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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

BeyondPlanck I. Global Bayesian analysis of the Planck Low Frequency Instrument data

We describe the BeyondPlanck project in terms of motivation, methodology and main products, and provide a guide to a set of companion papers that describe each result in fuller detail. Building directly on experience from ESA's Planck mission, we implement a complete end-to-end Bayesian analysis framework for the Planck Low Frequency Instrument (LFI) observations. The primary product is a joint posterior distribution P(omega|d), where omega represents the set of all free instrumental (gain, correlated noise, bandpass etc.), astrophysical (synchrotron, free-free, thermal dust emission etc.), and cosmological (CMB map, power spectrum etc.) parameters. Some notable advantages of this approach are seamless end-to-end propagation of uncertainties; accurate modeling of both astrophysical and instrumental effects in the most natural basis for each uncertain quantity; optimized computational costs with little or no need for intermediate human interaction between various analysis steps; and a complete overview of the entire analysis process within one single framework. As a practical demonstration of this framework, we focus in particular on low-l CMB polarization reconstruction, paying special attention to the LFI 44 GHz channel. We find evidence of significant residual systematic effects that are still not accounted for in the current processing, but must be addressed in future work. These include a break-down of the 1/f correlated noise model at 30 and 44 GHz, and scan-aligned stripes in the Southern Galactic hemisphere at 44 GHz. On the Northern hemisphere, however, we find that all results are consistent with the LCDM model, and we constrain the reionization optical depth to tau = 0.067 +/- 0.016, with a low-resolution chi-squared probability-to-exceed of 16%. The marginal CMB dipole amplitude is 3359.5 +/- 1.9 uK. (Abridged.)

Andersen, KJ↗
DOE OSTI2021

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The sum is greater than the parts: exploiting microbial communities to achieve complex functions

We report multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Using Information Automation and Human Technology Integration to Implement Integrated Operations for Nuclear

The purpose of the research effort described in this report is to develop and demonstrate an approach to the design and implementation of advanced, automated systems intended to increase operational efficiencies at nuclear power plants. In particular, we describe methods for considering human-technology integration (HTI) issues throughout the various phases of system design, test, and implementation and how these considerations help promote effective design. This research project will develop planning tools and comprehensive guidance on how HTI principles and methods, in combination with information automation technologies, can enable effective data integration and coordination for full nuclear plant modernization. Specifically, this research project will develop an approach to automate the mapping of data from plant systems and processes to application needs, thereby significantly reducing the amount of human workload currently required for the execution of these tasks. In addition to developing an automated solution as a replacement for these tasks, this research will also analyze digitalization’s effectiveness in reducing operational costs of compliance related activities. Compliance activities are estimated to account for as much as 50% of operations and maintenance (i.e., non-fuel and non-capital) costs of plant operation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported phosphopeptide identification and phosphosite localization results, underscoring a critical need for benchmarking. While efforts have been made to compare performance of computational pipelines using data from synthetic phosphopeptides, evaluations involving real application data have been largely limited to comparing the numbers of phosphopeptide identifications due to the lack of appropriate evaluation metrics. We investigated three deep learning-derived features as potential evaluation metrics: phosphosite probability, Delta RT and spectral similarity. Predicted phosphosite probability is computed by MusiteDeep, which provides high accuracy as previously reported; Delta RT is defined as the absolute retention time (RT) difference between RTs observed and predicted by AutoRT; and spectral similarity is defined as the Pearson’s correlation coefficient between spectra observed and predicted by pDeep2. Using a synthetic peptide dataset, we found that both Delta RT and spectral similarity provided excellent discrimination between correct and incorrect peptide-spectrum matches (PSMs) both when incorrect PSMs involved wrong peptide sequences and even when incorrect PSMs were caused by only incorrect phosphosite localization. Based on these results, we used all the three deep learning-derived features as evaluation metrics to compare different computational pipelines on diverse set of phosphoproteomic datasets and showed their utility in benchmarking performance of the pipelines. The benchmark metrics demonstrated in this study will enable users to select computational pipelines and parameters for routine analysis of phosphoproteomics data and will offer guidance for developers to improve computational methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantum Computing for Biomedical Computational and Data Sciences: A Joint DOE-NIH Roundtable

The overlap of quantum computing and biomedical research, while less explored, presents significant near-term opportunities. The Department of Energy (DOE) and the National Institutes of Health (NIH) are interested in exploiting the DOE community’s capabilities and expertise in quantum computing to potentially advance biomedical research, targeting fundamental studies of biological and molecular structures, understanding of human health as well as mental and physical disorders and diseases, and deriving insights from clinical data. NIH’s approach to quantum computing is guided by its Strategic Plan for Data Science, emphasizing the importance of findable, accessible, interoperable, and reusable (FAIR) data assets, security and privacy of data, and efficient computing and storage. DOE’s Office of Science (SC), and more specifically the Advanced Scientific Computing Research (ASCR) program, supports quantum information science (QIS) research, contributing to a unique portfolio of quantum computing and communications expertise. This roundtable was assembled to consider the opportunities and challenges in the near-, medium-, and long-term at the intersection of quantum computing, data science, and biomedical research and how these could be addressed through inter-agency collaboration and multi-disciplinary partnerships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Localizing Clinical Patterns of Blast Traumatic Brain Injury Through Computational Modeling and Simulation

Blast traumatic brain injury is ubiquitous in modern military conflict with significant morbidity and mortality. Yet the mechanism by which blast overpressure waves cause specific intracranial injury in humans remains unclear. Reviewing of both the clinical experience of neurointensivists and neurosurgeons who treated service members exposed to blast have revealed a pattern of injury to cerebral blood vessels, manifested as subarachnoid hemorrhage, pseudoaneurysm, and early diffuse cerebral edema. Additionally, a seminal neuropathologic case series of victims of blast traumatic brain injury (TBI) showed unique astroglial scarring patterns at the following tissue interfaces: subpial glial plate, perivascular, periventricular, and cerebral gray-white interface. The uniting feature of both the clinical and neuropathologic findings in blast TBI is the co-location of injury to material interfaces, be it solid-fluid or solid-solid interface. This motivates the hypothesis that blast TBI is an injury at the intracranial mechanical interfaces. In order to investigate the intracranial interface dynamics, we performed a novel set of computational simulations using a model human head simplified but containing models of gyri, sulci, cerebrospinal fluid (CSF), ventricles, and vasculature with high spatial resolution of the mechanical interfaces. Simulations were performed within a hybrid Eulerian—Lagrangian simulation suite (CTH coupled via Zapotec to Sierra Mechanics). Because of the large computational meshes, simulations required high performance computing resources. Twenty simulations were performed across multiple exposure scenarios—overpressures of 150, 250, and 500 kPa with 1 ms overpressure durations—for multiple blast exposures (front blast, side blast, and wall blast) across large variations in material model parameters (brain shear properties, skull elastic moduli). All simulations predict fluid cavitation within CSF (where intracerebral vasculature reside) with cavitation occurring deep and diffusely into cerebral sulci. These cavitation events are adjacent to high interface strain rates at the subpial glial plate. Larger overpressure simulations (250 and 500kPa) demonstrated intraventricular cavitation—also associated with adjacent high periventricular strain rates. Additionally, models of embedded intraparenchymal vascular structures—with diameters as small as 0.6 mm—predicted intravascular cavitation with adjacent high perivascular strain rates. The co-location of local maxima of strain rates near several of the regions that appear to be preferentially damaged in blast TBI (vascular structures, subpial glial plate, perivascular regions, and periventricular regions) suggest that intracranial interface dynamics may be important in understanding how blast overpressures leads to intracranial injury.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Self-Evolution Data Fusion Platform for Large-Scale Water Models

Focal Area: Data acquisition and assimilation enabled by machine learning (ML), artificial intelligence (AI), and advanced methods including experimental/network design/optimization, unsupervised learning (deep learning), leveraging advanced hardware (e.g., edge computing). This development is to enable solving the science questions regarding the human and climatic factors that interact with and drive global water scarcity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Simulation-aided occupant-centric building design: A critical review of tools, methods, and applications

Occupants are active participants in their built environment, affecting its performance while simultaneously being affected by its design and indoor environmental conditions. With recent advances in computer modeling, simulation tools, and analysis techniques, topics such as human-building interactions and occupant behavior have gained significant interest in the literature given their premise of improving building design processes and operating strategies. In practice, the focus of occupant-centric literature has been mostly geared towards the latter (i.e., operation), leaving the implications on building design practices underexplored. This paper fills the gap by providing a critical review of existing studies applying computer-based modeling and simulation to guide occupant-centric building design. The reviewed papers are organized along four main themes, namely occupant-centric: (i) metrics of building performance, (ii) modeling and simulation approaches, (iii) design methods and applications, and (iv) supporting practices and mechanisms. Important barriers are identified for a more effective application of occupant-centric building design practices, including the limited consideration of metrics beyond energy efficiency (e.g., occupant well-being and space planning), the limited implementation and validation of the proposed methods, and the lack of integration of occupant behavior modeling in existing building performance simulation tools. Finally, future research directions are discussed, covering large-scale international data collection efforts to move from generic assumptions about occupant behavior to specific/localized knowledge, improved metrics of measuring building performance, and improved industry practices, such as building codes, to promote an occupant-in-the-loop approach to the building design process.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Translating nanoparticle dosimetry from conventional in vitro systems to occupational inhalation exposures

As encouraged by Toxicity Testing in the 21st Century, researchers increasingly apply high-throughput in vitro approaches to identify and characterize nanoparticle hazards, including conventional aqueous cell culture systems to assess respiratory hazards. Translating nanoparticle dose from conventional toxicity testing systems to relevant human exposures remains a major challenge for assessing occupational risk of nanoparticle exposures. Here, we explored existing computational tools and data available to translate nanoparticle dose metrics from cellular test systems to inhalation exposures of silver nanoparticles in humans. We used the Multiple-Path Particle Dosimetry (MPPD) Model to predict deposition of humans exposed to 20 and 110 nm silver nanoparticles at 0.9 µg/m3 over an 8 hr period, the proposed a National Institute of Occupational Safety and Health (NIOSH) recommended exposure limit (REL). MPPD predicts 1.88 and 0.98 µg of silver deposited in an 8 hr period for 20 and 110 nm nanoparticles, respectively, with 20 nm particles displaying nearly 11-fold higher total surface area deposited. Peak nanoparticle concentrations occurred more proximal in the pulmonary tract compared to mass deposition patterns (generation 5 vs. generations 20-21, respectively) due to regional differences in lung lining fluid volumes. Assuming 0.4% nanoparticle dissolution by mass as previously measured, we predict peak concentrations of silver ions in cells of 0.24 and 0.17 µg/mL for 20 and 110 nm particles, respectively. Both predicted concentrations are below the measured toxic threshold of 1.7 µg/mL of silver ions in cells from in vitro assessments. Assuming 4% dissolution by mass, we predict 10-fold higher silver concentrations in tissues, peaking at 2.4 and 1.7 µg/mL, for 20 and 110 nm nanoparticles respectively, exceeding the observed in vitro toxic threshold and highlighting the importance and sensitivity of dissolution rates. Overall, this approach offers a framework for extrapolating nanotoxicity results from in vitro cell culture systems to human exposures. Aligning appropriate dose metrics from in vitro and in vivo hazard characterizations and human pulmonary doses from occupational exposures are critical components for successful nanoparticle risk assessment and worker protection and provide guidance for designing future in vitro studies aimed at relevant human exposures.

Smith, Jordan N.↗
DOE OSTI2021

2019 Computing Sciences Strategic Plan

Computing has transformed nearly every aspect of scientific inquiry — across disciplines and across scales — from the behavior of subatomic particles to the formation of structures in the early universe, from the assembly of the human genome to the evolution of earth systems. Over the past two decades, computing has become an integral part of how Berkeley Lab is “Bringing Science Solutions to the World.” Advances in computing and mathematics have been key, with new mathematical models of complex physical phenomena, new methods for analyzing complex data, new algorithms for accuracy and scaling and sophisticated software systems that encapsulate these techniques into open, reusable tools. The performance of NERSC computers and the ESnet network have grown by several orders of magnitude, along with our understanding of how to map scientific computations and workflows onto these systems. From research to facility operations, the passion, talent and dedication of the Computing Sciences Area staff has been the cornerstone of our success. The plan outlined in this document describes the next step in a journey to expand the influence and impact of our efforts, building an increasingly connected global enterprise for science that places more powerful instruments in the hands of scientists, along with more powerful methods and tools for modeling, analysis and prediction.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The Ground Truth Program: Simulations as Test Beds for Social Science Research Methods.

Social systems are uniquely complex and difficult to study, but understanding them is vital to solving the world’s problems. The Ground Truth program developed a new way of testing the research methods that attempt to understand and leverage the Human Domain and its associated complexities. The program developed simulations of social systems as virtual world test beds. Not only were these simulations able to produce data on future states of the system under various circumstances and scenarios, but their causal ground truth was also explicitly known. Research teams studied these virtual worlds, facilitating deep validation of causal inference, prediction, and prescription methods. The Ground Truth program model provides a way to test and validate research methods to an extent previously impossible, and to study the intricacies and interactions of different components of research.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

An expanded registry of candidate cis -regulatory elements

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Moore, Jill E. [Univ. of Massachusetts, Worchester↗
DOE OSTI2021

Human-Constrained Indicators of Gatekeeping Behavior as a Role in Information Suppression: Finding Invisible Information and the Significant Unsaid

To date, disinformation research has focused largely on the production of false information ignoring the suppression of select information. We term this alternative form of disinformation information suppression. Information suppression occurs when facts are withheld with the intent to mislead. In order to detect information suppression, we focus on understanding the actors who withhold information. In this research, we use knowledge of human behavior to find signatures of different gatekeeping behaviors found in text. Specifically, we build a model to classify the different types of edits on Wikipedia using the added text alone and compare a human-informed feature engineering approach to a featureless algorithm. Being able to computationally distinguish gatekeeping behaviors is a first step towards identifying when information suppression is occurring.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization

Apoptosis is important for development and tissue homeostasis, and its dysregulation can lead to diseases, including cancer. As an apoptotic effector, BAK undergoes conformational changes that promote mitochondrial outer membrane disruption, leading to cell death. This is termed “activation” and can be induced by peptides from the human proteins BID, BIM, and PUMA. To identify additional peptides that can regulate BAK, we used computational protein design, yeast surface display screening, and structure-based energy scoring to identify 10 diverse new binders. We discovered peptides from the human proteins BNIP5 and PXT1 and three non-native peptides that activate BAK in liposome assays and induce cytochrome c release from mitochondria. Crystal structures and binding studies reveal a high degree of similarity among peptide activators and inhibitors, ruling out a simple function-determining property. Our results shed light on the vast peptide sequence space that can regulate BAK function and will guide the design of BAK-modulating tools and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The kinetics of SARS-CoV-2 infection based on a human challenge study

Studying the early events that occur after viral infection in humans is difficult unless one intentionally infects volunteers in a human challenge study. Here, we use data about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in such a study in combination with mathematical modeling to gain insights into the relationship between the amount of virus in the upper respiratory tract and the immune response it generates. We propose a set of dynamic models of increasing complexity to dissect the roles of target cell limitation, innate immunity, and adaptive immunity in determining the observed viral kinetics. We introduce an approach for modeling the effect of humoral immunity that describes a decline in infectious virus after immune activation. We fit our models to viral load and infectious titer data from all the untreated infected participants in the study simultaneously. We found that a power-law with a power h < 1 describes the relationship between infectious virus and viral load. Viral replication at the early stage of infection is rapid, with a doubling time of ~2 h for viral RNA and ~3 h for infectious virus. We estimate that adaptive immunity is initiated ~7 to 10 d postinfection and appears to contribute to a multiphasic viral decline experienced by some participants; the viral rebound experienced by other participants is consistent with a decline in the interferon response. Altogether, we quantified the kinetics of SARS-CoV-2 infection, shedding light on the early dynamics of the virus and the potential role of innate and adaptive immunity in promoting viral decline during infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A bacterial sensor taxonomy across earth ecosystems for machine learning applications

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and “transduce” signals to adjust internal processes. We hypothesized that an ecosystem’s unique stimuli leave a sensor “fingerprint,” able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection’s nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient’s disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

DRAS: Deep Reinforcement Learning for Cluster Scheduling in High Performance Computing

Cluster schedulers are crucial in high-performance computing (HPC). They determine when and which user jobs should be allocated to available system resources. Existing cluster scheduling heuristics are developed by human experts based on their experience with specific HPC systems and workloads. However, the increasing complexity of computing systems and the highly dynamic nature of application workloads have placed tremendous burden on manually designed and tuned scheduling heuristics. More aggressive optimization and automation are needed for cluster scheduling in HPC. In this work, we present an automated HPC scheduling agent named DRAS (Deep Reinforcement Agent for Scheduling) by leveraging deep reinforcement learning. DRAS is built on a hierarchical neural network incorporating special HPC scheduling features such as resource reservation and backfilling. An efficient training strategy is presented to enable DRAS to rapidly learn the target environment. Once being provided a specific scheduling objective given by the system manager, DRAS automatically learns to improve its policy through interaction with the scheduling environment and dynamically adjusts its policy as workload changes. We implement DRAS into a HPC scheduling platform called CQGym. CQGym provides a common platform allowing users to flexibly evaluate DRAS and other scheduling methods such as heuristic and optimization methods. Furthermore, the experiments using CQGym with different production workloads demonstrate that DRAS outperforms the existing heuristic and optimization approaches by up to 50%.

97 MATHEMATICS AND COMPUTING↗