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At least 1,171 records · Page 65

Covariance matrices for variance-suppressed simulations

ABSTRACT Cosmological N-body simulations provide numerical predictions of the structure of the Universe against which to compare data from ongoing and future surveys, but the growing volume of the Universe mapped by surveys requires correspondingly lower statistical uncertainties in simulations, usually achieved by increasing simulation sizes at the expense of computational power. It was recently proposed to reduce simulation variance without incurring additional computational costs by adopting fixed-amplitude initial conditions. This method has been demonstrated not to introduce bias in various statistics, including the two-point statistics of galaxy samples typically used for extracting cosmological parameters from galaxy redshift survey data, but requires us to revisit current methods for estimating covariance matrices of clustering statistics for simulations. In this work, we find that it is not trivial to construct covariance matrices analytically for fixed-amplitude simulations, but we demonstrate that ezmock (Effective Zel’dovich approximation mock catalogue), the most efficient method for constructing mock catalogues with accurate two- and three-point statistics, provides reasonable covariance matrix estimates for such simulations. We further examine how the variance suppression obtained by amplitude-fixing depends on three-point clustering, small-scale clustering, and galaxy bias, and propose intuitive explanations for the effects we observe based on the ezmock bias model.

79 ASTRONOMY AND ASTROPHYSICS↗

Persistent Octrees for Parallel Mesh Refinement Through Non-Volatile Byte-Addressable Memory

We report that octree-based mesh adaptation has enabled simulations of complex physical phenomena. Existing meshing algorithms were proposed with the assumption that computer memory is volatile. Consequently, for failure recovery, the in-core algorithms need to save memory states as snapshots with slow file I/Os. The out-of-core algorithms store octants on disks for persistence. However, neither of them was designed to leverage unique characteristics of non-volatile byte-addressable memory (NVBM). In this paper, we propose a novel data structure Distributed Persistent Merged octree (DPM-octree) for both meshing and in-memory storage of persistent octrees using NVBM. It is a multi-version data structure and can recover from failures using its earlier persistent version stored in NVBM. In addition, we design a feature-directed sampling approach to help dynamically transform the DPM-octree layout for reducing NVBM-induced memory write latency. DPM-octree uses parity trees which are created using erasure coding and stored in NVBM to support low-latency in-memory octant recovery after data loss. DPM-octree has been successfully integrated with Gerris software for simulation of fluid dynamics. Finally, our experimental results with real-world scientific workloads show that DPM-octree scales up to 1.1 billion mesh elements with 1000 processors on the Titan supercomputer.

97 MATHEMATICS AND COMPUTING↗

Using computer graphics to enhance astronaut and systems safety

Computer graphics is being employed at the NASA Johnson Space Center as a tool to perform rapid, efficient and economical analyses for man-machine integration, flight operations development and systems engineering. The Operator Station Design System (OSDS), a computer-based facility featuring a highly flexible and versatile interactive software package, PLAID, is described. This unique evaluation tool, with its expanding data base of Space Shuttle elements, various payloads, experiments, crew equipment and man models, supports a multitude of technical evaluations, including spacecraft and workstation layout, definition of astronaut visual access, flight techniques development, cargo integration and crew training. As OSDS is being applied to the Space Shuttle, Orbiter payloads (including the European Space Agency's Spacelab) and future space vehicles and stations, astronaut and systems safety are being enhanced. Typical OSDS examples are presented. By performing physical and operational evaluations during early conceptual phases. supporting systems verification for flight readiness, and applying its capabilities to real-time mission support, the OSDS provides the wherewithal to satisfy a growing need of the current and future space programs for efficient, economical analyses.

Computer Simulation↗

Automatic programming of simulation models

The concepts of software engineering were used to improve the simulation modeling environment. Emphasis was placed on the application of an element of rapid prototyping, or automatic programming, to assist the modeler define the problem specification. Then, once the problem specification has been defined, an automatic code generator is used to write the simulation code. The following two domains were selected for evaluating the concepts of software engineering for discrete event simulation: manufacturing domain and a spacecraft countdown network sequence. The specific tasks were to: (1) define the software requirements for a graphical user interface to the Automatic Manufacturing Programming System (AMPS) system; (2) develop a graphical user interface for AMPS; and (3) compare the AMPS graphical interface with the AMPS interactive user interface.

Schroer, Bernard J.↗

Sorption Modeling and Verification for Off-Gas Treatment

This project was successfully executed to provide valuable adsorption data and improve a comprehensive model developed in previous work by the authors. Data obtained were used in an integrated computer program to predict the behavior of adsorption columns. The model is supported by experimental data and has been shown to predict capture of off gas similar to that evolving during the reprocessing of nuclear waste. The computer program structure contains (a) equilibrium models of off-gases with the adsorbate; (b) mass-transfer models to describe off-gas mass transfer to a particle, diffusion through the pores of the particle, and adsorption on the active sites of the particle; and (c) incorporation of these models into fixed bed adsorption modeling, which includes advection through the bed. These models are being connected with the MOOSE (Multiphysics Object-Oriented Simulation Environment) software developed at the Idaho National Laboratory through DGOSPREY (Discontinuous Galerkin Off-gas SeParation and REcoverY) computer codes developed in this project. Experiments for iodine and water adsorption have been conducted on reduced silver mordenite (Ag0Z) for single layered particles. Adsorption apparatuses have been constructed to execute these experiments over a useful range of conditions for temperatures ranging from ambient to 250°C and water dew points ranging from -69 to 19°C. Experimental results were analyzed to determine mass transfer and diffusion of these gases into the particles and to determine which models best describe the single and binary component mass transfer and diffusion processes. The experimental results were also used to demonstrate the capabilities of the comprehensive models developed to predict single-particle adsorption and transients of the adsorption-desorption processes in fixed beds. Models for adsorption and mass transfer have been developed to mathematically describe adsorption kinetics and transport via diffusion and advection processes. These models were built on a numerical framework for solving conservation law problems in one-dimensional geometries such as spheres, cylinders, and lines. Coupled with the framework are specific models for adsorption in commercial adsorbents, such as zeolites and mordenites. Utilizing this modeling approach, the authors were able to accurately describe and predict adsorption kinetic data obtained from experiments at a variety of different temperatures and gas phase concentrations. A demonstration of how these models, and framework, can be used to simulate adsorption in fixed- bed columns is provided. The CO 2 absorption work involved modeling with supportive experimental information. A dynamic model was developed to simulate CO 2 absorption using high alkaline content water solutions. The model is based upon transient mass and energy balances for chemical species commonly present in CO 2 absorption. A computer code was developed to implement CO 2 absorption with a chemical reaction model. Experiments were conducted in a laboratory scale column to determine the model parameters. The influence of geometric parameters and operating variables on CO 2 absorption was studied over a wide range of conditions. Continuing work could employ the model to control column operation and predict the absorption behavior under various input conditions and other prescribed experimental perturbations. The value of the validated models and numerical frameworks developed in this project is that they can be used to predict the sorption behavior of off-gas evolved during the reprocessing of nuclear waste and thus reduce the cost of the experiments. They can also be used to design sorption processes based on concentration limits and flow-rates determined at the plant level.

42 ENGINEERING↗

The LSST DESC data challenge 1: generation and analysis of synthetic images for next-generation surveys

Data Challenge 1 (DC1) is the first synthetic data set produced by the Rubin Observatory Legacy Survey of Space and Time (LSST) Dark Energy Science Collaboration (DESC). DC1 is designed to develop and validate data reduction and analysis and to study the impact of systematic effects that will affect the LSST data set. DC1 is comprised of r -band observations of 40 deg 2 to 10 yr LSST depth. In this paper, we present each stage of the simulation and analysis process: (a) generation, by synthesizing sources from cosmological N -body simulations in individual sensor-visit images with different observing conditions; (b) reduction using a development version of the LSST Science Pipelines; and (c) matching to the input cosmological catalogue for validation and testing. We verify that testable LSST requirements pass within the fidelity of DC1. We establish a selection procedure that produces a sufficiently clean extragalactic sample for clustering analyses and we discuss residual sample contamination, including contributions from inefficiency in star–galaxy separation and imperfect deblending. We compute the galaxy power spectrum on the simulated field and conclude that: (i) survey properties have an impact of 50 per cent of the statistical uncertainty for the scales and models used in DC1; (ii) a selection to eliminate artefacts in the catalogues is necessary to avoid biases in the measured clustering; and (iii) the presence of bright objects has a significant impact (2σ–6σ) in the estimated power spectra at small scales (ℓ > 1200), highlighting the impact of blending in studies at small angular scales in LSST.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effects of stratification on overshooting and waves atop the convective core of M ⊙ main-sequence stars

As a massive star evolves along the main sequence, its core contracts, leaving behind a stable stratification in helium. We simulate two-dimensional convection in the core at three different stages of evolution of a $5\,\mathrm{ M}_{\odot }$ star, with three different stratifications in helium atop the core. We study the propagation of internal gravity waves in the stably stratified envelope, along with the overshooting length of convective plumes above the convective boundary. We find that the stratification in helium in evolved stars hinders radial motions and effectively shields the radiative envelope against plume penetration. This prevents convective overshooting from being an efficient mixing process in the radiative envelope. In addition, internal gravity waves are less excited in evolved models compared to the zero-age-main-sequence model, and are also more damped in the stratified region above the core. As a result, the wave power is several orders of magnitude lower in mid- and terminal-main-sequence models compared to zero-age-main-sequence stars.

79 ASTRONOMY AND ASTROPHYSICS↗

Long-lived neutron-star remnants from asymmetric binary neutron star mergers: element formation, kilonova signals and gravitational waves

We present 3D general-relativistic neutrino-radiation hydrodynamics simulations of two asymmetric binary neutron star mergers producing long-lived neutron stars remnants and spanning a fraction of their cooling time scale. The mergers are characterized by significant tidal disruption with neutron rich material forming a massive disc around the remnant. The latter develops one-armed dynamics that is imprinted in the emitted kilo-Hertz gravitational waves. Angular momentum transport to the disc is initially driven by spiral-density waves and enhanced by turbulent viscosity and neutrino heating on longer timescales. The mass outflows are composed by neutron-rich dynamical ejecta of mass ∼10 −3 –10 −2 M ⊙ followed by a persistent spiral-wave/neutrino-driven wind of ≳ 10 −2 M ⊙ with material spanning a wide range of electron fractions, ∼0.1–0.55. Dynamical ejecta (winds) have fast velocity tails up to ∼0.8 (∼0.4) c. The outflows are further evolved to days timescale using 2D ray-by-ray radiation-hydrodynamics simulations that include an online nuclear network. We find complete r-process yields and identify the production of 56 Ni and the subsequent decay chain to 56 Co and 56 Fe. Synthetic kilonova light curves predict an extended (near-) infrared peak a few days postmerger originating from r-process in the neutron-rich/high-opacity ejecta and UV/optical peaks at a few hours (ten minutes) postmerger originating from weak r-process (free-neutron decay) in the faster ejecta components. Additionally, the fast tail of tidal origin generates kilonova afterglows potentially detectable in radio and X band on a few to ten years time scale. Quantitative effects originating from the tidal disruption merger dynamics are reflected in the multimessenger emissions.

abundances↗

SU-F-BRD-16: Relative Biological Effectiveness of Double-Strand Break Induction for Modeling Cell Survival in Pristine Proton Beams of Different Dose-Averaged Linear Energy Transfers

Purpose: High throughput in vitro experiments assessing cell survival following proton radiation indicate that both the alpha and the beta parameters of the linear quadratic model increase with increasing proton linear energy transfer (LET). We investigated the relative biological effectiveness (RBE) of double-strand break (DSB) induction as a means of explaining the experimental results. Methods: Experiments were performed with two lung cancer cell lines and a range of proton LET values (0.94 – 19.4 keV/µm) using an experimental apparatus designed to irradiate cells in a 96 well plate such that each column encounters protons of different dose-averaged LET (LETd). Traditional linear quadratic survival curve fitting was performed, and alpha, beta, and RBE values obtained. Survival curves were also fit with a model incorporating RBE of DSB induction as the sole fit parameter. Fitted values of the RBE of DSB induction were then compared to values obtained using Monte Carlo Damage Simulation (MCDS) software and energy spectra calculated with Geant4. Other parameters including alpha, beta, and number of DSBs were compared to those obtained from traditional fitting. Results: Survival curve fitting with RBE of DSB induction yielded alpha and beta parameters that increase with proton LETd, which follows from the standard method of fitting; however, relying on a single fit parameter provided more consistent trends. The fitted values of RBE of DSB induction increased beyond what is predicted from MCDS data above proton LETd of approximately 10 keV/µm. Conclusion: In order to accurately model in vitro proton irradiation experiments performed with high throughput methods, the RBE of DSB induction must increase more rapidly than predicted by MCDS above LETd of 10 keV/µm. This can be explained by considering the increased complexity of DSBs or the nature of intra-track pairwise DSB interactions in this range of LETd values. NIH Grant 2U19CA021239-35.

60 APPLIED LIFE SCIENCES↗

Tidal disruption discs formed and fed by stream–stream and stream–disc interactions in global GRHD simulations

When a star passes close to a supermassive black hole (BH), the BH’s tidal forces rip it apart into a thin stream, leading to a tidal disruption event (TDE). In this work, we study the post-disruption phase of TDEs in general relativistic hydrodynamics (GRHD) using our GPU-accelerated code h-amr. We carry out the first grid-based simulation of a deep-penetration TDE (β = 7) with realistic system parameters: a black hole-to-star mass ratio of 10 6 , a parabolic stellar trajectory, and a non-zero BH spin. We also carry out a simulation of a tilted TDE whose stellar orbit is inclined relative to the BH midplane. We show that for our aligned TDE, an accretion disc forms due to the dissipation of orbital energy with ~20 percent of the infalling material reaching the BH. The dissipation is initially dominated by violent self-intersections and later by stream–disc interactions near the pericentre. The self-intersections completely disrupt the incoming stream, resulting in five distinct self-intersection events separated by approximately 12 h and a flaring in the accretion rate. We also find that the disc is eccentric with mean eccentricity e ≈ 0.88. For our tilted TDE, we find only partial self-intersections due to nodal precession near pericentre. Although these partial intersections eject gas out of the orbital plane, an accretion disc still forms with a similar accreted fraction of the material to the aligned case. These results have important implications for disc formation in realistic tidal disruptions. For instance, the periodicity in accretion rate induced by the complete stream disruption may explain the flaring events from Swift J1644+57.

79 ASTRONOMY AND ASTROPHYSICS↗

A Mechanism-Based Approach to Predict the Relative Biological Effectiveness of Protons and Carbon Ions in Radiation Therapy

Purpose: The physical and potential biological advantages of proton and carbon ions have not been fully exploited in radiation therapy for the treatment of cancer. In this work, an approach to predict proton and carbon ion relative biological effectiveness (RBE) in a representative spread-out Bragg peak (SOBP) is derived using the repair-misrepair-fixation (RMF) model. Methods and Materials: Formulas linking dose-averaged linear-quadratic parameters to DSB induction and processing are derived from the RMF model. The Monte Carlo Damage Simulation (MCDS) software is used to quantify the effects of radiation quality on the induction of DNA double-strand breaks (DSB). Trends in parameters {alpha} and {beta} for clinically relevant proton and carbon ion kinetic energies are determined. Results: Proton and carbon ion RBE are shown to increase as particle energy, dose, and tissue {alpha}/{beta} ratios decrease. Entrance RBE is {approx}1.0 and {approx}1.3 for protons and carbon ions, respectively. For doses in the range of 0.5 to 10 Gy, proton RBE ranges from 1.02 (proximal edge) to 1.4 (distal edge). Over the same dose range, the RBE for carbon ions ranges from 1.5 on the proximal edge to 6.7 on the distal edge. Conclusions: The proposed approach is advantageous because the RBE for clinically relevant particle distributions is guided by well-established physical and biological (track structure) considerations. The use of an independently tested Monte Carlo model to predict the effects of radiation quality on DSB induction also minimizes the number of ad hoc biological parameters that must be determined to predict RBE. Large variations in predicted RBE across an SOBP may produce undesirable biological hot and cold spots. These results highlight the potential for the optimization of physical dose for a uniform biological effect.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

OpenUniverse2024: a shared, simulated view of the sky for the next generation of cosmological surveys

The OpenUniverse2024 simulation suite is a cross-collaboration effort to produce matched simulated imaging for multiple surveys as they would observe a common simulated sky. Both the simulated data and associated tools used to produce it are intended to uniquely enable a wide range of studies to maximize the science potential of the next generation of cosmological surveys. We have produced simulated imaging for approximately 70 deg 2 of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) Wide-Fast-Deep survey and the Nancy Grace Roman Space Telescope High-Latitude Wide-Area Survey, as well as overlapping versions of the ELAIS-S1 Deep-Drilling Field for LSST and the High-Latitude Time-Domain Survey for Roman. OpenUniverse2024 includes (i) an early version of the updated extragalactic model called Diffsky, which substantially improves the realism of optical and infrared photometry of objects, compared to previous versions of these models; (ii) updated transient models that extend through the wavelength range probed by Roman and Rubin; and (iii) improved survey, telescope, and instrument realism based on up-to-date survey plans and known properties of the instruments. It is built on a new and updated suite of simulation tools that improves the ease of consistently simulating multiple observatories viewing the same sky. The approximately 400 TB of synthetic survey imaging and simulated universe catalogs are publicly available, and we preview some scientific uses of the simulations.

large-scale structure of Universe↗

Metabolic skinflint or spendthrift? Insights into ground sloth integument and thermophysiology revealed by biophysical modeling and clumped isotope paleothermometry

Abstract Remains of megatheres have been known since the 18th -century and were among the first megafaunal vertebrates to be studied. While several examples of preserved integument show a thick coverage of fur for smaller ground sloths living in cold climates such as Mylodon and Nothrotheriops , comparatively very little is known about megathere skin. Assuming a typical placental mammal metabolism, it was previously hypothesized that megatheres would have had little-to-no fur as they achieved giant body sizes. Here the “hairless model of integument” is tested using geochemical analyses to estimate body temperature to generate novel models of ground sloth metabolism, fur coverage, and paleoclimate with Niche Mapper software. The simulations assuming metabolic activity akin to those of modern xenarthrans suggest that sparse fur coverage would have resulted in cold stress across most latitudinal ranges inhabited by extinct ground sloths. Specifically, Eremotherium predominantly required dense 10 mm fur with implications for seasonal changes of coat depth in northernmost latitudes and sparse fur in the tropics; Megatherium required dense 30 mm fur year-round in its exclusive range of cooler, drier climates; Mylodon and Nothrotheriops required dense 10–50 mm fur to avoid thermal stress, matching the integument remains of both genera, and further implying the use of behavioral thermoregulation. Moreover, clumped isotope paleothermometry data from the preserved teeth of four genera of ground sloth yielded reconstructed body temperatures lower than those previously reported for large terrestrial mammals (29 ± 2°–32 ± 3° C). This combination of low metabolisms and thick fur allowed ground sloths to inhabit various environments.

Deak, Michael D.↗

Mechanical Testing of Innovated Composite Polymer Material for using in Manufacture of Railway Sleepers

Faculty of Engineering at Shoubra has been funded to start a project for manufacturing railway sleepers from plastic wastes and iron slag to replace imported wooden sleepers. In this paper, performance of wooden sleepers in tracks of Egyptian Railways, including high cost and material defects as well as reasons to find out a new sleeper will be presented. Previous studies for using composite materials in manufacturing railway sleepers are illustrated. Mechanical testing has been carried out to determine the important properties of the new mixture; hence results are compared with the minimum requirements of the international railway standards. Linear analysis has been conducted using 3D-SAP2000 software to simulate the actual performance of the proposed sleeper. It is found that the testing results are larger than the required values. Thus; it is concluded that the tested material is effective and adequate to be used in manufacture of railway sleepers.

36 MATERIALS SCIENCE↗

An efficient three-dimensional rhizosphere modeling capability to study the effect of root system architecture on soil water and reactive transport

This research was to develop a rhizosphere modeling capability for plant-soil interactions by integrating water and ion uptake and release from three dimensional (3D) root systems and 3D variably saturated flow and multicomponent reactive transport in soil. We combined open source software for simulating plant and soil interactions with parallel processing computational technologies to address highly-resolved root system architecture and soil hydrobiogeochemical processes. Simulation capability was demonstrated on Brachypodium distachyon . Our demonstration problem showed that availability of water and plant nutrients is controlled by the interplay between 1) transpiration-driven cycles of water uptake, root zone saturation and desaturation; 2) sorption and desorption via competitive ion exchange; 3) buildup of ions not taken up during kinetic uptake of nutrients/ions from pore water; and 4) advection, dispersion, and diffusion of ions in the soil. The uptake of water and ions by individual roots leads to dynamic, local gradients in ion concentrations. The resulting higher solution ionic strength can lead to increasing sorption of K+ and NH4+ on the soil exchange sites, despite their preferential absorption by roots. The modeling framework makes it possible to explore alternative conceptual models and improve the understanding of the biogeochemical and physical environment within the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗

Sustain: An experimental test bed for building energy simulation

Current building energy simulation technology requires extensive labor, time and expertise to create building energy models, substantial computational time for accurate simulations, and generates data in formats that make results difficult to interpret. These deficiencies can be ameliorated using modern graphical user interfaces and algorithms which take advantage of modern computer architectures and display capabilities. This paper describes a novel test bed environment which offers an interactive graphical interface, provides access to simulation modules that run at accelerated computational speeds, and presents new graphic visualization methods for the interpretation of simulation results. Its modular structure makes it suitable for use in early stage building design, for use as a research platform for the investigation of new simulation methods, and for use as a tool for teaching concepts of sustainable design. Improvements in the accuracy and execution speed of many of the simulation modules are based on the modification of advanced computer graphics rendering algorithms. Significant performance improvements are illustrated in several computationally expensive energy simulation modules.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗