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At least 1,711 records · Page 95

Accelerating Radiation Computations for Dynamical Models With Targeted Machine Learning and Code Optimization

Abstract Atmospheric radiation is the main driver of weather and climate, yet due to a complicated absorption spectrum, the precise treatment of radiative transfer in numerical weather and climate models is computationally unfeasible. Radiation parameterizations need to maximize computational efficiency as well as accuracy, and for predicting the future climate many greenhouse gases need to be included. In this work, neural networks (NNs) were developed to replace the gas optics computations in a modern radiation scheme (RTE+RRTMGP) by using carefully constructed models and training data. The NNs, implemented in Fortran and utilizing BLAS for batched inference, are faster by a factor of 1–6, depending on the software and hardware platforms. We combined the accelerated gas optics with a refactored radiative transfer solver, resulting in clear‐sky longwave (shortwave) fluxes being 3.5 (1.8) faster to compute on an Intel platform. The accuracy, evaluated with benchmark line‐by‐line computations across a large range of atmospheric conditions, is very similar to the original scheme with errors in heating rates and top‐of‐atmosphere radiative forcings typically below 0.1 K day −1 and 0.5 W m −2 , respectively. These results show that targeted machine learning, code restructuring techniques, and the use of numerical libraries can yield material gains in efficiency while retaining accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

60 APPLIED LIFE SCIENCES↗

Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signalling

Canonical fibroblast growth factors (FGFs) activate FGF receptors (FGFRs) through paracrine or autocrine mechanisms in a process that requires cooperation with heparan sulfate proteoglycans, which function as co-receptors for FGFR activation. By contrast, endocrine FGFs (FGF19, FGF21 and FGF23) are circulating hormones that regulate critical metabolic processes in a variety of tissues. FGF19 regulates bile acid synthesis and lipogenesis, whereas FGF21 stimulates insulin sensitivity, energy expenditure and weight loss. Endocrine FGFs signal through FGFRs in a manner that requires klothos, which are cell-surface proteins that possess tandem glycosidase domains. Here we describe the crystal structures of free and ligand-bound β-klotho extracellular regions that reveal the molecular mechanism that underlies the specificity of FGF21 towards β-klotho and demonstrate how the FGFR is activated in a klotho-dependent manner. β-Klotho serves as a primary ‘zip code’-like receptor that acts as a targeting signal for FGF21, and FGFR functions as a catalytic subunit that mediates intracellular signalling. Our structures also show how the sugar-cutting enzyme glycosidase has evolved to become a specific receptor for hormones that regulate metabolic processes, including the lowering of blood sugar levels. Lastly, we describe an agonistic variant of FGF21 with enhanced biological activity and present structural insights into the potential development of therapeutic agents for diseases linked to endocrine FGFs.

59 BASIC BIOLOGICAL SCIENCES↗

Milestone in predicting core plasma turbulence: successful multi-channel validation of the gyrokinetic code GENE

On the basis of several recent breakthroughs in fusion research, many activities have been launched around the world to develop fusion power plants on the fastest possible time scale. In this context, high-fidelity simulations of the plasma behavior on large supercomputers provide one of the main pathways to accelerating progress by guiding crucial design decisions. When it comes to determining the energy confinement time of a magnetic confinement fusion device, which is a key quantity of interest, gyrokinetic turbulence simulations are considered the approach of choice – but the question, whether they are really able to reliably predict the plasma behavior is still open. The present study addresses this important issue by means of careful comparisons between state-of-the-art gyrokinetic turbulence simulations with the GENE code and experimental observations in the ASDEX Upgrade tokamak for an unprecedented number of simultaneous plasma observables.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multi-beam X-ray ptychography using coded probes for rapid non-destructive high resolution imaging of extended samples

Imaging large areas of a sample non-destructively and with high resolution is of great interest for both science and industry. For scanning coherent X-ray diffraction microscopy, i. e., ptychography, the achievable scan area at a given spatial resolution is limited by the coherent photon flux of modern X-ray sources. Multibeam X-ray ptychography can improve the scanning speed by scanning the sample with several parallel mutually incoherent beams, e. g., generated by illuminating multiple focusing optics in parallel by a partially coherent beam. The main difficulty with this scheme is the robust separation of the superimposed signals from the different beams, especially when the beams and the illuminated sample areas are quite similar. We overcome this difficulty by encoding each of the probing beams with its own X-ray phase plate. This helps the algorithm to robustly reconstruct the multibeam data. We compare the coded multibeam scans to uncoded multibeam and single beam scans, demonstrating the enhanced performance on a microchip sample with regular and repeating structures.

47 OTHER INSTRUMENTATION↗

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

97 MATHEMATICS AND COMPUTING↗

The FLUKA code: Overview and new developments

The FLUKA Monte Carlo Radiation Transport and Interaction code package is widely used to simulate the interaction of particles with matter in a variety of fields, including high energy physics, space radiation, medical applications, radiation protection and shielding assessments, accelerator studies, astrophysical studies and well logging. This paper gives a brief overview of the FLUKA program and describes recent developments, in particular, improvements in the modelling of particle interactions and transport are described in detail. In addition, an overview of selected applications is given.

Ballarini, Francesca↗

Status of GPU capabilities within the Shift Monte Carlo radiation transport code

Shift is a general-purpose Monte Carlo (MC) radiation transport code for fission, fusion, and national security applications. Shift has been adapted to efficiently run on GPUs in order to leverage leadership-class supercomputers. This work presents Shift’s current GPU capabilities. These include core radiation transport capabilities for eigenvalue and fixed-source simulations, and support for non-uniform domain decomposition, Doppler broadening, free-gas elastic scattering, general-purpose geometry, hybrid MC/deterministic transport, and depletion. Transport results demonstrate a 2–5× GPU-to-CPU speedup on a per-node basis for an eigenvalue problem on the Frontier supercomputer and a 28× speedup for a fixed-source problem on the Summit supercomputer.

Biondo, Elliott [ORNL] (ORCID:0000000290881360)↗

Classical trajectory Monte Carlo code for simulating ion beam focusing or defocusing with magnetic elements modeled as current loops or current lines

A computational tool is described that can be used for designing magnetic focusing or defocusing systems. A fully three-dimensional classical trajectory Monte Carlo simulation has been developed. Ion trajectories are simulated in the presence of magnetic elements that can be modeled as any combination of current loops and current lines. Each current loop or line may be located anywhere in the system and oriented along any of the three coordinate axes. The configuration need not be axisymmetric. The solutions are obtained using normalized parameters, which can be used for easily scaling the results. Examples are provided of the utility of the code.

43 PARTICLE ACCELERATORS↗

Spin wave based parallel logic operations for binary data coded with domain walls

We numerically investigate the feasibility of spin wave (SW) based parallel logic operations, where the phase of SW packet (SWP) is exploited as a state variable and the phase shift caused by the interaction with domain wall (DW) is utilized as a logic inversion functionality. A designed functional element consists of parallel ferromagnetic nanowires (6 nm-thick, 36 nm-width, 5120 nm-length, and 200 nm separation) with the perpendicular magnetization and sub-μm scale overlaid conductors. The logic outputs for binary data, coded with the existence (“1”) or absence (“0”) of the DW, are inductively read out from interferometric aspect of the superposed SWPs, one of them propagating through the stored data area. A practical exclusive-or operation, based on 2π periodicity in the phase logic, is demonstrated for the individual nanowire with an order of different output voltage V{sub out}, depending on the logic output for the stored data. The inductive output from the two nanowires exhibits well defined three different signal levels, corresponding to the information distance (Hamming distance) between 2-bit data stored in the multiple nanowires.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Pressure distribution based optimization of phase-coded acoustical vortices

Based on the acoustic radiation of point source, the physical mechanism of phase-coded acoustical vortices is investigated with formulae derivations of acoustic pressure and vibration velocity. Various factors that affect the optimization of acoustical vortices are analyzed. Numerical simulations of the axial, radial, and circular pressure distributions are performed with different source numbers, frequencies, and axial distances. The results prove that the acoustic pressure of acoustical vortices is linearly proportional to the source number, and lower fluctuations of circular pressure distributions can be produced for more sources. With the increase of source frequency, the acoustic pressure of acoustical vortices increases accordingly with decreased vortex radius. Meanwhile, increased vortex radius with reduced acoustic pressure is also achieved for longer axial distance. With the 6-source experimental system, circular and radial pressure distributions at various frequencies and axial distances have been measured, which have good agreements with the results of numerical simulations. The favorable results of acoustic pressure distributions provide theoretical basis for further studies of acoustical vortices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A model code for the radiative theta pinch

A model for the theta pinch is presented with three modelled phases of radial inward shock phase, reflected shock phase, and a final pinch phase. The governing equations for the phases are derived incorporating thermodynamics and radiation and radiation-coupled dynamics in the pinch phase. A code is written incorporating correction for the effects of transit delay of small disturbing speeds and the effects of plasma self-absorption on the radiation. Two model parameters are incorporated into the model, the coupling coefficient f between the primary loop current and the induced plasma current and the mass swept up factor f{sub m}. These values are taken from experiments carried out in the Chulalongkorn theta pinch.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Analysis of stimulated Raman backscatter and stimulated Brillouin backscatter in experiments performed on SG-III prototype facility with a spectral analysis code

Experiments about the observations of stimulated Raman backscatter (SRS) and stimulated Brillouin backscatter (SBS) in Hohlraum were performed on Shenguang-III (SG-III) prototype facility for the first time in 2011. In this paper, relevant experimental results are analyzed for the first time with a one-dimension spectral analysis code, which is developed to study the coexistent process of SRS and SBS in Hohlraum plasma condition. Spectral features of the backscattered light are discussed with different plasma parameters. In the case of empty Hohlraum experiments, simulation results indicate that SBS, which grows fast at the energy deposition region near the Hohlraum wall, is the dominant instability process. The time resolved spectra of SRS and SBS are numerically obtained, which agree with the experimental observations. For the gas-filled Hohlraum experiments, simulation results show that SBS grows fastest in Au plasma and amplifies convectively in C{sub 5}H{sub 12} gas, whereas SRS mainly grows in the high density region of the C{sub 5}H{sub 12} gas. Gain spectra and the spectra of backscattered light are simulated along the ray path, which clearly show the location where the intensity of scattered light with a certain wavelength increases. This work is helpful to comprehend the observed spectral features of SRS and SBS. The experiments and relevant analysis provide references for the ignition target design in future.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Overcoming inherent magnetic instability, preventing spin canting and magnetic coding in an assembly of ferrimagnetic nanoparticles

The authors find that for mechanically milled Ni{sub 0.5}Zn{sub 0.5}Fe{sub 2}O{sub 4} (∼10 nm), the mechanical strain induced enhancement of anisotropy energy helps to retain stable magnetic order. The reduction of magnetization can be prevented by keeping the cation distribution of nanometric ferrites at its equilibrium ratio. Moreover, the sample can be used in coding, storing, and retrieving of binary bit (“0” and “1”) through magnetic field change.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Three dimensional nonlinear simulations of edge localized modes on the EAST tokamak using BOUT++ code

Experimental measurements of edge localized modes (ELMs) observed on the EAST experiment are compared to linear and nonlinear theoretical simulations of peeling-ballooning modes using the BOUT++ code. Simulations predict that the dominant toroidal mode number of the ELM instability becomes larger for lower current, which is consistent with the mode structure captured with visible light using an optical CCD camera. The poloidal mode number of the simulated pressure perturbation shows good agreement with the filamentary structure observed by the camera. The nonlinear simulation is also consistent with the experimentally measured energy loss during an ELM crash and with the radial speed of ELM effluxes measured using a gas puffing imaging diagnostic.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Development of a Monte Carlo code for the data analysis of the {sup 18}F(p,α){sup 15}O reaction at astrophysical energies

Novae are astrophysical events (violent explosion) occurring in close binary systems consisting of a white dwarf and a main-sequence star or a star in a more advanced stage of evolution. They are called 'narrow systems' because the two components interact with each other: there is a process of mass exchange with resulting in the transfer of matter from the companion star to the white dwarf, leading to the formation of this last of the so-called accretion disk, rich mainly of hydrogen. Over time, more and more material accumulates until the pressure and the temperature reached are sufficient to trigger nuclear fusion reactions, rapidly converting a large part of the hydrogen into heavier elements. The products of 'hot hydrogen burning' are then placed in the interstellar medium as a result of violent explosions. Studies on the element abundances observed in these events can provide important information about the stages of evolution stellar. During the outbursts of novae some radioactive isotopes are synthesized: in particular, the decay of short-lived nuclei such as {sup 13}N and {sup 18}F with subsequent emission of gamma radiation energy below 511 keV. The gamma rays from products electron-positron annihilation of positrons emitted in the decay of {sup 18}F are the most abundant and the first observable as soon as the atmosphere of the nova starts to become transparent to gamma radiation. Hence the importance of the study of nuclear reactions that lead both to the formation and to the destruction of {sup 18}F. Among these, the {sup 18}F(p,α){sup 15}O reaction is one of the main channels of destruction. This reaction was then studied at energies of astrophysical interest. The experiment done at Riken, Japan, has as its objective the study of the {sup 18}F(p,α){sup 15}O reaction, using a beam of {sup 18}F produced at CRIB, to derive important information about the phenomenon of novae. In this paper we present the experimental technique and the Monte Carlo code developed to be used in the data analysis process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Magnetic enhancement and coding in mechanosynthesized Ni{sub 0.3}Zn{sub 0.7}Fe{sub 2}O{sub 4} nanoparticles

The nanosized Ni{sub 0.3}Zn{sub 0.7}Fe{sub 2}O{sub 4} (∼ 15 nm) has been synthesized by high energy ball milling of the bulk powder sample. The sample has been characterized by powder x-ray diffraction, field emission and transmission electron microscopic and dc magnetic measurement techniques. The dc magnetic measurement on the sample indicates that the sample exhibit enhancement of magnetization compared to its counterparts synthesized by chemical methods. Moreover, the system stores the memory of either decrease or increase of magnetic field enabling a magnetic coding of “0” and “1” which can be profitably used in magnetic storage and sensing devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗