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At least 181 records · Page 10

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 ( ZmCIPK15 )

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.

59 BASIC BIOLOGICAL SCIENCES↗

The expressivity of classical and quantum neural networks on entanglement entropy

Abstract Analytically continuing the von Neumann entropy from Rényi entropies is a challenging task in quantum field theory. While then-th Rényi entropy can be computed using the replica method in the path integral representation of quantum field theory, the analytic continuation can only be achieved for some simple systems on a case-by-case basis. In this work, we propose a general framework to tackle this problem using classical and quantum neural networks with supervised learning. We begin by studying several examples with known von Neumann entropy, where the input data is generated by representing$${\text {Tr}}\rho _A^n$$ Tr ρ A n with a generating function. We adopt KerasTuner to determine the optimal network architecture and hyperparameters with limited data. In addition, we frame a similar problem in terms of quantum machine learning models, where the expressivity of the quantum models for the entanglement entropy as a partial Fourier series is established. Our proposed methods can accurately predict the von Neumann and Rényi entropies numerically, highlighting the potential of deep learning techniques for solving problems in quantum information theory.

Physics↗

GraphReduce: Processing Large-Scale Graphs on Accelerator-Based Systems

Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the host and device.

Architecture optimization, reuse, performance, ene↗

UNITY: Unified Memory and File Space. In: ROSS '17 Proceedings of the 7th International Workshop on Runtime and Operating Systems for Supercomputers ROSS 2017, Article No. 6

This paper describes the vision for UNITY, a new high-performance computing focused data storage abstraction that places the entire memory hierarchy, including both traditionally separated memory-and file-based data storage, into one storage continuum. Through the use of a novel API and a set of services centered around a smart runtime system, UNITY is able to provide a number of valuable and interesting benefits. The unified storage space provides a scalable and resilient data environment that dynamically manages the mapping of data onto available resources based on multiple factors, including desired persistence and energy budget considerations. By eliminating the need for high-performance computing domain scientists to develop architecture-dependent optimizations for rapidly evolving data storage technologies, UNITY addresses both ease-of-use and performance.

Jones, Terry↗

If We Build Them, They Will Run: Automated HPC Apps Deployment and Profiling with eBPF in Cloud

The high performance computing (HPC) community is in a period of transition. The rise of AI/ML coupled with a changing landscape of resources deems portability a new metric of performance, and methods to move between on-premises and cloud environments and assess compatibility are paramount. Here we design and test a strategy for bridging the gap between traditional HPC and Kubernetes environments – first containerizing applications, providing automated orchestration to run studies, and packaging the setup with automated means to assess performance using low overhead eXtended Berkeley Packet Filter (eBPF) programs. We first assess different designs for eBPF collection, demonstrating a tradeoff between number of programs deployed on a node and overhead added. We develop 5 low overhead eBPF programs that combine with streaming ML models to assess CPU, futex, TCP, shared memory, and file access across four different builds of an HPC application for CPU and GPU. We use eBPF data to generate insights into the possible underlying etiology of scaling issues. We then assess compatibility of a well-known benchmark, HPCG, across matrices of micro-architectures and optimization levels (217 containers across 24 instance types and over 7500 runs). We provide to the community 30 applications to deploy in our automated setup and perform a scaling study from 4 to a maximum of 256 nodes for both CPU and GPU applications. Finally, we use our gained knowledge about performance to generate compatibility artifacts that are used by a newly developed Kubernetes controller to intelligently select instance type based on optimizing a figure of merit. Along with insights to scaling in this environment with a collection of applications and templates to work from, we provide an overall strategy for approaching HPC application deployment and image selection based on compatibility in cloud.

Computer science↗

Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean

Fundamental to biological decision-making is the ability to generate bimodal expression patterns where two alternate expression states simultaneously exist. Here in this study, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV’s fate decision between active replication and viral latency. We find that the HIV Tat protein manipulates the intrinsic toggling of HIV’s promoter, the LTR, to generate bimodal ON-OFF expression, and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuit’s non-cooperative ‘non-latching’ feedback architecture is optimized to slow the promoter’s toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that non-latching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean-expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIV’s decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels.

59 BASIC BIOLOGICAL SCIENCES↗

Performance Portability of HPC Discovery Science Software: Fusion Energy Turbulence Simulations at Extreme Scale

As HPC R&D moves forward on a variety of “path to exascale” architectures today, an associated objective is to demonstrate performance portability of discovery-science-capable software. Important application domains, such as Magnetic Fusion Energy (MFE), have improved modelling of increasingly complex physical systems -- especially with respect to reducing “time-to-solution” as well as “energy to solution.” The emergence of new insights on confinement scaling in MFE systems has been aided significantly by efficient software capable of harnessing powerful supercomputers to carry out simulations with unprecedented resolution and temporal duration to address increasing problem sizes. Specifically, highly scalable particle-in-cell (PIC) programing methodology is used in this paper to demonstrate how modern scientific applications can achieve efficient architecture-dependent optimizations of performance scaling and code portability for path-to-exascale platforms.

97 MATHEMATICS AND COMPUTING↗

Cooperative Research and Development Agreement between National Energy Technology Laboratory and The Pennsylvania State University (Final Report)

This project will use bipolar membranes to produce efficient vapor-phase electrolysis cells for splitting CO 2 to CO and oxygen. CO is a valuable chemical feedstock that can be combined catalytically with hydrogen in the Fischer-Tropsch process to make liquid fuels. CO is arguably the best target for CO 2 reduction since, as a gaseous product, it is easily collected and is relatively immune to membrane crossover losses. The keys to success in this project are to design and synthesize hydrophilic, low resistance bipolar membranes and to create optimized electrode/catalyst/electrolyte architectures based on these new membranes and advanced catalysts in order to achieve high current density at low overpotentials for CO 2 conversion. High current density is key to achieving industrially relevant throughput for the process and low overpotentials maintain high overall efficiency for the process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advanced Anion Exchange Membranes with Tunable Water Transport for PGM-Free AEMFCs

This project advanced the synthesis, characterization, and testing of anion exchange membranes for use in fuel cells. Our goal was to improve the water transport in anion exchange membrane fuel cells to improve their performance and durability. Through the work in this project we: 1) developed new composite anion exchange membranes through polymer synthesis and membrane casting into mechanical supports; 2) optimized electrode architecture and cell conditions to achieve; 3) demonstrated an integrated approach to achieving over 1 W/cm 2 in an operating device. While we did not achieve 1000 hours of continuous operation, we demonstrated multiple runs of more than 300 hours of device performance at steady-state.

08 HYDROGEN↗

Microreactor Program Technology Maturation MACS system reports

This submission contains several reports associated with the DOE Microreactor Program Technology Maturation MACS system. These include milestone reports: M3AT-24IN0804031-Optimized MACS architecture M3AT-24IN0804033-Light and temp sensor integration M4AT-23IN0804055-Update Microreactor Automated Control System (MACS) hardware based on input from demonstration M2AT-23IN0804054-Demonstrate actuation of control system using Microreactor Automated Control System (MACS)

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Learning from Arctic Microgrids: Cost and Resiliency Projections for Renewable Energy Expansion with Hydrogen and Battery Storage

Electricity in rural Alaska is provided by more than 200 standalone microgrid systems powered predominantly by diesel generators. Incorporating renewable energy generation and storage to these systems can reduce their reliance on costly imported fuel and improve sustainability; however, uncertainty remains about optimal grid architectures to minimize cost, including how and when to incorporate long-duration energy storage. This study implements a novel, multi-pronged approach to assess the techno-economic feasibility of future energy pathways in the community of Kotzebue, which has already successfully deployed solar photovoltaics, wind turbines, and battery storage systems. Using real community load, resource, and generation data, we develop a series of comparison models using the HOMER Pro software tool to evaluate microgrid architectures to meet over 90% of the annual community electricity demand with renewable generation, considering both battery and hydrogen energy storage. We find that near-term planned capacity expansions in the community could enable over 50% renewable generation and reduce the total cost of energy. Additional build-outs to reach 75% renewable generation are shown to be competitive with current costs, but further capacity expansion is not currently economical. We additionally include a cost sensitivity analysis and a storage capacity sizing assessment that suggest hydrogen storage may be economically viable if battery costs increase, but large-scale seasonal storage via hydrogen is currently unlikely to be cost-effective nor practical for the region considered. While these findings are based on data and community priorities in Kotzebue, we expect this approach to be relevant to many communities in the Arctic and Sub-Arctic regions working to improve energy reliability, sustainability, and security.

25 ENERGY STORAGE↗

Emulating aerosol optics with randomly generated neural networks

Abstract. Atmospheric aerosols have a substantial impact on climate and remain one of the largest sources of uncertainty in climate prediction. Accurate representation of their direct radiative effects is a crucial component of modern climate models. However, direct computation of the radiative properties of aerosol populations is far too computationally expensive to perform in a climate model, so optical properties are typically approximated using a parameterization. This work develops artificial neural networks (ANNs) capable of replacing the current aerosol optics parameterization used in the Energy Exascale Earth System Model (E3SM). A large training dataset is generated by using Mie code to directly compute the optical properties of a range of atmospheric aerosol populations given a large variety of particle sizes, wavelengths, and refractive indices. Optimal neural architectures for shortwave and longwave bands are identified by evaluating ANNs with randomly generated wirings. Randomly generated deep ANNs are able to outperform conventional multilayer-perceptron-style architectures with comparable parameter counts. Finally, the ANN-based parameterization produces significantly more accurate bulk aerosol optical properties than the current parameterization when compared with direct Mie calculations using mean absolute error. The success of this approach makes possible the future inclusion of much more sophisticated representations of aerosol optics in climate models that cannot be captured by extension of the existing parameterization scheme and also demonstrates the potential of random-wiring-based neural architecture search in future applications in the Earth sciences.

54 ENVIRONMENTAL SCIENCES↗

Parallel computation of manipulator inverse dynamics

In this article, parallel computation of manipulator inverse dynamics is investigated. A hierarchical graph-based mapping approach is devised to analyze the inherent parallelism in the Newton-Euler formulation at several computational levels, and to derive the features of an abstract architecture for exploitation of parallelism. At each level, a parallel algorithm represents the application of a parallel model of computation that transforms the computation into a graph whose structure defines the features of an abstract architecture, i.e., number of processors, communication structure, etc. Data-flow analysis is employed to derive the time lower bound in the computation as well as the sequencing of the abstract architecture. The features of the target architecture are defined by optimization of the abstract architecture to exploit maximum parallelism while minimizing architectural complexity. An architecture is designed and implemented that is capable of efficient exploitation of parallelism at several computational levels. The computation time of the Newton-Euler formulation for a 6-degree-of-freedom (dof) general manipulator is measured as 187 microsec. The increase in computation time for each additional dof is 23 microsec, which leads to a computation time of less than 500 microsec, even for a 12-dof redundant arm.

Fijany, Amir↗

Sixth Goddard Conference on Mass Storage Systems and Technologies Held in Cooperation with the Fifteenth IEEE Symposium on Mass Storage Systems

This document contains copies of those technical papers received in time for publication prior to the Sixth Goddard Conference on Mass Storage Systems and Technologies which is being held in cooperation with the Fifteenth IEEE Symposium on Mass Storage Systems at the University of Maryland-University College Inn and Conference Center March 23-26, 1998. As one of an ongoing series, this Conference continues to provide a forum for discussion of issues relevant to the management of large volumes of data. The Conference encourages all interested organizations to discuss long term mass storage requirements and experiences in fielding solutions. Emphasis is on current and future practical solutions addressing issues in data management, storage systems and media, data acquisition, long term retention of data, and data distribution. This year's discussion topics include architecture, tape optimization, new technology, performance, standards, site reports, vendor solutions. Tutorials will be available on shared file systems, file system backups, data mining, and the dynamics of obsolescence.

Kobler, Benjamin↗

High Power Electric Propulsion for Outer Planet Missions

Focused technology trade studies for Nuclear Electric Propulsion vehicle concepts for outer planet missions are presented; representative mission, vehicle and technology characterizations illustrate samples of work done under the NASA Marshall Space Flight Center-Boeing-SAIC In-Space Technology Assessment (ISTA) contract. An objective of ISTA is to identify and present sound technical and programtic options for the formulation and implementation of advanced electric and chemical propulsion solar system exploration missions. Investigations to date include a variety of outer planet destinations, trip times, science payload allotments, orbital capture techniques, all conducted to illustrate how advanced technology would maximize mission benefits. Architecture wide optimizations that facilitate good propulsion technology investments for advanced electric and chemical propulsion systems were conducted, including those relevant to the nuclear system initiative. Representative analyses of vehicles utilizing fission reactors with advanced power generation, Conversion, processing and electric propulsion systems, which would enable scientifically rich robotic exploration missions, are presented.

Donahue, Benjamin B.↗

Touch modulates gravity sensing to regulate the growth of primary roots of Arabidopsis thaliana

Plants must sense and respond to diverse stimuli to optimize the architecture of their root system for water and nutrient scavenging and anchorage. We have therefore analyzed how information from two of these stimuli, touch and gravity, are integrated to direct root growth. In Arabidopsis thaliana, touch stimulation provided by a glass barrier placed across the direction of growth caused the root to form a step-like growth habit with bends forming in the central and later the distal elongation zones. This response led to the main root axis growing parallel to, but not touching the obstacle, whilst the root cap maintained contact with the barrier. Removal of the graviperceptive columella cells of the root cap using laser ablation reduced the bending response of the distal elongation zone. Similarly, although the roots of the gravisensing impaired pgm1-1 mutant grew along the barrier at the same average angle as wild-type, this angle became more variable with time. These observations imply a constant gravitropic re-setting of the root tip response to touch stimulation from the barrier. In wild-type plants, transient touch stimulation of root cap cells, but not other regions of the root, inhibited both subsequent gravitropic growth and amyloplast sedimentation in the columella. Taken together, these results suggest that the cells of the root cap sense touch stimuli and their subsequent signaling acts on the columella cells to modulate their graviresponse. This interaction of touch and gravity signaling would then direct root growth to avoid obstacles in the soil while generally maintaining downward growth.

NASA Discipline Plant Biology↗

Animal models for osteoporosis

Animal models will continue to be important tools in the quest to understand the contribution of specific genes to establishment of peak bone mass and optimal bone architecture, as well as the genetic basis for a predisposition toward accelerated bone loss in the presence of co-morbidity factors such as estrogen deficiency. Existing animal models will continue to be useful for modeling changes in bone metabolism and architecture induced by well-defined local and systemic factors. However, there is a critical unfulfilled need to develop and validate better animal models to allow fruitful investigation of the interaction of the multitude of factors which precipitate senile osteoporosis. Well characterized and validated animal models that can be recommended for investigation of the etiology, prevention and treatment of several forms of osteoporosis have been listed in Table 1. Also listed are models which are provisionally recommended. These latter models have potential but are inadequately characterized, deviate significantly from the human response, require careful choice of strain or age, or are not practical for most investigators to adopt. It cannot be stressed strongly enough that the enormous potential of laboratory animals as models for osteoporosis can only be realized if great care is taken in the choice of an appropriate species, age, experimental design, and measurements. Poor choices will results in misinterpretation of results which ultimately can bring harm to patients who suffer from osteoporosis by delaying advancement of knowledge.

NASA Discipline Regulatory Physiology↗