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At least 433 records · Page 24

mTOR regulates aerobic glycolysis through NEAT1 and nuclear paraspeckle-mediated mechanism in hepatocellular carcinoma

Hepatocellular Carcinoma (HCC) is a major form of liver cancer and a leading cause of cancer-related death worldwide. New insights into HCC pathobiology and mechanism of drug actions are urgently needed to improve patient outcomes. HCC undergoes metabolic reprogramming of glucose metabolism from respiration to aerobic glycolysis, a phenomenon known as the ‘Warburg Effect’ that supports rapid cancer cell growth, survival, and invasion. mTOR is known to promote Warburg Effect, but the underlying mechanism(s) remains poorly defined. The aim of this study is to understand the mechanism(s) and significance of mTOR regulation of aerobic glycolysis in HCC. We profiled mTORC1-dependent long non-coding RNAs (lncRNAs) by RNA-seq of HCC cells treated with rapamycin. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were used to explore the transcriptional regulation of NEAT1 by mTORC1. [U- 13 C]-glucose labeling and metabolomic analysis, extracellular acidification Rate (ECAR) by Seahorse XF Analyzer, and glucose uptake assay were used to investigate the role of mTOR-NEAT1-NONO signaling in the regulation of aerobic glycolysis. RNA immunoprecipitation (RIP) and NONO-binding motif scanning were performed to identify the regulatory mechanism of pre-mRNA splicing by mTOR-NEAT1. Myristoylated AKT1 (mAKT1)/NRASV 12 -driven HCC model developed by hydrodynamic transfection (HDT) was employed to explore the significance of mTOR-NEAT1 signaling in HCC tumorigenesis and mTOR-targeted therapy. mTOR regulates lncRNA transcriptome in HCC and that NEAT1 is a major mTOR transcriptional target. Interestingly, although both NEAT1_1 and NEAT1_2 are down-regulated in HCC, only NEAT1_2 is significantly correlated with poor overall survival of HCC patients. NEAT1_2 is the organizer of nuclear paraspeckles that sequester the RNA-binding proteins NONO and SFPQ. We show that upon oncogenic activation, mTORC1 suppresses NEAT1_2 expression and paraspeckle biogenesis, liberating NONO/SFPQ, which in turn, binds to U5 within the spliceosome, stimulating mRNA splicing and expression of key glycolytic enzymes. This series of actions lead to enhanced glucose transport, aerobic glycolytic flux, lactate production, and HCC growth both in vitro and in vivo. Furthermore, the paraspeckle-mediated mechanism is important for the anticancer action of US FDA-approved drugs rapamycin/temsirolimus. These findings reveal a molecular mechanism by which mTOR promotes the ‘Warburg Effect’, which is important for the metabolism and development of HCC, and anticancer response of mTOR-targeted therapy.

59 BASIC BIOLOGICAL SCIENCES↗

HYPHY: Deep Generative Conditional Posterior Mapping of Hydrodynamical Physics

Generating large-volume hydrodynamical simulations for cosmological observables is a computationally demanding task necessary for next-generation observations. In this work, we construct a novel fully convolutional variational autoencoder (VAE) to synthesize hydrodynamic fields conditioned on dark matter fields from N -body simulations. After training the model on a single hydrodynamical simulation, we are able to probabilistically map new dark-matter-only simulations to corresponding full hydrodynamical outputs. By sampling over the latent space of our VAE, we can generate posterior samples and study the variance of the mapping. We find that our reconstructed field provides an accurate representation of the target hydrodynamical fields as well as reasonable variance estimates. This approach has promise for the rapid generation of mocks as well as for implementation in a full inverse model of observed data.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling Solids in Nuclear Astrophysics with Smoothed Particle Hydrodynamics

Abstract Smoothed particle hydrodynamics (SPH) is a frequently applied tool in computational astrophysics to solve the fluid dynamics equations governing the systems under study. For some problems, for example when involving asteroids and asteroid impacts, the additional inclusion of material strength is necessary in order to accurately describe the dynamics. In compact stars, that is white dwarfs and neutron stars, solid components are also present. Neutron stars have a solid crust, which is the strongest material known in nature. However, their dynamical evolution, when modeled via SPH or other computational fluid dynamics codes, is usually described as a purely fluid dynamics problem. Here, we present the first 3D simulations of neutron star crustal toroidal oscillations including material strength with the Los Alamos National Laboratory SPH code FleCSPH. In the first half of the paper, we present the numerical implementation of solid material modeling together with standard tests. The second half is on the simulation of crustal oscillations in the fundamental toroidal mode. Here, we dedicate a large fraction of the paper to approaches that can suppress numerical noise in the solid. If not minimized, the latter can dominate the crustal motion in the simulations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Characterization of volcanic tuff pores pre- and post-underground nuclear detonation using ultra-small and small angle neutron scattering

The ability to accurately model the subsurface transport of radionuclides is fundamental to the remote detection and characterization of underground nuclear explosion (UNE) events. Developing more sophisticated transport models presents a significant opportunity to enhance monitoring capabilities, particularly in the reliable prediction of signature migration. Experimentally determined characterization of geologic materials associated with transport properties is the pertinent base information for such robust model development and calibration. Here, we report results from an unprecedented study demonstrating changes to the pore and fracture network structures in geological materials in response to UNEs over nanometer to micrometer length scales. Volcanic tuffs of five different lithological formations from pre- and post-UNE environments were collected from the Nevada National Security Site. Combined ultra-small and small-angle neutron scattering techniques were used to characterize the tuff pore structure. The results demonstrate measurable differences in the specific surface area and porosity of samples pre- and post-shot from texturally similar lithological formations, indicating that pore properties can serve as a direct physical signature of a UNE. The results also provide experimentally determined transport parameters in support of advanced model development through the integration of gas migration, hydrodynamic simulations, and geologic framework models.

54 ENVIRONMENTAL SCIENCES↗

Definition of the Stiesdal Offshore TetraSpar Floating Wind System for OC6 Phase IV

The Offshore Code Comparison Collaboration, Continued, with Correlation, and unCertainty (OC6) is an international project focused on verifying and validating modeling tools used in the analysis of floating offshore wind systems. The fourth phase of the project aims to assess the ability of the tools to model a novel floating wind design. The TetraSpar was designed by Stiesdal Offshore Technologies and was selected as the subject platform for the project. The platform is a unique design that features spar-like stability with a very low center of gravity, but does not require rare deep-water ports. This combination is achieved with a system made of two separate steel structures, a hull at the water's surface that supports the wind turbine tower, and a keel that is suspended below the main body. This lower keel has a very high density and drives the total platform's low center of gravity. The TetraSpar, with hull and keel, spar-type stability, and relatively slender components, is unique compared to platforms studied in earlier phases of OC3-OC6 projects, and it offers an opportunity to evaluate the applicability of modeling tools to a novel design, especially unique hydrodynamics and compliant cables. Scaled model tests of the TetraSpar design were performed in 2018-2019 by the University of Maine. The data collected in the model tests provides a detailed description of the response of the platform in various controlled and relatively well understood conditions. Comparison with this data provides a good opportunity for validation of numerical models. The OC6 Phase IV work focuses on the specific parameters used in these scaled model tests. Descriptions of the platform and the test campaign in this document are based on the report written by Allen and Fowler of the University of Maine in 2019.

17 WIND ENERGY↗

Bayesian analysis of (3 +1)⁢D relativistic nuclear dynamics with the RHIC beam energy scan data

This work presents a Bayesian inference study for relativistic heavy-ion collisions in the beam energy scan program at the BNL Relativistic Heavy-Ion Collider. The theoretical model simulates event-by-event (3+1)-dimensional [(3+1)⁢D] collision dynamics using hydrodynamics and hadronic transport theory. We analyze the model's 20-dimensional posterior distributions obtained using three model emulators with different accuracy and demonstrate the essential role of training an accurate model emulator in the Bayesian analysis. Our analysis provides robust constraints on the quark-gluon plasma's transport properties and various aspects of (3+1)⁢D relativistic nuclear dynamics. By running full model simulations with 100 parameter sets sampled from the posterior distribution, we make predictions for p T -differential observables and estimate their systematic theory uncertainty. Here, a sensitivity analysis is performed to elucidate how individual experimental observables respond to different model parameters, providing useful physics insights into the phenomenological model for heavy-ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Precision measurements of EFT parameters and BAO peak shifts for the Lyman- α forest

We present precision measurements of the bias parameters of the one-loop power spectrum model of the Lyman- α (Ly- α ) forest, derived within the effective field theory (EFT) of large-scale structure. We fit our model to the three-dimensional flux power spectrum measured from the ACCEL 2 hydrodynamic simulations. The EFT model fits the data with an accuracy of below 2% up to k = 2 h Mpc − 1 . Further, we analytically derive how nonlinearities in the three-dimensional clustering of the Ly- α forest introduce biases in measurements of the baryon acoustic oscillations (BAOs) scaling parameters in radial and transverse directions. From our EFT parameter measurements, we obtain a theoretical error budget of Δ α ∥ = − 0.2 % ( Δ α ⊥ = − 0.3 % ) for the radial (transverse) parameters at redshift z = 2.0 . This corresponds to a shift of − 0.3 % (0.1%) for the isotropic (anisotropic) distance measurements. We provide an estimate for the shift of the BAO peak for Ly- α -quasar cross-correlation measurements assuming analytical and simulation-based scaling relations for the nonlinear quasar bias parameters resulting in a shift of − 0.2 % ( − 0.1 % ) for the radial (transverse) dilation parameters, respectively. This analysis emphasizes the robustness of Ly- α forest BAO measurements to the theory modeling. We provide informative priors and an error budget for measuring the BAO feature—a key science driver of the currently observing Dark Energy Spectroscopic Instrument (DESI). Our work paves the way for full-shape cosmological analyses of Ly- α forest data from DESI and upcoming surveys such as the Prime Focus Spectrograph, WEAVE-QSO, and 4MOST. Published by the American Physical Society 2025

de Belsunce, Roger (ORCID:0000000336604028)↗

Energy transfer and scale dynamics in 2D and 3D laser-driven jets

We demonstrate a methodology for diagnosing the multiscale dynamics and energy transfer in complex HED flows with realistic driving and boundary conditions. The approach separates incompressible, compressible, and baropycnal contributions to energy scale-transfer and quantifies the direction of these transfers in (generalized) wavenumber space. We use this to compare the kinetic energy (KE) transfer across scales in simulations of 2D axisymmetric vs fully 3D laser-driven plasma jets. Using the FLASH code, we model a turbulent jet ablated from an aluminum cone target in the configuration outlined. We show that, in addition to its well known bias for underestimating hydrodynamic instability growth, 2D modeling suffers from significant spurious energization of the bulk flow by a turbulent upscale cascade. In 2D, this arises as vorticity and strain from instabilities near the jet's leading edge transfer KE upscale, sustaining a coherent circulation that helps propel the axisymmetric jet farther (⁠ ≈25% by 3.5 ns) and helps keep it collimated. In 3D, the coherent circulation and upscale KE transfer are absent. Here, the methodology presented here may also help with inter-model comparison and validation, including future modeling efforts to alleviate some of the 2D hydrodynamic artifacts highlighted in this study.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fusion burn-propagation simulations using the collisional and radiative particle-in-cell code TRIFORCE

The ability to accurately model burn propagation in inertial confinement fusion plasmas is crucial for advancing fusion energy research. This work presents enhancements to the triforce hybrid fluid-kinetic multiphysics code, focusing on its kinetic half, which employs the particle-in-cell (PIC) method with Monte Carlo collisions (MCC). We use a moment-preserving collision model that mitigates numerical noise, particularly in spherical geometries where particle weights vary significantly. Additionally, we refine the treatment of inverse bremsstrahlung to account for electron–ion collision frequency reductions in degenerate plasmas and incorporate a blackbody radiation source to enable realistic photon injection. These improvements enable the simulation of 1-dimensional (1D) spherical fusion burn propagation in deuterium–tritium plasmas. Benchmark comparisons with the hydra radiation-hydrodynamics code confirm that triforce accurately captures the dynamics of hot-spot expansion and burn propagation, demonstrating sensitivity to ignition thresholds consistent with theoretical models. Findings show the ignition cliff to be less steep in our work compared to radiation-hydrodynamic modeling. These results highlight the role of kinetic effects in fusion ignition physics and underscore the necessity of hybrid fluid-kinetic models for advancing predictive capabilities in high-energy-density plasma systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Toward a machine-guided approach to energetic material discovery

In this article, we trained a machine learning (ML) model to connect microstructural details of an energetic material formulation to its performance for the purpose of guiding the discovery of new explosive formulations. Our hypothesis was that the algorithm would robustly learn the training data and produce an accurate surrogate model. Specifically, the algorithm learned the relationship between details of the void size distribution (VSD), initiating shock pressure, and the energetic material performance. We used realistic constraints on the VSD and a range of cases were ingested by a physically informed reactive flow model working within a hydrodynamic solver running on high-performance computing resources. The ML algorithm produced a surrogate model that accurately predicted known test points around the parameter space. In addition to the utility of the model and the process used for its development, we noted interesting comparisons between what we, the authors—subject matter experts, would heuristically conclude from the training data and the surrogate model predictions. We detected nuanced details that were missed by the surrogate model; however, these details are not important to an energetic material formulator. We concluded that the algorithm did indeed robustly learn the training data and produce an accurate surrogate model. We further concluded that the surrogate model is a powerful tool to guide the formulator in the absence of subject matter experts and limited-access computing resources.

42 ENGINEERING↗

SPH modeling of biomass granular flow: Theoretical implementation and experimental validation

The commercialization of biomass-derived energy is impeded by flowability challenges arising from the feeding and handling of granular biomass materials in full-scale biorefineries. To overcome these obstacles, a robust and accurate model to simulate the flow of granular biomass is indispensable. However, conventional mesh-based numerical codes are limited by inherent mesh distortion in simulating large deformation that commonly occurs in granular biomass handling. Here, in this study, we propose a graphics processing unit (GPU)-accelerated meshless Smoothed Particle Hydrodynamics (SPH) code to model the flow of granular biomass materials. A modified void ratio-based mass conversation, a hybrid particle-to-particle/surface frictional boundary treatment, and a hypoplastic constitutive model are implemented. Four numerical examples, an elastic block sliding on inclined planes, sand column collapse, Angle of Repose, and axial compression tests for pine chips, were simulated using the developed SPH code. The results demonstrate good agreement between numerical predictions and analytical and experimental data for all four examples, validating the SPH code and increasing confidence that it can be applied to simulate more complex granular biomass handling processes, such as hopper feeding or auger conveyance.

09 BIOMASS FUELS↗

StaNdaRT: a repository of standardised test models and outputs for supernova radiative transfer

We present the first results of a comprehensive supernova (SN) radiative-transfer (RT) code-comparison initiative (StaNdaRT), where the emission from the same set of standardised test models is simulated by currently used RT codes. We ran a total of ten codes on a set of four benchmark ejecta models of Type Ia SNe. We consider two sub-Chandrasekhar-mass (M tot = 1.0 M ⊙ ) toy models with analytic density and composition profiles and two Chandrasekhar-mass delayed-detonation models that are outcomes of hydrodynamical simulations. We adopt spherical symmetry for all four models. The results of the different codes, including the light curves, spectra, and the evolution of several physical properties as a function of radius and time are provided in electronic form in a standard format via a public repository. We also include the detailed test model profiles and several Python scripts for accessing and presenting the input and output files. We also provide the code used to generate the toy models studied here. In this paper, we describe the test models, radiative-transfer codes, and output formats in detail, and provide access to the repository. We present example results of several key diagnostic features.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Dust supply to close binary systems

Binary systems can be born surrounded by circumbinary discs. The gaseous disc around either of the two stellar companions can have its life extended by the supply of mass arriving from the circumbinary disc. The objective of this study is to investigate the gravitational interactions exerted by a compact and eccentric binary system on the circumbinary and circumprimary discs, and the resulting transport of gas and solids between the disc components. We assume that the gas in the system behaves as a fluid, and we model its evolution by means of high-resolution hydrodynamical simulations. Dust grains are modelled as Lagrangian particles that interact with the gas and the stars. Our models indicate that significant fluxes of gas and dust proceed from the circumbinary disc towards the circumprimary disc. For the applied system parameters, grains of certain sizes are segregated outside the tidal gap generated by the stars. Consequently, the size distribution of the transported dust is not continuous, but presents a gap in the millimetre size range. In close binaries, the lifetime of an isolated circumprimary disc is found to be short, ~10 5 years, because of its low mass. However, because of the influx of gas from beyond the tidal gap, the disc around the primary star can survive much longer, ~10 6 years, as long as gas accretion from the circumbinary disc continues. The supply of solids and the extended lifetime of a circumbinary disc also aids in the possible formation of giant planets. Compared to close binary systems without a circumbinary disc, we expect a higher frequency of singleplanet or multiple-planet systems. Additionally, a planetesimal or debris belt can form in the proximity of the truncation radius of the circumprimary disc and/or around the location of the exterior edge of the tidal gap.

79 ASTRONOMY AND ASTROPHYSICS↗

FY2021 Improvements to the New CTH Code Verification & Validation Test Suite

Over the past few years, the CTH multiphysics hydrocode has overhauled its software quality and testing processes, implementing current best practices in software quality and building a robust V&V test suite comprised of traditional hydrocode verification problems, including ASC Tri-Lab Test Suite and Enhanced Tri-Lab Test Suite problems, as well as validation problems for some of CTH’s most frequently used equations of state, materials models, and other key capabilities. Substantial progress towards building this new test suite was made in FY19 and FY20. In FY21, the test suite has been expanded to include verification and validation tests of the Steinberg-Guinan-Lund (ST) viscoplastic model and the Johnson Cook (JFRAC) fracture model. Additionally, two new verification tests were added, covering hydrodynamics and high explosive (HE) modeling capabilities: the Kidder Gaussian density problem and the Escape of HE Products (EHEP) problem from the Tri-Lab Test Suite. This report discusses each of these test problems in detail. Verification test results are compared to analytic solutions. Validation test results are compared to experimental data. Wherever possible, convergence or mesh refinement studies are included. Additionally, while implementing the Kidder verification problem, a bug was identified that affects the use of tables to initialize pressure or density in 1D or 2D calculations. A brief discussion of the bug and its fix is included. CTH demonstrates good performance overall on the new test suite problems. Simulation results showed good agreement with analytic solutions for the Kidder problem, with convergence rates ranging between 1.8 and sub-linear, and relatively good agreement for the EHEP problem, though convergence rates for pressure and density were nearly 0. The ST and JFRAC strain rate loading verification tests show good agreement with analytic solutions. Likewise, CTH simulation results show good agreement with experimental validation data, including Taylor rod impact testing, for the materials tested. Future V&V work will focus on adding 2D and 3D versions of existing verification tests as well as adding validation tests of other frequently used capabilities such as other fracture models.

42 ENGINEERING↗

Climate projections over the Great Lakes Region: using two-way coupling of a regional climate model with a 3-D lake model

Abstract. Warming trends in the Laurentian Great Lakes and surrounding areas have been observed in recent decades, and concerns continue to rise about the pace and pattern of future climate change over the world's largest freshwater system. To date, most regional climate models used for Great Lakes projections either neglected the lake-atmosphere interactions or are only coupled with a 1-D column lake model to represent the lake hydrodynamics. This study presents a Great Lakes climate change projection that has employed the two-way coupling of a regional climate model with a 3-D lake model (GLARM) to resolve 3-D hydrodynamics essential for large lakes. Using the three carefully selected Coupled Model Intercomparison Project Phase 5 (CMIP5) general circulation models (GCMs), we show that the GLARM ensemble average substantially reduces surface air temperature and precipitation biases of the driving GCM ensemble average in present-day climate simulations. The improvements are not only displayed from an atmospheric perspective but are also evident in the accurate simulations of lake temperature and ice coverage. We further present the GLARM projected climate change for the mid-21st century (2030–2049) and the late 21st century (2080–2099) in the Representative Concentration Pathway (RCP) 4.5 and RCP 8.5 scenarios. Under RCP 8.5, the Great Lakes basin is projected to warm by 1.3–2.1 ∘C by the mid-21st century and 4.1–5.0 ∘C by the end of the century relative to the early century (2000–2019). Moderate mitigation (RCP 4.5) reduces the mid-century warming to 0.8–1.8 ∘C and late-century warming to 1.8–2.7 ∘C. Annual precipitation in GLARM is projected to increase for the entire basin, varying from 0 % to 13 % during the mid-century and from 9 % to 32 % during the late century in different scenarios and simulations. The most significant increases are projected in spring and fall when current precipitation is highest and a minimal increase in winter when it is lowest. Lake surface temperatures (LSTs) are also projected to increase across the five lakes in all of the simulations, but with strong seasonal and spatial variability. The most significant LST increases occur in Lakes Superior and Ontario. The strongest warming is projected in spring that persists into the summer, resulting from earlier and more intense stratification in the future. In addition, diminishing winter stratification in the future suggests the transition from dimictic lakes to monomictic lakes by the end of the century. In contrast, a relatively smaller increase in LSTs during fall and winter is projected with heat transfer to the deep water due to the strong mixing and energy required for ice melting. Correspondingly, the highest monthly mean ice cover is projected to reduce to 3 %–15 % and 10 %–40 % across the lakes by the end of the century in RCP 8.5 and RCP 4.5, respectively. In the coastal regions, ice duration is projected to decrease by up to 60 d.

Xue, Pengfei (ORCID:000000025702421X)↗