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At least 145 records · Page 8

Data Quality of Salt Property Measurements

Data quality is a key element to assessing technical uncertainties in property values of salt mixtures that are pivotal in molten salt reactor (MSR) design and safety assessments under both normal operating conditions and accident scenarios. Key properties for the salt mixtures being evaluated for use in MSRs have not been measured and the few values for relevant salt compositions available in the literature are inconsistent and not suitable for use in licensing. The applications of established techniques commonly used for property measurements to molten salts are still experimental in nature and vetted consensus standards are not yet available. Work is in progress to develop and standardize methods through DOE and commercially funded projects. The quality of measured property values limits the current ability to reliably design equipment and model normal MSR operation and the effects of operational upsets. Insights from experimental measurements pertinent to reducing technical uncertainty for regulatory development are summarized in this report. Quality controls are recommended for key properties based on the mathematical calculations used to derive property values and methods used to measure experimental values and salt produced for use in the measurements.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

59 BASIC BIOLOGICAL SCIENCES↗

Prevalence of human papillomavirus genotypes in high-grade cervical precancer and invasive cervical cancer from cancer registries before and after vaccine introduction in the United States

Background. US population-based cancer registries can be used for surveillance of human papillomavirus (HPV) types found in HPV-associated cancers. Using this framework, HPV prevalence among high-grade cervical precancers and invasive cervical cancers were compared before and after HPV vaccine availability. Methods. Archived tissue from 2 studies of cervical precancers and invasive cervical cancers diagnosed from 1993-2005 (prevaccine) were identified from 7 central cancer registries in Florida; Hawaii; Iowa; Kentucky; Louisiana; Los Angeles County, California; and Michigan; from 2014 through 2015 (postvaccine) cases were identified from 3 registries in Iowa, Kentucky, and Louisiana. HPV testing was performed using L1 consensus polymerase chain reaction analysis. HPV-type–specific prevalence was examined grouped by hierarchical attribution to vaccine types: HPV 16, 18, HPV 31, 33, 45, 52, 58, other oncogenic HPV types, and other types/HPV negative. Generalized logit models were used to compare HPV prevalence in the prevaccine study to the postvaccine study by patient age, adjusting for sampling factors. Results. A total of 676 precancers (328 prevaccine and 348 postvaccine) and 1140 invasive cervical cancers (777 prevaccine and 363 postvaccine) were typed. No differences were observed in HPV-type prevalence by patient age between the 2 studies among precancers or invasive cancers. Conclusions. The lack of reduction in vaccine-type prevalence between the 2 studies is likely explained by the low number of cases and low HPV vaccination coverage among women in the postvaccine study. Monitoring HPV-type prevalence through population-based strategies will continue to be important in evaluating the impact of the HPV vaccine.

59 BASIC BIOLOGICAL SCIENCES↗

Why Do Oceanic Nonlinearities Contribute Only Weakly to Extreme El Niño Events?

Abstract Extreme El Niño events have outsized global impacts and control the El Niño Southern Oscillation (ENSO) warm/cold phases asymmetries. Yet, a consensus regarding the relative contributions of atmospheric and oceanic nonlinearities to their genesis remains elusive. Here, we isolate the contribution of oceanic nonlinearities by conducting paired experiments forced with opposite wind stress anomalies in an oceanic general circulation model, which realistically simulates extreme El Niño events and oceanic nonlinearities thought to contribute to ENSO skewness (Tropical Instability Waves (TIWs), Nonlinear Dynamical Heating (NDH)). Our findings indicate a weak contribution of oceanic nonlinearities to extreme El Niño events in the eastern Pacific, owing to compensatory effects between lateral (NDH and TIWs) and vertical processes. These results hold across different vertical mixing schemes and modifications of the upper‐ocean heat budget mixed layer criterion. Our study reinforces previous research underscoring the pivotal role of atmospheric nonlinearities in shaping extreme El Niño events.

Geology↗

Distributed Optimal Power Management for Battery Energy Storage Systems: A Novel Accelerated Tracking ADMM Approach

Optimal power management (OPM) is critical for large-scale battery energy storage systems. Today’s methods often require formidable computational effort due to the design based on centralized numerical optimization. Thus, this paper investigates computationally distributed OPM where the agents based on the cells communicate over a network to cooperatively solve the OPM problem. We propose an accelerated tracking alternating direction method of multipliers (ADMM) algorithm to solve the distributed OPM. The proposed algorithm embeds dynamic average consensus and Nesterov’s acceleration technique in the ADMM algorithm. Not only is the proposed algorithm fully distributed without a need for fusion or aggregating nodes, but it also accelerates convergence. The paper formulates the OPM in a model predictive control framework where it seeks to regulate the charging/discharging power of each battery cell to minimize the total power losses and promote balanced use of the constituent cells while complying with the safety constraints. The paper provides ample simulation results to demonstrate the effectiveness and advantages of the proposed distributed OPM in terms of computation and convergence.

Farakhor, Amir↗

Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations

Abstract Mutations within the mtrR gene are commonly found amongst multidrug resistant clinical isolates of Neisseria gonorrhoeae, which has been labelled a superbug by the Centers for Disease Control and Prevention. These mutations appear to contribute to antibiotic resistance by interfering with the ability of MtrR to bind to and repress expression of its target genes, which include the mtrCDE multidrug efflux transporter genes and the rpoH oxidative stress response sigma factor gene. However, the DNA-recognition mechanism of MtrR and the consensus sequence within these operators to which MtrR binds has remained unknown. In this work, we report the crystal structures of MtrR bound to the mtrCDE and rpoH operators, which reveal a conserved, but degenerate, DNA consensus binding site 5′-MCRTRCRN4YGYAYGK-3′. We complement our structural data with a comprehensive mutational analysis of key MtrR-DNA contacts to reveal their importance for MtrR-DNA binding both in vitro and in vivo. Furthermore, we model and generate common clinical mutations of MtrR to provide plausible biochemical explanations for the contribution of these mutations to multidrug resistance in N. gonorrhoeae. Collectively, our findings unveil key biological mechanisms underlying the global stress responses of N. gonorrhoeae.

59 BASIC BIOLOGICAL SCIENCES↗

Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors

Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goal. Herein, we use molecular modeling approaches to identify and target potential novel pockets specific to Class IIA HDAC-HDAC4 at the interface between HDAC4 and the transcriptional corepressor component protein NCoR. These pockets were screened using an ensemble docking approach combined with consensus scoring to identify compounds with a different binding mechanism than the currently known HDAC modulators. Binding was compared in experimental assays between HDAC4 and HDAC3, which belong to a different family of HDACs. HDAC4 was significantly inhibited by compound 88402 but not HDAC3. Two other compounds (67436 and 134199) had IC50 values in the low micromolar range for both HDACs, which is comparable to the known inhibitor of HDAC4, SAHA (Vorinostat). However, both of these compounds were significantly weaker inhibitors of HDAC3 than SAHA and thus more selective, albeit to a limited extent. Five compounds exhibited activity on human breast carcinoma and/or urothelial carcinoma cell lines. The present result suggests potential mechanistic and chemical approaches for developing selective HDAC4 modulators.

60 APPLIED LIFE SCIENCES↗

Investigation of the Use of Dynamic Probabilistic Risk Assessment Methodologies for Identifying Digital I&C System Common Cause Failures

Digital Instrumentation and Control (I&C) systems have a key role in nuclear power plants in the upgrade of aging analog systems. Digital systems improve plant safety and reliability through features such as increased hardware reliability and stability and improved failure detection capability. There is no consensus on which of the current probabilistic risk assessment methods are most suitable for use in the reliability analysis of digital I&C systems. While the traditional event-tree/fault-tree (ET/FT) approach is still used for their reliability modeling, there are concerns regarding this approach in properly accounting for dynamic interactions among system components since potentially significant dependencies among failure events may not be identified and/or their likelihood may not be properly quantified. Dynamic methodologies are expected to provide a much more accurate representation of probabilistic evolution of the I&C systems in time due to their capability to more properly account for complex interactions than the static approach. The applicability of dynamic PRA methodologies for digital I&C system is investigated using the criteria presented in the NUREG/CR-6901, and the comparisons made in NUREG/CR-6901 are updated in light of the latest studies. The Dynamic Event Tree (DET) approach has been identified as one of the top dynamic methods when evaluated against the requirements for the reliability modeling of digital I&C systems. The DET method is a strong candidate for integration into existing PRA studies, as it bears many similarities to the traditional ET approach. In this study, the DET approach has been applied to the Plant Protection System of the APR1400 design, and the results are compared to results from its available traditional ET/FT analysis. Possible approaches to evaluate and quantify the effects of common cause failures on system safety using dynamic methods are also examined.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

No One Size Fits All: Semiconductor Nanocrystal Sizing Curves

Although colloidal quantum dots or nanocrystals (NCs) are now long past their infancy, there remain basic issues that must be addressed to fully establish their fundamental, size-dependent properties. This is especially true for model systems such as CdSe where confinement effects are responsible for changes in their optical response and where significant effort has been invested in developing theories of their underlying electronic structure. Surprisingly, there still appears to be a lack of consensus on one of the most fundamental metrics for NCs, their sizing curves. As shown here, these are empirical functions that link the size of isotropically shaped semiconductor NCs (such as the diameter, d, for spherical NCs and edge length, l, for cube-shaped ones) to corresponding changes in optical response.

36 MATERIALS SCIENCE↗

diffReplication - An Energy-Aware Fault Tolerance Model for Silent Error Detection and Mitigation in Heterogeneous Extreme-scale Computing Environment

At extreme scale, the frequency of silent errors – a class of errors that remain undetected by low-level error detection mechanisms – increases significantly with the computational complexity of the application and the scale of the computing infrastructure. As hardware and software advances are made to usher in the next scientific era of computing, developing new approaches to mitigate the impact of silent errors remains a challenging problem. In this work, we propose an energy-aware fault-tolerance model, referred to diffReplication to overcome silent errors. In the proposed model, the main process is associated with one replica that executes at the same rate as the main process, and one diffReplica that is executed at a fraction of the main process' execution rate. If the main and its replica reach consensus at the end of a computation phase, the state of the diffReplica is updated and computation is resumed. If the synchronization attempt results in a disagreement, however, the diffReplica increases its execution speed to complete the computation and quickly reach the synchronization barrier. Assuming a single error over any given synchronization interval, a majority voting is used to reach consensus and tolerate silent errors. To further enhance its performance, diffReplication is augmented with speculative execution, whereby the main or its fast replica is selected to continue execution without waiting for the diffReplica. The selection process is based on the previous behaviour of the main and its replica. A performance analysis study is carried out to assess the performance of diffReplication, in terms of the energy saving and time-to-completion reduction achieved by the diffReplication scheme. The experiment shows that speculative execution reduces the time to completion with additional energy, and dynamic decision-making balances the energy consumption and time to completion.

97 MATHEMATICS AND COMPUTING↗

Parameter identification methods for low-order gray box building energy models: A critical review

The body of knowledge on gray box building energy modeling (GBBEM) has been developed over the past few decades and has undergone some important changes recently. Starting with simple methods and simple buildings, the science of GBBEM has grown to encompass complex and more computationally intensive techniques and complex commercial buildings. Numerous works including a recent review have considered model structure and inputs in a nearly systematic way, but no extant work systematically reviews the approaches for GBBEM parameter search initialization and final identification, despite this being arguably the most difficult and impactful part of the modeling process. To this end, we critically review 55 extant works describing advantages, limitations, and domain of applicability of several classes of parameter initialization and optimization techniques specifically for GBBEM. We categorize the classes of methods and analyze the evidence of their applicability for different applications within the field of GBBEM. We find an emerging consensus that initialization of parameter searches for anything other than the simplest building elements is often challenging and sometimes requires a stochastic approach to begin the parameter identification process. After this initial process, faster methods have been used in some cases but often the nature of the problem requires stochastic methods for this portion of the process as well. For less complex systems, more deterministic and efficient methods have been shown to be effective. Finally, we draw conclusions as to the domain of applicability of different classes of initialization and optimization techniques for GBBEEM and offer suggestions for research directions that are likely to prove fruitful.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes

The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene expression.

59 BASIC BIOLOGICAL SCIENCES↗

The effects of anthropogenic and volcanic aerosols and greenhouse gases on twentieth century Sahel precipitation

Abstract There is little scientific consensus on the importance of external climate forcings—including anthropogenic aerosols, volcanic aerosols, and greenhouse gases (GHG)—relative to each other and to internal variability in dictating past and future Sahel rainfall. We address this query by relating a 3-tiered multi-model mean (MMM) over the Climate Model Intercomparison Project phase 5 “twentieth century” and pre-Industrial control simulations to observations. The comparison of single-forcing and historical simulations highlights the importance of anthropogenic and volcanic aerosols over GHG in generating forced Sahel rainfall variability in models. However, the forced MMM only accounts for a small fraction of observed variance. A residual consistency test shows that simulated internal variability cannot explain the residual observed multidecadal variability, and points to model deficiency in simulating multidecadal variability in the forced response, internal variability, or both.

54 ENVIRONMENTAL SCIENCES↗

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å −1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q -range to <0.5 Å −1 , but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H 2 O and in D 2 O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å −1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

59 BASIC BIOLOGICAL SCIENCES↗

In situ irradiation of spent nuclear fuels

To improve the economics of commercial nuclear reactors, nuclear vendors and utilities are seeking approval for increased burnup usage of the existing nuclear fleet. This is especially critical for meeting the clean energy initiative by the United States Government, Department of Energy (DOE). However, one of the key challenges the nuclear industry faces in this regard is that the regions exposed to high burnup and low temperatures exhibit a fine-grained microstructure with large bubbles known as high-burnup structure (HBS) [1]. The formation of HBS has been correlated to the diminished performance of the reactor, as well as fuel fragmentation and pulverization during transient and accidental conditions [2]. Therefore, it is paramount to understand the mechanisms for HBS formation along with its impact on the properties and performance of nuclear fuels. While existing programs, such as Nuclear Energy Advanced Modeling and Simulation (NEAMS) and Advanced Fuel Campaign (AFC) are focusing on evaluating the performance impact of HBS, the physical mechanisms contributing to HBS formation are still not fully understood. In addition, having predictive capabilities and sound understanding of the microstructural evolution of nuclear fuel is essential for accelerated development, qualification, and deployment of new nuclear materials and novel reactor designs for advanced nuclear reactors. There is a lack of consensus among researchers regarding the mechanisms leading to such restructuring observed in HBS. Grain subdivision due to polygonization versus recrystallization, continuous versus discrete recrystallization occurring in tandem or conjunction, etc., have been proposed and debated. In general, it is hypothesized that defect accumulation and dislocation interaction within the grains cause the realignment of dislocations into grain boundaries, leading to the new subgrain formation, which over time transforms into new grains. However, due to the lack of transient data, the importance of fission rate, irradiation, thermal, and stress history of the fuel on the restructuring could not be assessed. In situ microstructural evolution under various irradiation conditions is desired to bridge this gap. Alternatively, phase-field-based models have been developed to capture HBS formation via discrete recrystallization utilizing the classical nucleation approach [3–5]. However, in these models, the grain nucleation criteria are often defined based on empirical relations for burnup and fission gas density leading to dislocation density change. A mechanistic approach to capture the dislocation interaction with the microstructural features leading to grain subdivision is lacking.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Audacity of huge: overcoming challenges of data scarcity and data quality for machine learning in computational materials discovery

Machine learning (ML)-accelerated discovery requires large amounts of high-fidelity data to reveal predictive structure–property relationships. For many properties of interest in materials discovery, the challenging nature and high cost of data generation has resulted in a data landscape that is both scarcely populated and of dubious quality. Data-driven techniques starting to overcome these limitations include the use of consensus across functionals in density functional theory, the development of new functionals or accelerated electronic structure theories, and the detection of where computationally demanding methods are most necessary. When properties cannot be reliably simulated, large experimental data sets can be used to train ML models. In the absence of manual curation, increasingly sophisticated natural language processing and automated image analysis are making it possible to learn structure–property relationships from the literature. Finally, models trained on these data sets will improve as they incorporate community feedback.

36 MATERIALS SCIENCE↗

Controlling the pandemic during the SARS-CoV-2 vaccination rollout

There is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario.

60 APPLIED LIFE SCIENCES↗

Evaluating Ensemble Predictions of South Asian Monsoon Low Pressure System Genesis

Abstract Synoptic-scale vortices known as monsoon low pressure systems (LPSs) frequently produce intense precipitation and hydrological disasters in South Asia, so accurately forecasting LPS genesis is crucial for improving disaster preparedness and response. However, the accuracy of LPS genesis forecasts by numerical weather prediction models has remained unknown. Here, we evaluate the performance of two global ensemble models—the U.S. Global Ensemble Forecast System (GEFS) and the Ensemble Prediction System of the European Centre for Medium-Range Weather Forecasts (ECMWF)—in predicting LPS genesis during the years 2021–22. The GEFS successfully predicted about half the observed LPS genesis events 1–2 days in advance; the ECMWF model captured an additional 10% of observed genesis events. Both models had a false alarm ratio (FAR) of around 50% for 1–2-day lead times. In both ensembles, the control run typically exhibited a higher probability of detection (POD) of observed events and a lower FAR compared to the perturbed ensemble members. However, a consensus forecast, in which genesis is predicted when at least 20% of ensemble members forecast LPS formation, had POD values surpassing those of the control run for all lead times. Moreover, probabilistic predictions of genesis over the Bay of Bengal, where most LPSs form, were skillful, with the fraction of ensemble members predicting LPS formation over a 5-day lead time approximating the observed frequency of genesis, without any adjustment or bias correction.

Suhas, D. L.↗