Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Mathematics and Computing, Information sciences”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

An AI-Enabled MODEX Framework for Improving Predictability of Subsurface Water Storage across Local and Continental Scales

Focal Area: (2) Predictive modeling through the use of AI techniques and AI-derived model components. (3) Insight gleaned from complex data using AI, big data analytics, and other advanced methods. We propose an AI-enabled model-experiment (MODEX) framework to improve the predictability of subsurface water storage (SWS) from local to conus scales in a changing environment by taking advantage of DOE’s observation and simulation capabilities, as well as to inform the model and the observation development.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Agent-based Disease Surveillance and Transmission Model

The SARS-CoV-2 pandemic has driven a need for models that can predict transmission among populations and test the effectiveness of proposed interventions to control it such as testing, quarantining, vaccinations, and nonpharmaceutical interventions. Some questions of interest include:1. How rapidly will the virus spread if no action is taken? 2. How frequently should people be tested and quarantined if necessary? 3. Should unvaccinated persons be tested more frequently than the vaccinated? 4. If test results are delayed, how will that affect the spread? 5. How do test false negative rates affect the overall efficacy of testing programs? 6. How do constraints on testing resources impact the overall efficacy of testing programs? 7. How does the patient’s failure to recognize COVID symptoms and quarantine affect the spread? 8. What level of vaccination coverage is needed to suppress the epidemic? 9. What is the risk of a large outbreak (probability exceeding x infections)? 10. What is the cost effectiveness of interventions (dollars per avoided infection)? This report describes the structure of a discrete event simulation model that provides actionable information to address these questions. Parameter inputs and results of analyses have been reported in briefings provided to LLNL management and are not discussed here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Enhancing risk and crisis communication with computational methods: A systematic literature review

Abstract Recent developments in risk and crisis communication (RCC) research combine social science theory and data science tools to construct effective risk messages efficiently. However, current systematic literature reviews (SLRs) on RCC primarily focus on computationally assessing message efficacy as opposed to message efficiency. We conduct an SLR to highlight any current computational methods that improve message construction efficacy and efficiency. We found that most RCC research focuses on using theoretical frameworks and computational methods to analyze or classify message elements that improve efficacy. For improving message efficiency, computational and manual methods are only used in message classification. Specifying the computational methods used in message construction is sparse. We recommend that future RCC research apply computational methods toward improving efficacy and efficiency in message construction. By improving message construction efficacy and efficiency, RCC messaging would quickly warn and better inform affected communities impacted by current hazards. Such messaging has the potential to save as many lives as possible.

Mathematical Methods In Social Sciences↗
DOE OSTI2023

Automated Credibility Assessments of User Features in Scientific Software

Scientific software (SciSoft) is complex, often containing a mixture of production capabilities co-mingled with features under active research and development. Furthermore, SciSoft is often developed over decades by non-computer scientists who may not have a strong background in or prioritize software architecture design, testing, and quality (e.g., test coverage). These conditions lead to difficulty in understanding which software components or functions implement what user-facing features and therefore those features’ software quality pedigree. This lack of understanding poses challenges in assessing readiness and credibility of user features, and often relies on a SciSoft subject matter expert’s (SME) laborious investigation and assertion. This final report of a one-year Computing and Information Sciences Lab Directed Research and Development project presents a general framework for modeling SciSoft architecture as a direct relationship between user features and the software components/functions that implement them. Our approach leverages automated labeling of the SciSoft’s regression test suite and employs machine learning algorithms to construct the architecture model. We demonstrate this framework on the Solid Mechanics component of the SIERRA multi-physics engineering analysis suite developed at Sandia National Laboratories.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Symposium: Quantum Theory, Quantum Materials, Quantum Computing (Final Report, DE-SC0022551)

Quantum mechanics is fundamental to understanding, predicting, and controlling many physical processes in a vast range of scientific and technological areas. In molecules and materials, the quantum mechanics of Coulombic many-body systems determines far more than the ground state and bulk properties. Quantum mechanics governs magnetism, electron and spin transport, chemical reactions and catalysis, superconductivity, photosynthesis, etc. Each plays a vital role in modern society. As digital technologies push both temporal and length-scale limits, fundamental quantum principles become the current focus for a new class of technologies: quantum computing, quantum sensing, quantum encryption, etc. This oncoming quantum information sciences wave is manifest recently in frontier foci of all six Department of Energy Office of Science programs. The Sanibel Symposium offers a proven, influential platform for facilitating and advancing cross-fertilization among theoretical and computational chemists and physicists, computer scientists, and materials engineers. The Symposia have a long, successful record of driving progress on theory and computation of materials, nanostructures, and their molecular constituents. The Symposia thus are well-suited for advancing the quantum information science thrust in the Office of Basic Energy Sciences (BES). With that QIS thrust as the focus, we propose five sessions of the 61st Sanibel Symposium on the theme Quantum Theory, Quantum Materials, Quantum Computing. From a longer perspective, this thematic program for 2022 is the second year of a five year plan of program segments addressed at challenges in quantum information sciences and quantum materials. The rest of the Symposium program will be of considerable relevance, with, for example, sessions on quantum molecular and material dynamics, and new directions in coupled cluster theory. New ideas for methods and applications can be expected to emerge from the stimulus of the formal presentations and informal discussions. The proposed award is targeted at students, post-docs, and junior scientists. Conscious effort, characteristic of the Sanibel Symposia, to stimulate the participation of women and under-represented minorities will continue.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Vessel Rupture Thresholds for Vessel–Bubble Interactions Using an Earthworm Vasculature Model

Intravenous microbubble oscillation in the presence of ultrasound has the potential to yield a wide range of therapeutic benefits. However, the likelihood of vessel damage caused by mechanical effects has not been quantified as a function of the numerous important parameters in therapeutic ultrasound procedures. In this study, we examined the effects of microbubbles injected into the vasculature of the earthworm. It was found that the elastic properties of earthworm blood vessels are similar to those of arteries in older humans, and that earthworms are well suited to the large number of experiments necessary to investigate safety of procedures involving microbubble oscillation in sonicated vessels. Microbubbles were infused into earthworm vessels, and the rupture time during sonication was recorded as a function of ultrasound frequency, pulse repetition frequency and acoustic pressure. A modified mechanical index (MMI) was defined that successfully captured the trends in rupture probability and rupture time for the different parameter values, creating a database of vessel rupture thresholds. In the absence of bubbles, the product of MMI squared and rupture time was approximately constant, indicating a possible radiation-force effect. Here, the MMI was an effective correlating parameter in the presence of bubbles, though the mathematical dependence is not yet apparent. The results of the study are expected to be valuable in designing more refined studies in vertebrate models, as well as informing computational models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Parsimonious models of in-host viral dynamics and immune response

Mathematical models of in-host viral dynamics and immune response are a vital tool for patient-specific estimation of the initial viral load, prediction of the course of an infection, etc. The COVID-19 pandemics has given impetus to the development of models with an ever-increasing degree of complexity. We show that one of the most popular models---the Target Cell Limited model---fails the identifiability test, i.e., its parameters cannot be uniquely inferred from readily available data such as viral load measurements. Here, we present a model that is both identifiable and parsimonious according to information criteria. Our model's predictions match both reported observations of COVID-19 patients and predictions of its more complex counterparts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Prediction of histone post-translational modifications using deep learning

Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.

Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗
DOE OSTI2024

Beyond PCA: Additional Dimension Reduction Techniques to Consider in the Development of Climate Fingerprints

Abstract Dimension reduction techniques are an essential part of the climate analyst’s toolkit. Due to the enormous scale of climate data, dimension reduction methods are used to identify major patterns of variability within climate dynamics, to create compelling and informative visualizations, and to quantify major named modes such as El Niño–Southern Oscillation. Principal components analysis (PCA), also known as the method of empirical orthogonal functions (EOFs), is the most commonly used form of dimension reduction, characterized by a remarkable confluence of attractive mathematical, statistical, and computational properties. Despite its ubiquity, PCA suffers from several difficulties relevant to climate science: high computational burden with large datasets, decreased statistical accuracy in high dimensions, and difficulties comparing across multiple datasets. In this paper, we introduce several variants of PCA that are likely to be of use in climate sciences and address these problems. Specifically, we introduce non-negative , sparse , and tensor PCA and demonstrate how each approach provides superior pattern recognition in climate data. We also discuss approaches to comparing PCA-family results within and across datasets in a domain-relevant manner. We demonstrate these approaches through an analysis of several runs of the E3SM climate model from 1991 to 1995, focusing on the simulated response to the Mt. Pinatubo eruption; our findings are consistent with a recently identified stratospheric warming fingerprint associated with this type of stratospheric aerosol injection.

Weylandt, Michael↗
DOE OSTI2023

Impact Report: Quantum Systems Accelerator

The Quantum Systems Accelerator (QSA) is a U.S. National Quantum Information Science Research Center established in August 2020 and funded by the Department of Energy (DOE) Office of Science. QSA is composed of 15 partner institutions— universities and national laboratories—bringing together pioneers of many of today’s unique quantum information science (QIS) and engineering capabilities. Led by Lawrence Berkeley National Laboratory (Berkeley Lab), with Sandia National Laboratories (Sandia Labs) as the lead partner, 250+ QSA researchers are catalyzing U.S. leadership in a fast-growing field that seeks solutions to the Nation’s and the world’s most pressing problems by harnessing the laws of quantum mechanics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

hIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described by partial differential equations (PDEs) remains prohibitive with black-box Markov chain Monte Carlo (MCMC) methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two complementary libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems across a broad spectrum of scientific and engineering disciplines. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods available in the integrated software on several high-dimensional Bayesian inverse problems. These include problems characterized by both linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large (~ 50×) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log-posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Reactor System Safety: A case for New and Advanced Reactors

This presentation covers a generic overview of reactor system safety testing, analysis, and related research and development (R&D) focusing on new and advanced reactor systems. This presentation is prepared for graduate-level student seminar talks. No specific reactor design information is provided. Only publicly available information and related published articles and book contents are utilized.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗
DOE OSTI2022

MIDAS: Modeling Individual Differences using Advanced Statistics

This research explores novel methods for extracting relevant information from EEG data to characterize individual differences in cognitive processing. Our approach combines expertise in machine learning, statistics, and cognitive science, advancing the state-of-the art in all three domains. Specifically, by using cognitive science expertise to interpret results and inform algorithm development, we have developed a generalizable and interpretable machine learning method that can accurately predict individual differences in cognition. The output of the machine learning method revealed surprising features of the EEG data that, when interpreted by the cognitive science experts, provided novel insights to the underlying cognitive task. Additionally, the outputs of the statistical methods show promise as a principled approach to quickly find regions within the EEG data where individual differences lie, thereby supporting cognitive science analysis and informing machine learning models. This work lays methodological ground work for applying the large body of cognitive science literature on individual differences to high consequence mission applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

RCSB Protein Data Bank 1D tools and services

Abstract Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Advances in Kriging-Based Autonomous X-Ray Scattering Experiments

Autonomous experimentation is an emerging paradigm for scientific discovery, wherein measurement instruments are augmented with decision-making algorithms, allowing them to autonomously explore parameter spaces of interest. We have recently demonstrated a generalized approach to autonomous experimental control, based on generating a surrogate model to interpolate experimental data, and a corresponding uncertainty model, which are computed using a Gaussian process regression known as ordinary Kriging (OK). We demonstrated the successful application of this method to exploring materials science problems using x-ray scattering measurements at a synchrotron beamline. Here, we report several improvements to this methodology that overcome limitations of traditional Kriging methods. The variogram underlying OK is global and thus insensitive to local data variation. We augment the Kriging variance with model-based measures, for instance providing local sensitivity by including the gradient of the surrogate model. As with most statistical regression methods, OK minimizes the number of measurements required to achieve a particular model quality. However, in practice this may not be the most stringent experimental constraint; e.g. the goal may instead be to minimize experiment duration or material usage. We define an adaptive cost function, allowing the autonomous method to balance information gain against measured experimental cost. We provide synthetic and experimental demonstrations, validating that this improved algorithm yields more efficient autonomous data collection.

36 MATERIALS SCIENCE↗
DOE OSTI2023

3D track reconstruction of low-energy electrons in the MIGDAL low pressure optical time projection chamber

Here, we demonstrate three-dimensional track reconstruction of electrons in a low pressure (50 Torr) optical TPC consisting of two glass GEMs with an ITO strip readout in CF 4 and CF 4 /Ar mixtures. The reconstructed tracks show a variety of event topologies, including short tracks from photoelectrons induced by 55 Fe 5.9 keV X-rays and long tracks from gamma ray interactions and beta decays. Algorithms for event identification and track ridge detection are discussed as well as multiple methods for integrating information from the camera image and ITO waveforms with the goal of full 3D reconstruction of the track.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Power Grid Reliability Estimation via Adaptive Importance Sampling

Electricity production currently generates approximately 25% of greenhouse gas emissions in the USA. Thus, increasing the amount of renewable energy is a key step to carbon neutrality. However, integrating a large amount of fluctuating renewable generation is a significant challenge for power grid operating and planning. Grid reliability, i.e., an ability to meet operational constraints under power fluctuations, is probably the most important of them. In this letter, we propose computationally efficient and accurate methods to estimate the probability of line overflow, i.e., reliability constraints violation, under a known distribution of renewable energy generation. To this end, we investigate an importance sampling approach, a flexible extension of Monte-Carlo methods, which adaptively changes the sampling distribution to generate more samples near the reliability boundary. The approach allows to estimate overload probability in real-time based only on a few dozens of random samples, compared to thousands required by the plain Monte-Carlo. Our study focuses on high voltage direct current power transmission grids with linear reliability constraints on power injections and line currents. Herein, we propose a novel theoretically justified physics-informed adaptive importance sampling algorithm and compare its performance to state-of-the-art methods on multiple IEEE power grid test cases.

power system faults↗