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At least 1,027 records · Page 57

Development of a River Dynamical Core for E3SM to simulate compound flooding on Exascale-class heterogeneous supercomputers

Flooding events pose significant risk to human life, property, and infrastructure. Physically-consistent quantification of altered flood risks in global models requires hyper-resolution (~1 km) or fine flood simulations using two-dimensional (2D) physics schemes, both of which are unavailable in the current generation Earth System Models. Here, in this work, we have developed the River Dynamical Core (RDycore), which is an open-source, 2D shallow water equation (SWE) library for the U.S. Department of Energy's Energy Exascale Earth System Model (E3SM). RDycore uses PETSc and libCEED libraries that allows it to run efficiently on CPUs and GPUs, as well as select a time-integration algorithm at runtime without requiring any code modifications. RDycore achieves spatial error convergence rates for problems with analytical and manufactured solutions similar to those reported previously in the literature, or consistent with the implemented first-order spatial discretization scheme. RDycore's accuracy in predicting flooding for a well-studied dam break problem is comparable to existing SWE models. For a problem with 471 million grid cells, RDycore achieves a speedup of 6.6x and 7.6x on GPUs compared to CPUs when using 320 compute nodes on DOE's Perlmutter and Frontier supercomputers, respectively. The one-way coupling of the RDycore library within E3SM is demonstrated by performing multiple 5-day flooding simulations during Hurricane Harvey driven by five precipitation datasets. The E3SM--RDycore simulations at 30 m spatial resolution accurately simulate maximum water height during the hurricane when benchmarked against a previously published study and achieve a speedup of 15x (Perlmutter) and 21x (Frontier) on GPUs relative to CPUs. The work presented here is the foundational step in providing hardware and algorithmic portability framework for simulating kilometer-scale river dynamics within E3SM.

Flood Simulation↗

Chemoproteogenomic stratification of the missense variant cysteinome

Abstract Cancer genomes are rife with genetic variants; one key outcome of this variation is widespread gain-of-cysteine mutations. These acquired cysteines can be both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain unidentified via chemoproteomics; identification is a critical step to enable functional analysis, including assessment of potential druggability and susceptibility to oxidation. Here, we pair cysteine chemoproteomics—a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues—with genomics to reveal the hidden landscape of cysteine genetic variation. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized two-stage false discovery rate (FDR) error controlled proteomic search, which is further enhanced with a user-friendly FragPipe interface. Chemoproteogenomics analysis reveals that cysteine acquisition is a ubiquitous feature of both healthy and cancer genomes that is further elevated in the context of decreased DNA repair. Reference cysteines proximal to missense variants are also found to be pervasive, supporting heretofore untapped opportunities for variant-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and is compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.

Desai, Heta (ORCID:0000000343621707)↗

Real-time quantum error correction beyond break-even

The ambition of harnessing the quantum for computation is at odds with the fundamental phenomenon of decoherence. The purpose of quantum error correction (QEC) is to counteract the natural tendency of a complex system to decohere. This cooperative process, which requires participation of multiple quantum and classical components, creates a special type of dissipation that removes the entropy caused by the errors faster than the rate at which these errors corrupt the stored quantum information. Previous experimental attempts to engineer such a process faced an excessive generation of errors that overwhelmed the error-correcting capability of the process itself. Whether it is practically possible to utilize QEC for extending quantum coherence thus remains an open question. We answer it by demonstrating a fully stabilized and error-corrected logical qubit whose quantum coherence is significantly longer than that of all the imperfect quantum components involved in the QEC process, beating the best of them with a coherence gain of G=2.27±0.07. Here we achieve this performance by combining innovations in several domains including the fabrication of superconducting quantum circuits and model-free reinforcement learning.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An Experiment-based Distribution Level Performance Comparison among PMUs

This paper presents a experiment-based distribution level performance comparison among three Phasor Measurement Units (PMUs). Several evaluation criteria, including the total vector error, the phase angle error, the frequency error, the rate of change of frequency, the response time, the settling time, the overshoot, and the algorithm window size, are selected to compare the static and dynamic performances of the PMUs under steady state and step response test conditions. In order to have a more realistic test environment, a test is setup in which PMUs under evaluation have exactly the same input signals. The quantitative experiment result analysis gives an end-user guideline to the PMU selection regarding distribution level applications.

Yin, He↗

Automating Genetic Algorithm Mutations for Molecules Using a Masked Language Model

Inspired by the evolution of biological systems, genetic algorithms have been applied to generate solutions for optimization problems in a variety of scientific and engineering disciplines. For a given problem, a suitable genome representation must be defined along with a mutation operator to generate subsequent generations. Unlike natural systems which display a variety of complex rearrangements (e.g. mobile genetic elements), mutation for genetic algorithms commonly utilizes only random point-wise changes. Furthermore, generalizing beyond point-wise mutations poses a key difficulty as useful genome rearrangements depend on the representation and problem domain. To move beyond the limitations of manually defined point-wise changes, here we propose the use of techniques from masked language models to automatically generate mutations. As a first step, common subsequences within a given population are used to generate a vocabulary. The vocabulary is then used to tokenize each genome. A masked language model is trained on the tokenized data in order to generate possible rearrangements (i.e. mutations). In order to illustrate the proposed strategy, we use string representations of molecules and use a genetic algorithm to optimize for drug-likeness and synthesizability. Finally, our results show that moving beyond random point-wise mutations accelerates genetic algorithm optimization.

59 BASIC BIOLOGICAL SCIENCES↗

New insights gained on mechanisms of low-energy proton-induced SEUs by minimizing energy straggle

In this study, we present low-energy proton single-event upset (SEU) data on a 65 nm SOI SRAM whose substrate has been completely removed. Since the protons only had to penetrate a very thin buried oxide layer, these measurements were affected by far less energy loss, energy straggle, flux attrition, and angular scattering than previous datasets. The minimization of these common sources of experimental interference allows more direct interpretation of the data and deeper insight into SEU mechanisms. The results show a strong angular dependence, demonstrate that energy straggle, flux attrition, and angular scattering affect the measured SEU cross sections, and prove that proton direct ionization is the dominant mechanism for low-energy proton-induced SEUs in these circuits.

74 ATOMIC AND MOLECULAR PHYSICS↗

Total-Ionizing-Dose Effects on Read Noise of MLC 3-D NAND Memories T

This paper analyzes the total ionizing dose (TID) effects on noise characteristics of commercial multi-level-cell (MLC) 3-D NAND memory technology during the read operation. Additionally, the chips were exposed to a Co-60 gamma-ray source for up to 100 krad(Si) of TID. We find that the number of noisy cells in the irradiated chip increases with TID. Bit-flip noise was more dominant for cells in an erased state during irradiation compared to programmed cells.

3-D NAND Flash↗

Designing and Evaluating Redundancy-Based Soft-Error Masking on a Continuum of Energy versus Robustness

Near-threshold computing is an effective strategy to reduce the power dissipation of deeply-scaled CMOS logic circuits. However, near-threshold strategies exacerbate the impact of delay variations on device performance and increase the susceptibility to soft errors due to narrow voltage margins. The objective of this work is to develop and assess design approaches that leverage tradeoffs between performance and the resilience of fault masking coverage for various soft-error mitigation techniques. The primary insight from this work is identification of redundancy-based hardening techniques that can deliver increased benefits in terms of the fault coverage energy ratio (FCER) for the leveraged tradeoffs within iso-energy constraints at near-threshold voltage (NTV). Simulation results demonstrate that temporal redundancy approaches offer favorable tradeoffs in terms of FCER. They exhibit reduced impact on performance variations and achieve extensive soft fault masking, therefore improving the system robustness within acceptable delay constraints. Meanwhile, it is shown that a hybrid redundancy approach can be used to protect a low-power system to maintain throughput while tolerating soft errors. We demonstrate how the FCER metric can be used as an optimization parameter to guide circuit synthesis to meet performance and robustness goals. Lastly, the impact of design diversity on spatial and hybrid redundancy at NTV is assessed in terms of FCER and delay variation to form overall recommendations regarding soft-error mitigation at NTV.

97 MATHEMATICS AND COMPUTING↗

Flight test of a stall sensor and evaluation of its application to an aircraft stall deterrent system using the NASA LRC general aviation simulator

A series of flight maneuvers were developed to cover the range of flight conditions and to define the repeatability and hysteresis of the sensors. Initial flights were made with two sensors at the + or - 68 percent span and 60 percent and 70 percent chord stations. The primary effort in simulation program development was to modify the LRC General Aviation Simulator (GAS) Fortran programs to allow execution on the MSU UNIVAC 1106. A simple model of the sensor-servo stall deterrent system was developed. A one degree of freedom model of pitch dynamics of the airplane and stall deterrent system was developed to make initial estimates of the control system gains. A position error plus rate damping control algorithm was found to have acceptable characteristics.

Bennett, G.↗

Multispectral data acquisition and classification - Statistical models for system design

In this paper we relate the statistical processes that are involved in multispectral data acquisition and classification to a simple radiometric model of the earth surface and atmosphere. If generalized, these formulations could provide an analytical link between the steadily improving models of our environment and the performance characteristics of rapidly advancing device technology. This link is needed to bring system analysis tools to the task of optimizing remote sensing and (real-time) signal processing systems as a function of target and atmospheric properties, remote sensor spectral bands and system topology (e.g., image-plane processing), radiometric sensitivity and calibration accuracy, compensation for imaging conditions (e.g., atmospheric effects), and classification rates and errors.

Huck, F. O.↗

Analyzing Multirate-Sampled Systems

New method available for monitoring stability of system on basis of data sampled at multiple rates--in particular, at two rates, one of which is twice frequency of other. Method is called Multirate Matrix Frequency Response (MMFR) analysis. MMFR was used in Space Shuttle to evaluate effect of decreasing sample rate of error loop in ascent-phase digital autopilot. Should also be useful to designers of other control systems and to structural, civil, and mechanical engineers for structure and vibration analysis.

Hendrix, N.↗

Motion-base simulator results of advanced supersonic transport handling qualities with active controls

Handling qualities of the unaugmented advanced supersonic transport (AST) are deficient in the low-speed, landing approach regime. Consequently, improvement in handling with active control augmentation systems has been achieved using implicit model-following techniques. Extensive fixed-based simulator evaluations were used to validate these systems prior to tests with full motion and visual capabilities on a six-axis motion-base simulator (MBS). These tests compared the handling qualities of the unaugmented AST with several augmented configurations to ascertain the effectiveness of these systems. Cooper-Harper ratings, tracking errors, and control activity data from the MBS tests have been analyzed statistically. The results show the fully augmented AST handling qualities have been improved to an acceptable level.

Feather, J. B.↗

Earth feature identification for onboard multispectral data editing: Computational experiments

A computational model of the processes involved in multispectral remote sensing and data classification is developed as a tool for designing smart sensors which can process, edit, and classify the data that they acquire. An evaluation of sensor system performance and design tradeoffs involves classification rates and errors as a function of number and location of spectral channels, radiometric sensitivity and calibration accuracy, target discrimination assignments, and accuracy and frequency of compensation for imaging conditions. This model provides a link between the radiometric and statistical properties of the signals to be classified and the performance characteristics of electro-optical sensors and data processing devices. Preliminary computational results are presented which illustrate the editing performance of several remote sensing approaches.

Aherron, R. M.↗

Fokker-Planck response of stochastic satellites

The present investigation is concerned with the effects of stochastic geometry and random environmental torques on the pointing accuracy of spinning and three-axis stabilized satellites. The study of pointing accuracies requires a knowledge of the rates of error growth over and above any criteria for the asymptotic stability of the satellites. For this reason the investigation is oriented toward the determination of the statistical properties of the responses of the satellites. The geometries of the satellites are considered stochastic so as to have a phenomenological model of the motions of the flexible structural elements of the satellites. A widely used method of solving stochastic equations is the Fokker-Planck approach where the equations are assumed to define a Markoff process and the transition probability densities of the responses are computed directly as a function of time. The Fokker-Planck formulation is used to analyze the response vector of a rigid satellite.

Huang, T. C.↗