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At least 37 records · Page 2

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

59 BASIC BIOLOGICAL SCIENCES

Virtual environment display for a 3D audio room simulation

The development of a virtual environment simulation system integrating a 3D acoustic audio model with an immersive 3D visual scene is discussed. The system complements the acoustic model and is specified to: allow the listener to freely move about the space, a room of manipulable size, shape, and audio character, while interactively relocating the sound sources; reinforce the listener's feeling of telepresence in the acoustical environment with visual and proprioceptive sensations; enhance the audio with the graphic and interactive components, rather than overwhelm or reduce it; and serve as a research testbed and technology transfer demonstration. The hardware/software design of two demonstration systems, one installed and one portable, are discussed through the development of four iterative configurations.

Chapin, William L.

Sequential multidimensional heteroepitaxy of chalcogen-sharing 3D ZnSe and 2D MoSe 2 with quasi van der Waals interface engineering

Two-dimensional (2D) materials are emerging as a promising platform for epitaxial growth, largely free from the constraints of lattice constant and thermal expansion coefficient mismatches. Among them, transition metal dichalcogenides (TMDs), known for their superior electrical properties, are ideal for ultrathin semiconductor applications. Their unique epitaxial characteristics enable seamless integration with 3D materials, facilitating the development of gate stacks and heterojunction devices. In this regard, developing a process for growing high-quality 3D epitaxial materials before and after the growth of 2D TMDs and understanding the 2D/3D interface are crucial. This study demonstrates the sequential growth of fully epitaxial ZnSe/MoSe 2 /ZnSe heterostructures using metal-organic chemical vapor deposition. ZnSe and MoSe 2 , sharing chalcogen elements, enable large-area quasi van der Waals epitaxy with sharp interfaces without intermediate phase. Multiscale analysis involving transmission electron microscopy and density functional theory calculation reveals lattice commensurability, van der Waals gaps, termination, and interfacial reconstruction. Understanding these interactions is crucial for advancing multidimensional integration of 2D and 3D materials.

36 MATERIALS SCIENCE

Calculation of fully three-dimensional separated flow with an unsteady viscous-inviscid interaction method

Three previous papers have shown that the viscous inviscid numerical methods were capable of calculating separated turbulent flows. The 'Semi-inverse method' and the models of the first author allow the computation of massive separations, stalled flows, and shock wave-boundary layer interactions, in two-dimensional or quasi-three-dimensional conditions, from low speeds to supersonic speeds. The 'Semi-implicit' method for time-consistent coupling allows for the computation of time-accurate transonic separated flow and buffer computations in two-dimensions. The present paper shows that the viscous-inviscid interaction approach is also able to compute the fully three-dimensional flow separation phenomena. The method is based on a thin-layer approximation of the theory of 'Defect-Formulation' that provides the viscous-inviscid splitting of the Navier-Stokes equations. A parametric analytical modelling of the 3D-turbulent velocity profiles is involved. Numerically, the 3D-velocity profiles are discretized in the normal z-direction and driven by parametric integral 3D-equations in direct or inverse modes in the x-direction. The viscous-inviscid coupling is fully 3D and solved the time-consistency problem with an extension of the 'Semi-implicit' method previously suggested in two-dimensions. A 3D inviscid subroutine with TSP approximation is used. Results are obtained for transonic steady flows over wings with shock-induced transonic separation. The method provides results for highly three-dimensional flow separations, such as induced by a three-dimensional through at the wall of a flat plate. The 3D viscous-inviscid coupling and the 3D model of the velocity field provide three-dimensional instantaneous skin-friction lines whose patterns exhibit the same complex topology as Navier-Stokes solvers, with foci, nodes, and saddle-points.

Leballeur, J. C.

pyTriBeam

SAND2025-01899O pyTriBeam is a software tool that creates automated processes for a scanning electron microscope including workflows for 3D serial sectioning dataset collection, high-res image montaging, and support for custom script use. This includes integration for 3D chemical mapping (EDS) and crystallographic (EBSD) data collection with select supported detectors. The application allows end users to setup and run customizable data collection workflows without requiring expertise in programming. 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.

Hovey, Chad

N -Terminal Octylated Peptoid Hydrogels as 3D-Printable Cell Scaffolds and Proteolytically Robust Cargo Depots

Supramolecular hydrogels that mimic the extracellular matrix (ECM) represent promising materials for tissue engineering and drug delivery. However, conventional hydrogels formed via the self-assembly of natural or synthetic building blocks often face a trade-off between biological functionality and biochemical stability, limiting their utility in long-term or protease-rich environments. Peptoids, a class of peptide-inspired, sequence-defined polymers, offer a compelling alternative due to their exceptional proteolytic resistance and bioactivity. Despite this potential, the development of supramolecular peptoid hydrogels has been hindered by the absence of backbone hydrogen bond donors, which limits long-range ordering necessary for efficient hydrogel formation. This work describes a short peptoid functionalized at the N-terminus with an octyl chain that readily self-assembles into hydrogels. Hydrophobic interactions among pendant octyl groups promote directional peptoid packing into highly ordered nanosheets, which interconnect to form a porous hydrogel network. These hydrogels exhibit tunable viscoelasticity, shear-thinning, and self-healing properties, enabling their use as inks for extrusion-based 3D printing. They support NIH-3T3 fibroblast adhesion, spreading, and proliferation, maintaining greater than 95% cell viability over 4 days. Moreover, the hydrogels retain their macroscopic integrity under protease-rich conditions, enabling sustained cargo release and uniform cellular uptake. Together, this study demonstrates a class of supramolecular peptoid hydrogelators that integrate biocompatibility, 3D printability, and proteolytic stability, providing a versatile platform for ECMmimetic scaffolds in regenerative medicine and long-term therapeutic delivery.

cargo delivery

Fully-coupled analysis of jet mixing problems. Three-dimensional PNS model, SCIP3D

Numerical procedures formulated for the analysis of 3D jet mixing problems, as incorporated in the computer model, SCIP3D, are described. The overall methodology closely parallels that developed in the earlier 2D axisymmetric jet mixing model, SCIPVIS. SCIP3D integrates the 3D parabolized Navier-Stokes (PNS) jet mixing equations, cast in mapped cartesian or cylindrical coordinates, employing the explicit MacCormack Algorithm. A pressure split variant of this algorithm is employed in subsonic regions with a sublayer approximation utilized for treating the streamwise pressure component. SCIP3D contains both the ks and kW turbulence models, and employs a two component mixture approach to treat jet exhausts of arbitrary composition. Specialized grid procedures are used to adjust the grid growth in accordance with the growth of the jet, including a hybrid cartesian/cylindrical grid procedure for rectangular jets which moves the hybrid coordinate origin towards the flow origin as the jet transitions from a rectangular to circular shape. Numerous calculations are presented for rectangular mixing problems, as well as for a variety of basic unit problems exhibiting overall capabilities of SCIP3D.

Wolf, D. E.

Validation of an integrated modeling framework for investigating 3D plasma responses in tokamak plasmas

As contemporary experimental tokamaks are pushed toward reactor-relevant operation, they provide essential testbeds for demonstrating and exploring ELM control strategies for deployment in future fusion pilot plants. Accurate predictions of full plasma responses are essential to guide and optimize these demonstrations. This paper introduces and validates an integrated modeling framework over a historical range of DIII-D operational space. The integrated modeling framework uses only scalar plasma parameters and optional reference boundary to self-consistently and flexibly scan through tokamak operational space and estimate the corresponding ELM-suppression relevant plasma response over 3D coil phase space. The framework generates tightly converged equilibria that satisfy a target set of plasma parameters (I p , β N , l i ), with kinetic profiles constrained by an EPED(NN)-computed pedestal and empirical core model. The plasma response of these modeled equilibria is calculated with GPEC. Validated against 55 distinct DIII-D equilibria, the framework consistently reproduces experimentally constrained equilibrium pressure, q, and other representative profiles using the time-varying information from only evolving scalar plasma parameters; plasma response validation is performed for the n=3 perturbation. In particular, the plasma response of a DIII-D discharge scanning q 95 in search of ELM suppression windows is quantitatively reproduced. By accurately reproducing experimental equilibria and plasma responses across wide parameter variation, the framework supports potential for synthetic parameter scans in key operational, stability, and plasma response dimensions to investigate RMP ELM-suppression experiments and inform predictive RMP scenario optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Ultra-thick three-dimensional interpenetrating graphene electrode architectures for high volumetric density energy storage

For electrochemical energy storage, increasing the electrode thickness is an effective approach to achieving higher energy density from a given material. However, this often compromises ion transport, leading to diminished performance. Here, in this study, we present a novel platform for fabricating complex 3D interpenetrating electrode structures via photo-polymerization 3D printing, integrated with computational structural optimization for energy storage. The platform employs an acrylate resin system infused with graphene oxide (GO), enabling high-fidelity printing of optimized porous structures and facilitating efficient electron and ion transport in ultra-thick electrodes. The optimized 3D layouts substantially enhance energy and power densities compared to conventional configurations, ensuring superior material utilization and minimal ohmic losses. Supercapacitors fabricated using this approach achieved an exceptional energy density of 4.7 Wh L−1 at a power density of 1689.0 W L−1, surpassing traditional designs. This work underscores the transformative role of structural optimization in advancing electrochemical performance and establishes a versatile pathway for developing next-generation energy storage systems with exceptional efficiency and functionality.

Wang, Zhen [University of California, Berkeley, CA

An ultra-fast method for generating synthetic down-scattered neutron data for inertial confinement fusion implosions

In inertial confinement fusion experiments at the National Ignition Facility, asymmetries are probed by a variety of neutron diagnostics, including neutron imaging systems, real-time neutron activation diagnostics (RTNADs), and neutron spectrometers. It is often useful to generate synthetic data based on these diagnostics to validate and tune models. However, current methods of doing so using Monte Carlo particle tracing are time-consuming. In this paper, an ultra-fast method is presented for generating synthetic neutron images, RTNAD data, and spectrometry data using line integrals and 3D convolutions. While it does not contain as much physics as particle tracing codes, it is thousands of times faster and produces nearly identical data. This enables analysis techniques that depend on generating large amounts of synthetic data, which will prove very useful for the study of asymmetries going forward.

Deuterium

Frontal polymerization of thermosets to enable vacuum-formed structural electronics

Material design and accessible manufacturing are often at odds with each other, calling for creative solutions to adapt high-performance materials to available processes. This challenge is represented well by in-mold electronics, an innovative approach to the manufacture of 3D circuitry and electronic components that offers game-changing advantages. In-mold electronics relies on vacuum forming processes, which are historically limited to thermoplastics. Extending these methods to include thermosets would enable manufacturing of robust components with desirable properties. Here, we provide a solution to make thermoset materials amenable to vacuum forming. Specifically, an ambient polymerization is used to transition a liquid monomeric solution to an elastomeric gel. These free-standing gels can then be vacuum formed, and the reaction can be completed via frontal polymerization. Thermoset materials produced with this method have properties that provide benefits over traditionally employed thermoplastic substrates and enable 3D device integration into environmentally demanding architectural, automotive, and extraterrestrial structures.

Fowler, Hayden Elise [Sandia National Laboratories

Impact of surface growth method and surface treatment in niobium-based superconducting devices

We explore the comparison between two growth methods for niobium film - sputtering and electron-cyclotron resonance growth - for niobium-based superconducting resonators. We discuss some of the key properties of the films, including surface characterization and residual resistance measurements metrics. We present our design of various devices used in this study including superconducting resonators and qubits, both in planar configurations and integrated in 3D cavities, as well as experimental characterization of coherence metrics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Global Methane Budget 2000–2020

Abstract. Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. CH4 is the second most important human-influenced greenhouse gas in terms of climate forcing after carbon dioxide (CO2), and both emissions and atmospheric concentrations of CH4 have continued to increase since 2007 after a temporary pause. The relative importance of CH4 emissions compared to those of CO2 for temperature change is related to its shorter atmospheric lifetime, stronger radiative effect, and acceleration in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in quantifying the factors responsible for the observed atmospheric growth rate arise from diverse, geographically overlapping CH4 sources and from the uncertain magnitude and temporal change in the destruction of CH4 by short-lived and highly variable hydroxyl radicals (OH). To address these challenges, we have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to improve, synthesise, and update the global CH4 budget regularly and to stimulate new research on the methane cycle. Following Saunois et al. (2016, 2020), we present here the third version of the living review paper dedicated to the decadal CH4 budget, integrating results of top-down CH4 emission estimates (based on in situ and Greenhouse Gases Observing SATellite (GOSAT) atmospheric observations and an ensemble of atmospheric inverse-model results) and bottom-up estimates (based on process-based models for estimating land surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations). We present a budget for the most recent 2010–2019 calendar decade (the latest period for which full data sets are available), for the previous decade of 2000–2009 and for the year 2020. The revision of the bottom-up budget in this 2025 edition benefits from important progress in estimating inland freshwater emissions, with better counting of emissions from lakes and ponds, reservoirs, and streams and rivers. This budget also reduces double counting across freshwater and wetland emissions and, for the first time, includes an estimate of the potential double counting that may exist (average of 23 Tg CH4 yr−1). Bottom-up approaches show that the combined wetland and inland freshwater emissions average 248 [159–369] Tg CH4 yr−1 for the 2010–2019 decade. Natural fluxes are perturbed by human activities through climate, eutrophication, and land use. In this budget, we also estimate, for the first time, this anthropogenic component contributing to wetland and inland freshwater emissions. Newly available gridded products also allowed us to derive an almost complete latitudinal and regional budget based on bottom-up approaches. For the 2010–2019 decade, global CH4 emissions are estimated by atmospheric inversions (top-down) to be 575 Tg CH4 yr−1 (range 553–586, corresponding to the minimum and maximum estimates of the model ensemble). Of this amount, 369 Tg CH4 yr−1 or ∼ 65 % is attributed to direct anthropogenic sources in the fossil, agriculture, and waste and anthropogenic biomass burning (range 350–391 Tg CH4 yr−1 or 63 %–68 %). For the 2000–2009 period, the atmospheric inversions give a slightly lower total emission than for 2010–2019, by 32 Tg CH4 yr−1 (range 9–40). The 2020 emission rate is the highest of the period and reaches 608 Tg CH4 yr−1 (range 581–627), which is 12 % higher than the average emissions in the 2000s. Since 2012, global direct anthropogenic CH4 emission trends have been tracking scenarios that assume no or minimal climate mitigation policies proposed by the Intergovernmental Panel on Climate Change (shared socio-economic pathways SSP5 and SSP3). Bottom-up methods suggest 16 % (94 Tg CH4 yr−1) larger global emissions (669 Tg CH4 yr−1, range 512–849) than top-down inversion methods for the 2010–2019 period. The discrepancy between the bottom-up and the top-down budgets has been greatly reduced compared to the previous differences (167 and 156 Tg CH4 yr−1 in Saunois et al. (2016, 2020) respectively), and for the first time uncertainties in bottom-up and top-down budgets overlap. Although differences have been reduced between inversions and bottom-up, the most important source of uncertainty in the global CH4 budget is still attributable to natural emissions, especially those from wetlands and inland freshwaters. The tropospheric loss of methane, as the main contributor to methane lifetime, has been estimated at 563 [510–663] Tg CH4 yr−1 based on chemistry–climate models. These values are slightly larger than for 2000–2009 due to the impact of the rise in atmospheric methane and remaining large uncertainty (∼ 25 %). The total sink of CH4 is estimated at 633 [507–796] Tg CH4 yr−1 by the bottom-up approaches and at 554 [550–567] Tg CH4 yr−1 by top-down approaches. However, most of the top-down models use the same OH distribution, which introduces less uncertainty to the global budget than is likely justified. For 2010–2019, agriculture and waste contributed an estimated 228 [213–242] Tg CH4 yr−1 in the top-down budget and 211 [195–231] Tg CH4 yr−1 in the bottom-up budget. Fossil fuel emissions contributed 115 [100–124] Tg CH4 yr−1 in the top-down budget and 120 [117–125] Tg CH4 yr−1 in the bottom-up budget. Biomass and biofuel burning contributed 27 [26–27] Tg CH4 yr−1 in the top-down budget and 28 [21–39] Tg CH4 yr−1 in the bottom-up budget. We identify five major priorities for improving the CH4 budget: (i) producing a global, high-resolution map of water-saturated soils and inundated areas emitting CH4 based on a robust classification of different types of emitting ecosystems; (ii) further development of process-based models for inland-water emissions; (iii) intensification of CH4 observations at local (e.g. FLUXNET-CH4 measurements, urban-scale monitoring, satellite imagery with pointing capabilities) to regional scales (surface networks and global remote sensing measurements from satellites) to constrain both bottom-up models and atmospheric inversions; (iv) improvements of transport models and the representation of photochemical sinks in top-down inversions; and (v) integration of 3D variational inversion systems using isotopic and/or co-emitted species such as ethane as well as information in the bottom-up inventories on anthropogenic super-emitters detected by remote sensing (mainly oil and gas sector but also coal, agriculture, and landfills) to improve source partitioning. The data presented here can be downloaded from https://doi.org/10.18160/GKQ9-2RHT (Martinez et al., 2024).

54 ENVIRONMENTAL SCIENCES

A comparison of upwind schemes for computation of three-dimensional hypersonic real-gas flows

The method of Suresh and Liou (1992) is extended, and the resulting explicit noniterative upwind finite-volume algorithm is applied to the integration of 3D parabolized Navier-Stokes equations to model 3D hypersonic real-gas flowfields. The solver is second-order accurate in the marching direction and employs flux-limiters to make the algorithm second-order accurate, with total variation diminishing in the cross-flow direction. The algorithm is used to compute hypersonic flow over a yawed cone and over the Ames All-Body Hypersonic Vehicle. The solutions obtained agree well with other computational results and with experimental data.

Gerbsch, R. A.

3D Printing of Polyelectrolyte Complex-Integrated Photocurable Hydrogel Resins

In this study, we developed a photocurable hydrogel resin incorporating a polyelectrolyte complex (PEC) for 3D printing. Acrylamide-based monomers were formulated with varying PEC contents (0–15 wt %) in an aqueous KBr medium to fabricate patterned porous hydrogel structures. The morphology of printed hydrogels was characterized by field-emission scanning electron microscopy and energy-dispersive X-ray spectroscopy. Notably, the PEC5 and PEC10 formulations exhibited optimal thermal stability and compressive properties, attributed to the homogeneous distribution of PEC domains within the hydrogel matrix. Furthermore, dye adsorption experiments demonstrated excellent removal efficiency, highlighting the potential of PEC-containing hydrogels for environmental remediation applications, particularly in the treatment of dye-contaminated wastewater.

Yang, Jinchul [University of Tennesse Knoxville]

Systematic analysis of magnetic equilibrium reconstruction with eddy currents on LTX- β

Magnetic equilibrium reconstruction in the Lithium Tokamak Experiment-Beta (LTX-β) is complicated by strong eddy currents and toroidal asymmetries arising from its segmented, close-fitting conducting shell. In the earlier experiment LTX, these three-dimensional (3D) conductor effects significantly distorted diagnostic signals and challenged conventional axisymmetric reconstruction methods. In this work, we demonstrate that accurate plasma equilibria can be recovered on LTX-β by incorporating a small number of dominant eddy current modes derived from realistic conductor models. Using the open-source $\tt{TokaMaker}$ Grad–Shafranov solver, we reconstruct equilibria across a systematically selected set of LTX-β discharges and validate them against the legacy $\tt{PSI-Tri}$ hybrid 2D-3D code. Our results show that fully 2D $\tt{TokaMaker}$ reconstructions achieve significantly improved agreement with flux loop and Mirnov probe measurements, reducing total chi-squared fitting errors, especially during startup. Finally, we develop new hybrid 2D-3D $\tt{TokaMaker}$ reconstructions by integrating the $\tt{ThinCurr}$ 3D eddy current model, which we optimize for significant further reduction of chi-squared in most scenarios. These findings underscore the importance of realistic wall-current modeling in short-pulse tokamaks, and establish a physics-based reconstruction framework that is extensible to devices with complex passive structures and 3D wall interactions.

Grad–Shafranov solver

An efficient formulation of the coupled finite element-integral equation technique for solving large 3D scattering problems

It is often desirable to calculate the electromagnetic fields inside and about a complicated system of scattering bodies, as well as in their far-field region. The finite element method (FE) is well suited to solving the interior problem, but the domain has to be limited to a manageable size. At the truncation of the FE mesh one can either impose approximate (absorbing) boundary conditions or set up an integral equation (IE) for the fields scattered from the bodies. The latter approach is preferable since it results in higher accuracy. Hence, the two techniques can be successfully combined by introducing a surface that encloses the scatterers, applying a FE model to the inner volume and setting up an IE for the tangential fields components on the surface. Here the continuity of the tangential fields is used bo obtain a consistent solution. A few coupled FE-IE methods have recently appeared in the literature. The approach presented here has the advantage of using edge-based finite elements, a type of finite elements with degrees of freedom associated with edges of the mesh. Because of their properties, they are better suited than the conventional node based elements to represent electromagnetic fields, particularly when inhomogeneous regions are modeled, since the node based elements impose an unnatural continuity of all field components across boundaries of mesh elements. Additionally, our approach is well suited to handle large size problems and lends itself to code parallelization. We will discuss the salient features that make our approach very efficient from the standpoint of numerical computation, and the fields and RCS of a few objects are illustrated as examples.

Cwik, T.

Attempting to Develop the World’s Most Cost-Effective Metal 3D Printing Technology Through Industrial Adoption of a High-Temperature Electro-Magnetic Nozzle for 3D Printing and Computer Numerical Control Integration

This project aimed to make a practical system capable of sustained metal deposition in air engineered with industrial integration and controls. The Al-Ce wire feedstock was tailored with appropriate deposition and solidification properties for direct reactive interface printing (DRIP), and the goal was to integrate onto a Hybrid Manufacturing Technologies system for producing test parts without a controlled environment.

36 MATERIALS SCIENCE