voltage. Furthermore, theoretical calculations indicate that the lattice oxygen reversibility in the anion framework of the optimized sample is obviously enhanced due to the higher content of O 2p states near the Fermi level than that of the pristine one. Meanwhile, the stronger Mo–O bond further reduces cell volume alteration, which improves the bulk structure stability of modified materials. Besides, the detailed charge compensation mechanism suggests that the average oxidation state of Ni is reduced, which induces more active Li + participating in the redox reactions, boosting the cell energy density. As a result, the uniquely designed cathode materials exhibit an extraordinary discharge capacity of 245.4 mAh g −1 at 0.1 C, remarkable rate performance of 169.3 mAh g −1 at 10 C at 4.5V, and a high capacity retention of 70.5% after 1000 cycles in full cells at a high cut-off voltage of 4.4V. Further, this strategy provides an valuable insight into constructing distinctive heterostructure on high-performance Ni-rich layered cathodes for LIBs.
25 ENERGY STORAGE↗
Comparing Liquid Vortex Capture & the Rapid Droplet Sampling Interface for Single Cell Mass Spectrometry
High-throughput single-cell mass spectrometry is a rapidly evolving field that requires innovative sampling and ionization techniques to balance speed, sensitivity, and reliability for metabolomic and lipidomic analyses. This study provides a comparative analysis of two cutting-edge ionization platforms for single-cell analysis: Liquid Vortex Capture (LVC) and Rapid Droplet Sampling Interface (RDSI). The performance was benchmarked by testing pharmaceuticals, EquiSPLASH, and single-cell experiments. RDSI demonstrated up to 100-fold improvements in sensitivity for drugs and lipids such as propranolol, amiodarone, atorvastatin, and phosphocholines in water and phosphate-buffered solutions. This was attributed to its low-flow rate operation (3 μL/min) and reduced dilution. Conversely, LVC excelled in handling higher liquid volumes with greater reproducibility due to its higher solvent flow rate (200 μL/min), enabling increased dilution, solubility, and cleaning. Single-cell uptake of atorvastatin incubated for 10 min, or amiodarone incubated for 24 h in HepG2 cells, similarly revealed up to 85-fold enhancement in sensitivity by RDSI for drugs and lipids. These findings highlight the potential of RDSI for enhancing sensitivity in single-cell drug monitoring and lipidomics.
Cahill, John [ORNL] (ORCID:0000000298664010)↗
Advancements in Manufacturing of High-Performance Perovskite Solar Cells and Modules Using Printing Technologies
Perovskite photovoltaic technology carries immense opportunity for the solar industries because of its remarkable efficiency and prospect for cost-effective production. However, the successful deployment of perovskite solar modules (PSMs) in the solar market necessitates tackling stability-based obstacles, scalability, and environmental considerations. This paper unveils a comprehensive examination of the cutting-edge advancements in the manufacturing of perovskite solar cells (PSCs) and modules, with an emphasis on high-speed, large-area printing. The paper underscores the substantial progress achieved in printed PSCs and PSMs, demonstrating promising electrical performance and long-term device durability. This review paper categorizes printing techniques compatible with large-area high-speed manufacturing into three distinct families: blade coating, slot die coating, and screen printing, as these common printing practices offer precise control, scalability, cost-effectiveness, high resolution, and efficient material usage. Additionally, this paper presents an in-depth investigation and comparison of superior PSCs and PSMs fabricated by printing on power conversion efficiency (PCE), stability, and scalability.
14 SOLAR ENERGY↗
Metallization and stringing for back-contact solar cells
Metallization and stringing methods for back-contact solar cells, and resulting solar cells, are described. In an example, in one embodiment, a method involves aligning conductive wires over the back sides of adjacent solar cells, wherein the wires are aligned substantially parallel to P-type and N-type doped diffusion regions of the solar cells. The method involves bonding the wires to the back side of each of the solar cells over the P-type and N-type doped diffusion regions. The method further includes cutting every other one of the wires between each adjacent pair of the solar cells.
Terao, Akira↗
Anisotropic Hot Spot Formation at a Grain Boundary in Shock-Compressed TATB High Explosive Crystal
Secondary high explosives (HEs) exhibit rich microstructure that promotes the formation of hot spots responsible for detonation initiation, but the role of microstructural interfaces remains poorly quantified. To this end, we develop extensions for the generalized crystal-cutting method (GCCM) to prepare molecular dynamics (MD) simulation cells containing grain boundaries (GBs) and other crystal–crystal interfaces with prescribed tilt and twist orientations. Using the GCCM, we perform MD simulations of shock interactions with a GB between the (001) and (100) crystal facets in the secondary HE TATB (1,3,5-triamino-2,4,6-trinitrobenzene). Our MD simulations reveal a strong directional dependence to the formation of a hot spot at the GB interface. In particular, transmission of the shock from the (001) grain to the (100) grain yields a hot spot in the (100) grain at the GB interface, whereas no hot spot is produced when an equivalent shock transits the GB in the opposite direction. We trace the origin of this GB anisotropy to three dominant factors: (1) the intrinsic differences in shock-deformation mechanisms and wave structures for the bulk (100) and (001) grains, which leads to distinct geometries and mechanical impedances upon shock arrival to the GB depending on which grains are donor or acceptor for the transmitted shock; (2) the different time intervals separating the initial shock rise and the formation of steady wave structures in the respective donor–acceptor configurations; and (3) the differences in time scales required to re-establish local thermal equilibrium. Interfacial hot spots form when these factors combine to impede development of a steady two-wave structure and instead induce a localized, pseudosingly shocked region that undergoes a higher rate of work production (resulting in a higher temperature) compared to when the steady two-wave structure develops further from the interface. The extensions to the GCCM approach presented here are anticipated to facilitate a wide range of MD studies that focus on understanding the role of crystal–crystal interfaces in molecular materials.
organic↗
Incorporation of Ion Transport Chains into Multivariate MOF for Improved Water Oxidation
The climate crisis demands clean energy technologies to cut CO 2 emissions from fossil fuels. Hydrogen fuel cells and solar-driven CO 2 reduction are promising, but both rely on efficient water oxidation. Polypyridyl ruthenium complexes are active catalysts for water oxidation; however, they exhibit poor stability and recyclability. Our group improved performance by embedding these complexes into metal−organic frameworks (MOFs). As water oxidation is pH-dependent, proton management further enhances reactivity. To address the issue, we introduced proton transfer pathways into the MOF structure. Specifically, we incorporated −SO 3 H groups onto the biphenyl linkers of UiO-67 loaded with [Ru(tpy)(dcbpy)OH 2 ]PF 6 catalyst (where tpy = 2,2′:6′,2″-terpyridine; dcbpy = 5,5-dicarboxy-2,2′- bipyridine). The sulfonated MOF exhibited a 2.5-fold increase in oxygen evolution compared to the nonsulfonated analogue. After 1 h of electrolysis, the sulfonated MOF exhibited a turnover number of 25 for oxygen evolution reaction compared to 10 for the native MOF, demonstrating the benefits of built-in proton management.
Catalysts↗
To immunity and beyond: the central role of jasmonate signalling in beneficial root–microbe–environment interactions
Jasmonates (JAs) have traditionally been studied for their defensive roles against wounding and detrimental organisms, but they are also crucial hormones for plant–microbe beneficial interactions. Here, we review the most recent advances in this overlooked field. We cover the evolutionary divergences of JA biosynthesis and signalling across various plant lineages and present the molecular mechanisms of action through which beneficial microbes interact with the host JA signalling pathway as well as environmental integration. Special emphasis is given to the cutting‐edge tools to study the spatial compartmentalization and cell and tissue specialization of JA signalling. This review underscores the role of the JA signalling pathway, with the MYELOCYTOMATOSIS2 transcription factor as a potential integrator of biotic and environmental cues, and highlights its significance in mutualistic interactions.
defence↗