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At least 1,351 records · Page 75

Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges

Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production have intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of ‘user-friendly’ biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically important plant species and can provide resources for application to precision breeding and natural product metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Logic in Memory Emulator

Logic in Memory Emulator (LiME) is a hardware/software tool specially designed for memory system evaluation and experiment. Emerging memories display a wide range of bandwidths, latencies, and capacities, making it challenging for the computer architect to navigate the design space of potential memory configurations, and for the application developer to assess performance implications of using such memories. With the LiME framework, architectural ideas can be prototyped in great detail yet with sufficient performance to support realistic evaluation on long running applications. LiME consists of two fundamental components: 1) the hardware and OS infrastructure for the emulator, and 2) a suite of benchmark applications to assist in characterizing the performance of current and future computer architectures. Some of the applications have been collected from other open source projects. Uses: Logging, replay and analysis of an application's memory behavior Evaluate impact of emerging memory technology on application performance. Emulate complex memory interactions in whole applications orders of magnitude faster than software simulation. Emulate acceleration hardware co-located with the memory subsystem. Features: Capture and log external memory accesses to a separate off-chip memory device without affecting application execution. Memory traces include the address, length, timestamp, and optionally the data for each transaction. Captured trace data can be saved to an SD card for off-line analysis. Configure a wide range of memory latencies in sub-nanosecond increments that encompass highbandwidth and storage class memories. Specify regions of interest (ROI) in applications to reduce the amount of trace data captured for analysis. Currently supports execution on Xilinx Zynq SoC which integrates an ARM processor with FPGA logic on a single device. Applications can be run under Linux or in bare metal mode on the ARM cores.

Jain, AbhishekK↗

WarpX: Delivering Unprecedented Particle-in-Cell Simulation Capability

Since 1939, more than 30 percent of all Nobel prizes in physics and four of the past 14 prizes in chemistry have been awarded for work with particle accelerators. These tools are now used to treat cancer and produce medical supplies, support research in applied fields such as pharmaceuticals, create microcircuits, and sterilize food—and the applications list continues to grow. However, the size of the facilities needed to house these machines—which are often dozens of kilometers long—has limited their future potential. Thus, researchers are motivated to create novel particle accelerator designs that provide new imaging capability but have a much smaller footprint. The Exascale Computing Project’s WarpX application captures the full complexity of the acceleration processes within plasma-based design, supporting the rapid and cost-efficient development of tens of thousands of new particle accelerators for various applications from improving human health to nuclear fusion reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Solar thermal power storage applications lead laboratory overview

The implementation of the applications elements of the thermal energy storage for Solar Thermal Applications program is described. The program includes the accelerated development of thermal storage technologies matched to solar thermal power system requirements and scheduled milestones. The program concentrates on storage development in the FY80 to 85 time period with emphasis on the more near-term solar thermal power system application.

Radosevich, L. G.↗

Electromagnetic and Engineering Design of a High-Current 15-MeV/u Cyclotron

The capability to produce high current, low loss, and extracted external ion beams presents an enabling technology for nuclear security, isotope production, and medical applications. We report on a novel, continuous-wave cyclotron for accelerating light ions with a charge-to-mass ratio of 1/2, which is designed for 1 mA maximum and 15 MeV/u energy. This article details the conceptual electromagnetic (EM) and engineering design including the 1.1 T sector magnets and 45 MHz, 200 kV radio frequency (RF) cavities. We discuss the cyclotron beam parameters with respect to potential commercial and industrial applications. The general concept and the accelerator’s layout are followed by a detailed EM design of magnets and RF cavities. Finally, practical engineering design considerations will be provided.

07 ISOTOPE AND RADIATION SOURCES↗

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗

Modeling and design of compact, permanent-magnet transport systems for highly divergent, broad energy spread laser-driven proton beams

Laser-driven (LD) ion acceleration has been explored in a newly constructed short focal length laser beamline at the BELLA petawatt facility (interaction point 2, iP2). For applications utilizing such LD ion beams, a beam transport system is required, which for reasons of compactness be ideally contained within 3 m. While they are generated from a micron-scale source, large divergence and energy spread of LD ion beams present a unique challenge to transporting them compared to beams from conventional accelerators. This study gives an overview of proposed compact transport designs using permanent magnets satisfying different requirements depending on the application for the iP2 laser beamline such as radiation biology, material science, and high-energy density science. These designs are optimized for different parameters such as energy spread and peak proton density according to the application’s need. The various designs consist solely of permanent magnet elements, which can provide high magnetic field gradients on a small footprint. While the field strengths are fixed, we have shown that the beam size is able to be tuned effectively by varying the placement of the magnets. The performance of each design was evaluated based on high-order particle tracking simulations of typical LD proton beams. We also examine the ability of certain configurations to tune and select beam energies, critical for specific applications. A more detailed investigation was carried out for a design to deliver 10 MeV LD accelerated ions for radiation biology applications. With these transport system designs, the iP2 laser beamline is ready to house various application experiments.

43 PARTICLE ACCELERATORS↗

Rational Design of Efficient Amine Reductant Initiators for Amine–Peroxide Redox Polymerization

Amine-peroxide redox polymerization (APRP) has been highly prevalent in industrial and medical applications since the 1950s, yet the initiation mechanism of this radical polymerization process is poorly understood so that innovations in the field are largely empirically driven and incremental. Through a combination of computational prediction and experimental analysis, we elucidate the mechanism of this important redox reaction between amines and benzoyl peroxide for the ambient production of initiating radicals. Our calculations show that APRP proceeds through S N 2 attack by the amine on the peroxide but that homolysis of the resulting intermediate is the rate-determining step. We demonstrate a correlation between the computationally predicted initiating rate and the experimentally measured polymerization rate with an R 2 = 0.80. The new mechanistic understanding was then applied to computationally predict amine reductant initiators with faster initiating kinetics. This led to our discovery of N-(4-methoxyphenyl)pyrrolidine (MPP) as amine reductant, which we confirmed significantly outperforms current state-of-the-art tertiary aromatic amines by ~20-fold, making it the most efficient amine-peroxide redox initiator to date. The application of amines with superior kinetics such as MPP in APRP could greatly accelerate existing industrial processes, facilitate new industrial manufacturing methods, and improve biocompatibility in biomedical applications conducted with reduced initiator concentrations yet higher overall efficiency.

36 MATERIALS SCIENCE↗

Nonrelativistic perpendicular shocks modeling young supernova remnants: Nonstationary dynamics and particle acceleration at forward and reverse shocks

For parameters that are applicable to the conditions at young supernova remnants, we present results of two-dimensional, three-vector (2D3V) particle-in-cell simulations of a non-relativistic plasma shock with a large-scale perpendicular magnetic field inclined at a 45{sup ∘} angle to the simulation plane to approximate three-dimensional (3D) physics. We developed an improved clean setup that uses the collision of two plasma slabs with different densities and velocities, leading to the development of two distinctive shocks and a contact discontinuity. The shock formation is mediated by Weibel-type filamentation instabilities that generate magnetic turbulence. Cyclic reformation is observed in both shocks with similar period, for which we note global variations due to shock rippling and local variations arising from turbulent current filaments. The shock rippling occurs on spatial and temporal scales produced by the gyro-motions of shock-reflected ions. The drift motion of electrons and ions is not a gradient drift, but is commensurate with E×B drift. We observe a stable supra-thermal tail in the ion spectra, but no electron acceleration because the amplitude of the Buneman modes in the shock foot is insufficient for trapping relativistic electrons. We see no evidence of turbulent reconnection. A comparison with other two-dimensional (2D) simulation results suggests that the plasma beta and the ion-to-electron mass ratio are not decisive for efficient electron acceleration, but the pre-acceleration efficacy might be reduced with respect to the 2D results once 3D effects are fully accounted for. Other microphysical factors may also play a part in limiting the amplitude of the Buneman waves or preventing the return of electrons to the foot region.

79 ASTRONOMY AND ASTROPHYSICS↗

Improvements of the boundary projection acceleration technique applied to the discrete-ordinates transport solver in XYZ geometries

In this paper we discuss the latest upgrades of the Boundary Projection Acceleration (BPA) applied to the XYZ transport solver of APOLLO3, namely IDT. The acceleration method is a well-known effective technique for the speed-up of the source iterations of the discrete-ordinates method. The BPA in IDT has been improved in three aspects: the taking into account of the residue on boundary conditions as a boundary source for the acceleration problem, the extension of the method to higher order angular moments in the case of anisotropic scattering and, finally, the application of the method to the multigroup iterations for the acceleration of the fission source and k-effective. The spectrum of the method has been Fourier-analyzed to explore the effectiveness. The 3D mock-up geometry of the ZPPR is presented as final study to test the performances of the acceleration on a realistic whole-core 3D calculation. (authors)

97 MATHEMATICS AND COMPUTING↗

Application of a new model of residual magnetization of iron for calculating the deflecting magnet of an accelerator

Allowing for residual magnetization of iron is necessary when calculating the magnetic field of elements of electron-optical channels in charged-particle accelerators because the contribution of residual magnetization to the field in the gap can be on the order of mT. Moreover, the magnitude and sign of this contribution depend on the magnetization process. Earlier, we proposed a model of residual magnetization of iron with the use of a small number of magnetic domain types. Here, an algorithm for magnetic-field calculation with the use of this model is described. The ability of the algorithm was demonstrated for the case of a simplest electromagnet with an O-shaped magnetic circuit. Comparison with the measurement results demonstrated a satisfactory accuracy of allowing for residual magnetization.

43 PARTICLE ACCELERATORS↗

A compact linear accelerator based on a scalable microelectromechanical-system RF-structure

Here, a new approach for a compact radio-frequency (RF) accelerator structure is presented. The new accelerator architecture is based on the Multiple Electrostatic Quadrupole Array Linear Accelerator (MEQALAC) structure that was first developed in the 1980s. The MEQALAC utilized RF resonators producing the accelerating fields and providing for higher beam currents through parallel beamlets focused using arrays of electrostatic quadrupoles (ESQs). While the early work obtained ESQs with lateral dimensions on the order of a few centimeters, using a printed circuit board (PCB), we reduce the characteristic dimension to the millimeter regime, while massively scaling up the potential number of parallel beamlets. Using Microelectromechanical systems scalable fabrication approaches, we are working on further red ucing the characteristic dimension to the sub-millimeter regime. The technology is based on RF-acceleration components and ESQs implemented in the PCB or silicon wafers where each beamlet passes through beam apertures in the wafer. The complete accelerator is then assembled by stacking these wafers. This approach has the potential for fast and inexpensive batch fabrication of the components and flexibility in system design for application specific beam energies and currents. For prototyping the accelerator architecture, the components have been fabricated using the PCB. In this paper, we present proof of concept results of the principal components using the PCB: RF acceleration and ESQ focusing. Finally, ongoing developments on implementing components in silicon and scaling of the accelerator technology to high currents and beam energies are discussed.

43 PARTICLE ACCELERATORS↗

Summary report of mission acceleration measurements for STS-60, SPACEHAB2, launched 11 February 1994

The STS-60 mission, which launched on 11 February 1994, carried seven accelerometer systems. This report describes the configuration of each of these systems, where they were located on the Orbiter and the name of a contact person for each system. The Space Acceleration Measurement System (SAMS) was one of the accelerometer systems on-board and this mission marked its eighth successful flight. Acceleration data are provided here for SAMS which flew under an agreement between the NASA Microgravity Science and Applications division and the NASA office of Advanced Concepts and Technology. Acceleration data for the other accelerometer systems are not presented here. SAMS was located in the commercial SPACEHAB laboratory, on its second flight. The SAMS system was configured with three triaxial sensor heads with filter cut-offs of 5, 10, and 50 Hz. The acceleration environment related to an experiment centrifuge, an experiment refrigerator freezer unit, a SAMS sensor head rotation, an Orbiter shudder, and payload deploy activities are discussed. In the Appendices, all of the data from SAMS Head B (10 Hz) are plotted to provide an overview of the environment during the majority of the STS-60 mission. An evaluation form is included at the end of the report to solicit users' comments about the usefulness of this series of reports.

Rogers, Melissa J. B.↗

Suppression of Beam Hosing in Plasma Accelerators with Ion Motion

Mitigation of the beam hose instability in plasma-based accelerators is required for the realization of many applications, including plasma-based colliders. The hose instability is analyzed in the blowout regime including plasma ion motion, and ion motion is shown to suppress the hose instability by inducing a head-to-tail variation in the focusing force experienced by the beam. Furthermore, stable acceleration in plasma-based accelerators is possible, while, by use of proper bunch shaping, minimizing the energy spread and preserving the transverse beam emittance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Photonuclear Physics in SCALE

Radiation shielding modeling involves a wide range of applications, such as power reactors, critical experiments, portable sources, linear accelerators, and fusion systems. Particle energy ranges vary from thermal energies to fast energy spectra. MAVRIC, as the radiation shielding sequence of the SCALE code system [1] developed and maintained by Oak Ridge National Laboratory, is capable of modeling both neutron and photon interactions in matter and is widely used by the US Nuclear Regulatory Commission, Department of Energy, the National Nuclear Security Administration, and radiation shielding practitioners all around the world. Although most applications don’t involve highly energetic photons that can cause photonuclear reactions and create coupled chains of high energy, ionized electrons and bremsstrahlung radiation within a material medium, when present, these reactions can have a significant impact upon the downstream particle fluxes from incident photons above 20 MeV. For example, linear accelerators used for medical isotope production are examples of applications in which high-energetic photons are generated and used for driving or controlling other components of a complex facility. Radiation shielding analyses of such a facility would require accounting for any and all significant sources of radiation. Unfortunately, MAVRIC included no data and methods to model either photonuclear reactions or the bremsstrahlung photons until this work, which enabled accounting for both. Photonuclear reaction cross sections were imported from the Evaluated Nuclear Data File libraries, and corresponding methods were implemented in the SCALE code system; see Section 2 for how the nuclear data are imported and used. Bremsstrahlung photons were modeled by assuming thick-target approximation whereby all generated electrons and positrons due to photon interactions are assumed to be absorbed within the same material in which they were born, yielding a quick particle transport simulation method by using fast lookup tables for generating subsequent gammas; see Section 4 for details. A suite of verification models was used to test implemented methods and associated data. Tests yielded satisfactory results for the new features. Enhancements will be released as part of the next major SCALE release (v7.0), which is anticipated to be deployed in 2025, with beta releases available in the interim.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Effect of Strain on the Resistivity and Thermal Conductivity of High Purity Niobium

High purity niobium (Nb) is a technologically important material for large-scale accelerator and nano-scale quantum computing applications in microwave frequency range. The high thermal conductivity and low resistivity of Nb are critical to the high performance at temperature range of 0.01–4.0 K. The presence of interstitials such as O, N, H, and C act as scattering centers and alter the mean free path, reducing resistivity and thermal conductivity, and contributing significantly to Nb's thermal performance for temperatures of 2.0 K and above. The residual resistivity ratio (RRR), defined as the ratio of the normal state resistivity at 300 K to that at 4.2 K (Nb, T c = 9.2 K), is an accepted direct estimate of the impurity content of fully recrystallized Nb. Complete re-crystallization of Nb is challenging unless very high temperatures are employed, which is often impractical, hence, in practice, dislocation and dislocation structures impact the thermal performance of Nb due to strong phonon scattering contributions. Furthermore, this paper reports on the degradation of thermal conductivity and RRR of high purity Nb large grain, single crystal with fixed impurity, varying strain, and dislocation content levels. Experimental thermal conductivity data fits the Boltzmann transport equation incorporating dislocation density.

36 MATERIALS SCIENCE↗

Characterizing laser-plasma ion accelerators driving an intense neutron beam via nuclear signatures

Compact, bright neutron sources are opening up several emerging applications including detection of nuclear materials for national security applications. At Los Alamos National Laboratory, we have used a short-pulse laser to accelerate deuterons in the relativistic transparency regime. These deuterons impinge on a beryllium converter to generate neutrons. During the initial experiments where these neutrons were used for active interrogation of uranium and plutonium, we observed β-delayed neutron production from decay of 9 Li, formed by the high-energy deuteron bombardment of the beryllium converter. Analysis of the delayed neutrons provides novel evidence of the divergence of the highest energy portion of the deuterons (i.e., above 10 MeV/nucleon) from the laser axis, a documented feature of the breakout afterburner laser-plasma ion acceleration mechanism. Furthermore, these delayed neutrons form the basis of non-intrusive diagnostics for determining the features of deuteron acceleration as well as monitoring neutron production for the next generation of laser-driven neutron sources.

43 PARTICLE ACCELERATORS↗

Advanced data analysis in inertial confinement fusion and high energy density physics

Bayesian analysis enables flexible and rigorous definition of statistical model assumptions with well-characterized propagation of uncertainties and resulting inferences for single-shot, repeated, or even cross-platform data. This approach has a strong history of application to a variety of problems in physical sciences ranging from inference of particle mass from multi-source high-energy particle data to analysis of black-hole characteristics from gravitational wave observations. The recent adoption of Bayesian statistics for analysis and design of high-energy density physics (HEDP) and inertial confinement fusion (ICF) experiments has provided invaluable gains in expert understanding and experiment performance. In this Review, we discuss the basic theory and practical application of the Bayesian statistics framework. We highlight a variety of studies from the HEDP and ICF literature, demonstrating the power of this technique. Due to the computational complexity of multi-physics models needed to analyze HEDP and ICF experiments, Bayesian inference is often not computationally tractable. Two sections are devoted to a review of statistical approximations, efficient inference algorithms, and data-driven methods, such as deep-learning and dimensionality reduction, which play a significant role in enabling use of the Bayesian framework. We provide additional discussion of various applications of Bayesian and machine learning methods that appear to be sparse in the HEDP and ICF literature constituting possible next steps for the community. We conclude by highlighting community needs, the resolution of which will improve trust in data-driven methods that have proven critical for accelerating the design and discovery cycle in many application areas.

47 OTHER INSTRUMENTATION↗