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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

PaRSEC: Scalability, flexibility, and hybrid architecture support for task-based applications in ECP

This paper highlights the most significant enhancements made to PaRSEC, a scalable task-based runtime system designed for hybrid machines, during the Exascale Computing Project (ECP). The enhancements focus on expanding the capabilities of PaRSEC to address the evolving landscape of parallel computing. Notable achievements include the integration of support for three major types of accelerators (NVIDIA, AMD, and Intel GPUs), the refinement and increased flexibility of the communication subsystem, and the introduction of new programming interfaces tailored for irregular applications. Additionally, the project resulted in the development of powerful debugging and performance analysis tools aimed at assisting users in understanding and optimizing their applications. We present a comprehensive demonstration of these advancements through a series of benchmarks and applications within ECP and beyond, thereby showcasing the enhanced capabilities of PaRSEC across the diverse architectures within the ECP, providing valuable insights into the runtime system’s adaptability and performance across varied computing environments.

Bouteiller, Aurelien↗
DOE OSTI2025

Preparing MPICH for exascale

The advent of exascale supercomputers heralds a new era of scientific discovery, yet it introduces significant architectural challenges that must be overcome for MPI applications to fully exploit its potential. Among these challenges is the adoption of heterogeneous architectures, particularly the integration of GPUs to accelerate computation. Additionally, the complexity of multithreaded programming models has also become a critical factor in achieving performance at scale. The efficient utilization of hardware acceleration for communication, provided by modern NICs, is also essential for achieving low latency and high throughput communication in such complex systems. In response to these challenges, the MPICH library, a high-performance and widely used Message Passing Interface (MPI) implementation, has undergone significant enhancements. Here, this paper presents four major contributions that prepare MPICH for the exascale transition. First, we describe a lightweight communication stack that leverages the advanced features of modern NICs to maximize hardware acceleration. Second, our work showcases a highly scalable multithreaded communication model that addresses the complexities of concurrent environments. Third, we introduce GPU-aware communication capabilities that optimize data movement in GPU-integrated systems. Finally, we present a new datatype engine aimed at accelerating the use of MPI derived datatypes on GPUs. These improvements in the MPICH library not only address the immediate needs of exascale computing architectures but also set a foundation for exploiting future innovations in high-performance computing. By embracing these new designs and approaches, MPICH-derived libraries from HPE Cray and Intel were able to achieve real exascale performance on OLCF Frontier and ALCF Aurora respectively.

Guo, Yanfei [Argonne National Laboratory (ANL), Ar↗
DOE OSTI2024

Mitigative Strategies for Recovering From Large Language Model Trust Violations

In this study, we investigated strategies to address trust issues arising from errors in large language models (LLMs). The study examined the impact of confidence scores, system capability explanations, and user feedback on trust restoration post-error. 68 participants viewed the responses of an LLM to 20 general trivia questions, with an error introduced on the third trial. Each participant was presented with one mitigation strategy. Participants rated their overall trust in the model and the reliability of the answer. Results showed an immediate drop in trust after the error; however, there were no differences across the three strategies in trust recovery. All conditions had a logarithmic trend in trust recovery following error. Differences in overall trust were predicted by perceived reliability of the answer, suggesting that participants were evaluating results critically and using that to inform their trust in the model. Qualitative data supported this finding; participants expressed lasting distrust despite the LLM’s later accuracy. Results showcase the need to prioritize accuracy in LLM deployment, because early errors may irrevocably damage user trust calibration and later adoption.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Quantum Advantage in Trading: A Game-Theoretic Approach

Quantum games, like quantum algorithms, exploit quantum entanglement to establish strong correlations between strategic player actions. This paper introduces quantum game-theoretic models applied to trading and demonstrates their implementation on an ion-trap quantum computer. The results showcase a quantum advantage, previously known only theoretically, realized as higher-paying market Nash equilibria. This advantage could help uncover alpha in trading strategies, defined as excess returns compared to established benchmarks. These findings suggest that quantum computing could significantly influence the development of financial strategies.

Khan, Faisal Shah [Taqtics LLC, USA, Rethinc. Labs↗
DOE OSTI2021

Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Quantitative phenotyping of crop roots with spectral electrical impedance tomography: a rhizotron study with optimized measurement design

Background: Root systems are key contributors to plant health, resilience, and, ultimately, yield of agricultural crops. To optimize plant performance, phenotyping trials are conducted to breed plants with diverse root traits. However, traditional analysis methods are often labour-intensive and invasive to the root system, therefore limiting high-throughput phenotyping. Spectral electrical impedance tomography (sEIT) could help as a non-invasive and cost-efficient alternative to optical root analysis, potentially providing 2D or 3D spatio-temporal information on root development and activity. Although impedance measurements have been shown to be sensitive to root biomass, nutrient status, and diurnal activity, only few attempts have been made to employ tomographic algorithms to recover spatially resolved information on root systems. In this study, we aim to establish relationships between tomographic electrical polarization signatures and root traits of different fine root systems (maize, pinto bean, black bean, and soy bean) under hydroponic conditions. Results: Our results show that, with the use of an optimized data acquisition scheme, sEIT is capable of providing spatially resolved information on root biomass and root surface area for all investigated root systems. We found strong correlations between the total polarization strength and the root biomass (R 2 = 0.82) and root surface area (R 2 = 0.8). Our findings suggest that the captured polarization signature is dominated by cell-scale polarization processes. Additionally, we demonstrate that the resolution characteristics of the measurement scheme can have a significant impact on the tomographic reconstruction of root traits. Conclusion: Our findings showcase that sEIT is a promising tool for the tomographic reconstruction of root traits in high-throughput root phenotyping trials and should be evaluated as a substitute for traditional, often time-consuming, root characterization methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Geothermal reservoir characterization using distributed temperature sensing at Brady Geothermal Field, Nevada

Distributed temperature sensing (DTS) systems provide near real-time data collection that captures borehole spatiotemporal temperature dynamics. For this study, temperature data was collected in an observation well at an active geothermal site for a period of eight days under geothermal production conditions. Collected temperature data showcase the ability of DTS systems to detect changes to the location of the steam-water interface, visualize borehole temperature recovery — following injection of a coldwater “slug” — and identify anomalously warm and/or cool zones. The high sampling rate and spatial resolution of DTS data also shows borehole temperature dynamics that are not captured by traditional pressure-temperature survey tools. Inversion of thermal recovery data using a finite-difference heat-transfer model produces a thermal-diffusivity profile that is consistent with laboratorymeasured values and correlates with identified lithologic changes within the borehole. Used alone or in conjunction with complementary data sets, DTS systems are useful tools for developing a better understanding of both reservoir rock thermal properties as well as within and near borehole fluid movement.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Challenges in Markov Chain Monte Carlo for Bayesian Neural Networks

Markov chain Monte Carlo (MCMC) methods have not been broadly adopted in Bayesian neural networks (BNNs). This paper initially reviews the main challenges in sampling from the parameter posterior of a neural network via MCMC. Such challenges culminate to lack of convergence to the parameter posterior. Nevertheless, this paper shows that a nonconverged Markov chain, generated via MCMC sampling from the parameter space of a neural network, can yield via Bayesian marginalization a valuable posterior predictive distribution of the output of the neural network. Further, classification examples based on multilayer perceptrons showcase highly accurate posterior predictive distributions. The postulate of limited scope for MCMC developments in BNNs is partially valid; an asymptotically exact parameter posterior seems less plausible, yet an accurate posterior predictive distribution is a tenable research avenue.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Dynamic mitigation of EDFA power excursions with machine learning

Dynamic optical networking has promising potential to support the rapidly changing traffic demands in metro and long-haul networks. However, the improvement in dynamicity is hindered by wavelength-dependent power excursions in gain-controlled erbium doped fiber amplifiers (EDFA) when channels change rapidly. We introduce a general approach that leverages machine learning (ML) to characterize and mitigate the power excursions of EDFA systems with different equipment and scales. An ML engine is developed and experimentally validated to show accurate predictions of the power dynamics in cascaded EDFAs. Recommended channel provisioning based on the ML predictions achieves within 1% error of the lowest possible power excursion over 94% of the time. In conclusion, we also showcase significant mitigation of EDFA power excursions in super-channel provisioning when compared to the first-fit wavelength assignment algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Distinctive molecular configuration of nanostructured silica deposited at a glancing angle

Glancing-angle deposition (GLAD) produces nanostructured silica, showcasing form birefringence, an attractive alternative to traditionally used crystalline materials for polarization control. This work aims to enhance the understanding of its internal structure and associated defects in its native form and after laser processing. Our observations show, for the first time, that the GLAD silica exhibits a unique Raman signature that converges to a typical silica spectrum following laser melting. Defects were also investigated with fluorescence spectroscopy. The new insight provided by this work informs our understanding of this birefringent material and drives optimization of its performance in GLAD-based polarization control devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

CMOS photonic integrated circuit for flex-grid polarization entanglement

We showcase a CMOS-fabricated silicon photonic integrated circuit employing a bidirectionally pumped microring and polarization splitter-rotators for high-fidelity polarization entanglement. Spanning the optical C+L-band, this source is ideal for wavelength-multiplexed entanglement distribution in multi-user networks.

Miloshevsky, Alex↗
DOE OSTI2024

Ultra-narrow-linewidth hybrid-integrated self-injection locked laser at 780 nm

Narrow-linewidth lasers are essential across a wide range of applications, including classical and quantum sensing, trapped ion systems, position/navigation/timing systems, optical clocks, and microwave frequency synthesizers. In the visible and near-visible spectrum, low-noise lasers are particularly important for laser trapping and cooling techniques, which are vital for trapped ion quantum computing, sensing, and atomic clocks. In this context, our work showcases a hybrid-integrated narrow-linewidth laser that operates at 780 nm, achieving a self-heterodyne linewidth of 105 Hz. To validate the experimental results, we performed a numerical analysis that combines insights from a many-body theory applied to the gain region with a travelling-wave model to capture the laser dynamics. Our investigation further delves into how the linewidth of the self-injection locked lasers is influenced by the parameters of micro-ring resonators, aiming to assess the potential for achieving Hz-level integrated laser linewidths at 780 nm. This work not only demonstrates the technical feasibility of Hz-level narrow-linewidth lasers but also lays the groundwork for future explorations in the field.

Prokoshin, Artem (ORCID:0009000699760238)↗
DOE OSTI2024

CMOS photonic integrated source of broadband polarization-entangled photons

We showcase a fully on-chip CMOS-fabricated silicon photonic integrated circuit employing a bidirectionally pumped microring and polarization splitter-rotators tailored for the generation of broadband (>9 THz), high-fidelity (90–98%) polarization-entangled photons. Spanning the optical C+L-band and producing over 116 frequency-bin pairs on a 38.4-GHz-spaced grid, this source is ideal for flex-grid wavelength-multiplexed entanglement distribution in multiuser networks.

42 ENGINEERING↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multiple social platforms reveal actionable signals for software vulnerability awareness: A study of GitHub, Twitter and Reddit

Software vulnerabilities are flaws in computer systems that leave users open to attack. In many cases, these vulnerabilities go unnoticed and remain unresolved in codebases. Thus, awareness of software vulnerabilities among the public is crucial to ensure effective cybersecurity practices, the development of high quality software, and ultimately national security. This awareness can be better understood by studying the spread and evolution of software vulnerability discussions in online communities. This work is the first to evaluate and contrast how discussions about software vulnerabilities spread on three social platforms -- Twitter, GitHub, and Reddit. To lay the groundwork, we showcase a novel fundamental framework for measuring information spread that identifies the spread mechanisms and observables across platforms, the units of information, and the groups of measurements that can be applied to focus on a specific phenomena e.g., information cascades. We then analyze and contrast social network topologies for three example social networks and measure the scale and speed of the spread of discussion of specific vulnerabilities to understand how far and how widely they spread, how many users participate in discussions, and the duration of their spread. To demonstrate the awareness of more impactful software vulnerabilities, a subset of our analysis focuses on vulnerabilities targeted during recent major cyber attacks as well as vulnerabilities exploited by advanced persistent threat groups. We discover that usually, vulnerability discussions start on GitHub, before occurring on Twitter and Reddit. While studying how some user-level and content-level characteristics influence vulnerability spread, we observe that Twitter discussions started by users predicted to be humans have larger size, breadth, depth, adoption rate, lifetime, and structural virality compared to those started by users predicted to be bots. On Reddit, we contrast the differences in thread structure that originate from posts with positive, negative and neutral polarity. We find that posts that are positive have larger, deeper and wider discussions compared to negative and neutral posts. We anticipate the results of our analysis to not only increase the understanding of software vulnerability awareness but also inform models for simulating information spread across multiple social environments online.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A large accessory genome and high recombination rates may influence global distribution and broad host range of the fungal plant pathogen Claviceps purpurea

Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (~ 38%), high recombination rates (ρ = 0.044), and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion may be controlled by frequent recombination. We additionally identified that within the ergoline biosynthetic cluster the lpsA1 and lpsA2 were the result of a recombination event. However, the high recombination rates observed in C. purpurea may be influencing an overall trend of purifying selection across the genome. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗