Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “sampling methods”

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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Computing equilibrium free energies through a nonequilibrium quench

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium “quench” process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications.

Chemistry↗
DOE OSTI2025

Computing Reaction Kinetics with MC-PDFT–OPESf: Combining Multireference Electronic Structure Theory and Enhanced Sampling

Accurate rate constants are crucial for understanding and optimizing catalytic reactions mediated by enzymes, metalloproteins, and heterogeneous catalysts. These systems frequently present a dual computational challenge. Multiconfigurational reaction sites require multireference techniques for the accurate treatment of the electronic structure, and high activation barriers prevent efficient sampling of unbiased reactive transitions. In this work, we combine multiconfiguration pair-density functional theory (MC-PDFT) as an accurate and efficient multireference electronic structure method with on-the-fly probability-enhanced sampling flooding (OPESf) as an enhanced sampling method capable of accelerating reactive transitions. We demonstrate the approach on the Diels–Alder [4+2] cycloaddition between cis-butadiene and ethene as a reaction characterized by a large activation barrier and multireference character. MC-PDFT–OPESf provides reaction rates in agreement with experiments at a fraction of the computational cost required by conventional unbiased ab initio calculations. Here, we propose MC-PDFT–OPESf as an efficient approach for computing kinetics in strongly correlated molecular systems.

Chemical calculations↗
DOE OSTI2020

XPS guide: Charge neutralization and binding energy referencing for insulating samples

This guide deals with methods to control surface charging during XPS analysis of insulating samples and approaches to extracting useful binding energy information. Furthermore, the guide summarizes the causes of surface charging, how to recognize when it occurs, approaches to minimize charge buildup, and methods used to adjust or correct XPS photoelectron binding energies when charge control systems are used. Additionally, there are multiple ways to control surface charge buildup during XPS measurements and examples of systems on advanced XPS instruments are described. There is no single, simple, and foolproof way to extract binding energies on insulating material, but advantages and limitations of several approaches are described. Because of the variety of approaches and limitations of each it is critical for researchers to accurately describe the procedures that have been applied in research reports and publications.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Controllable Thin‐Film Approaches for Doping and Alloying Transition Metal Dichalcogenides Monolayers

Abstract Two‐dimensional (2D) transition metal dichalcogenides (TMDs) exhibit exciting properties and versatile material chemistry that are promising for device miniaturization, energy, quantum information science, and optoelectronics. Their outstanding structural stability permits the introduction of various foreign dopants that can modulate their optical and electronic properties and induce phase transitions, thereby adding new functionalities such as magnetism, ferroelectricity, and quantum states. To accelerate their technological readiness, it is essential to develop controllable synthesis and processing techniques to precisely engineer the compositions and phases of 2D TMDs. While most reviews emphasize properties and applications of doped TMDs, here, recent progress on thin‐film synthesis and processing techniques that show excellent controllability for substitutional doping of 2D TMDs are reported. These techniques are categorized into bottom–up methods that grow doped samples on substrates directly and top–down methods that use energetic sources to implant dopants into existing 2D crystals. The doped and alloyed variants from Group VI TMDs will be at the center of technical discussions, as they are expected to play essential roles in next‐generation optoelectronic applications. Theoretical backgrounds based on first principles calculations will precede the technical discussions to help the reader understand each element's likelihood of substitutional doping and the expected impact on the material properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Oxygen K -edge X-ray absorption spectra of liquids with minimization of window contamination

We report oxygen K-edge X-ray absorption spectroscopy is used routinely to study a range of solid materials. However, liquid samples are studied less frequently at the oxygen K-edge due to the combined challenges of high-vacuum conditions and oxygen contamination of window materials. A modular sample holder design with a twist-seal sample containment system that provides a simple method to encapsulate liquid samples under high-vacuum conditions is presented. This work shows that pure silicon nitride windows have lower oxygen contamination than both diamond- and silicon-rich nitride windows, that the levels of oxygen contamination are related to the age of the windows, and provides a protocol for minimizing the background oxygen contamination. Acid-washed 100 nm-thick silicon nitride windows were found to give good quality oxygen K-edge data on dilute liquid samples.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Efficient sampling of free energy landscapes with functions in Sobolev spaces

Molecular simulations of biological and physical phenomena generally involve sampling complicated, rough energy landscapes characterized by multiple local minima. In this work, we introduce a new family of methods for advanced sampling that draw inspiration from functional representations used in machine learning and approximation theory. As shown here, such representations are particularly well suited for learning free energies using artificial neural networks. As a system evolves through phase space, the proposed methods gradually build a model for the free energy as a function of one or more collective variables, from both the frequency of visits to distinct states and generalized force estimates corresponding to such states. Implementation of the methods is relatively simple and, more importantly, for the representative examples considered in this work, they provide computational efficiency gains of up to several orders of magnitude over other widely used simulation techniques.

Approximation theory↗
DOE OSTI2023

Entropy-driven Optimal Sub-sampling of Fluid Dynamics for Developing Machine-learned Surrogates

Optimal sub-sampling of large datasets from fluid dynamics simulations is essential for training reduced-order machine learned models. A method using Shannon entropy was developed to weight flow features according to their level of information content, such that the most informative features can be extracted and used for training a surrogate model. The method is demonstrated in the canonical flow over a cylinder problem simulated with OpenFOAM. Both time-independent predictions and temporal forecasting were investigated as well as two types of prediction targets: local per-grid-point predictions and global per-time-step predictions. When tested on training a surrogate model, results indicate that our entropy-based sampling method typically outperforms random sampling and yields more reproducible results in less iterations. Finally, the method was used to train a surrogate model for modeling turbulence in magnetohydrodynamic flows, which revealed various challenges and opportunities for future research.

Brewer, Wes↗
DOE OSTI2021

Identifying crystallographic faces of the fluorites urania and thoria with rotational polarized Raman spectroscopy

Crystallite orientation identification is invaluable, but is often limited to small area identification or requires a large area sample. Nondestructive optical methods such as polarized Raman spectroscopy, in contrast, can be used to completely map a variety of sample sizes, but their potential is not yet fully realized. Here, we report a systematic study of polarized Raman scattering of high-quality, hydrothermally grown, single crystals of urania and thoria. The peak intensity variations for as-grown major crystal planes, post-growth polished crystal planes, and a post-growth polished non-crystallographic plane are directly linked to crystallographic orientation and crystal rotation, and agree with computed models. In particular, the parallel polarized peak intensity results are directly correlated with metal–oxygen–metal chains in the fluorite structure and can be used to determine both orientation and rotational alignment of a given crystal face if sufficiently small rotational steps are applied. These results are structure based, being applicable to the larger fluorite phase space, which is useful for optical, semiconductor, nuclear, and solid oxide fuel cell industries. Further, these results suggest that Raman spectroscopy can identify non-crystallographic orientations that are not discernable by traditional means.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Computational Optimization of 133m Xe Production via Neutron Irradiation in a TRIGA Reactor

Here, the Comprehensive Nuclear-Test-Ban Treaty bans all nuclear tests worldwide. As part of treaty compliance, the concentration of radioactive nuclides in the atmosphere is monitored to detect nuclear weapons tests. Radioactive noble gas fission products, specifically radioxenon, can vent into the atmosphere after a nuclear weapons test, even if the test is well contained underground or underwater. Radioxenon thus serves as a signal for nuclear weapons tests. All atmospheric monitoring systems require samples of radioxenon isotopes for detector calibration, quality control, and certification. Here, we present a novel, improved method for creating samples of 133m Xe via neutron irradiation of 132 Xe in the Washington State University TRIGA reactor. 132 Xe neutron absorption results in either 133 Xe or 133m Xe—thermal neutron absorption results in 133m Xe 12% of the time, while fast neutron absorption (above ~1 MeV) results in 133m Xe ~50% of the time. To optimize the production of 133m Xe via neutron absorption in 132 Xe in the thermal TRIGA reactor, spectral tuning using an irradiation chamber is required to maximize the fraction of fast neutrons being absorbed and minimize the number of thermal neutrons interacting with the 132 Xe. We used MCNP to tally 132 Xe absorptions with the isotopic tally function, flux tallies and neutron attenuation to estimate the number of neutrons reaching the 132 Xe through the irradiation chamber, and the adjoint importance function to improve the source strength estimate. Additionally, we performed a heat transfer analysis for safety considerations. It was determined that the use of a 96% enriched 10 B boron carbide chamber, placed next to the fuel elements in reactor position D8, increases the 133m Xe/ 133 Xe activity ratio from a baseline value of 0.3 to 1.0, a 233% increase. Additionally, it was determined that the alpha heating produced in the boron does not become an unmanageable problem in the Washington State University reactor.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
DOE OSTI2020

Novel Geometric Operations for Linear Programming

This report summarizes the work performed under the project "Linear Programming in Strongly Polynomial Time." Linear programming (LP) is a classic combinatorial optimization problem heavily used directly and as an enabling subroutine in integer programming (IP). Specifically IP is the same as LP except that some solution variables must take integer values (e.g. to represent yes/no decisions). Together LP and IP have many applications in resource allocation including general logistics, and infrastructure design and vulnerability analysis. The project was motivated by the PI's recent success developing methods to efficiently sample Voronoi vertices (essentially finding nearest neighbors in high-dimensional point sets) in arbitrary dimension. His method seems applicable to exploring the high-dimensional convex feasible space of an LP problem. Although the project did not provably find a strongly-polynomial algorithm, it explored multiple algorithm classes. The new medial simplex algorithms may still lead to solvers with improved provable complexity. We describe medial simplex algorithms and some relevant structural/complexity results. We also designed a novel parallel LP algorithm based on our geometric insights and implemented it in the Spoke-LP code. A major part of the computational step is many independent vector dot products. Our parallel algorithm distributes the problem constraints across processors. Current commercial and high-quality free LP solvers require all problem details to fit onto a single processor or multicore. Our new algorithm might enable the solution of problems too large for any current LP solvers. We describe our new algorithm, give preliminary proof-of-concept experiments, and describe a new generator for arbitrarily large LP instances.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A Review of Online Monitoring within Used Nuclear Fuel Recycling Processes

The processing of used nuclear fuels and related materials is often complex and variable. The ability to quickly optimize conditions to the material being processed can aid in increasing efficiency and safety, but requires very quick determination of the conditions present in the feedstock, the process, and the product. Furthermore, accurate quantification of materials such as enriched uranium and plutonium aids in maintaining material accountancy and avoiding nuclear proliferation risks. Traditional analytical methods require process samples to be collected and analyzed in a laboratory, which often takes days to weeks. Online monitoring is suitable for collecting this information nearly instantaneously, enabling much faster optimization of the process or detection of material diversion. Online monitoring is also beneficial as it is typically based on robust and nondestructive analytical methods, so no material is removed as samples. This review examines online monitoring relevant to used nuclear fuel processing for the determination of both chemical and physical parameters. The chemical parameters include quantities such as concentration, isotopic composition, and speciation. These values are often well suited to spectroscopic or spectrometric measurements as they are fast, nondestructive, and easily implemented in an online manner. Physical quantities are often more varied and include temperature, pressure, tank fill levels, and others. Due to the specificity of these quantities, specialized instrumentation is often used. However, this instrumentation is often amendable to online monitoring.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Scalable deep learning for watershed model calibration

Watershed models such as the Soil and Water Assessment Tool (SWAT) consist of high-dimensional physical and empirical parameters. These parameters often need to be estimated/calibrated through inverse modeling to produce reliable predictions on hydrological fluxes and states. Existing parameter estimation methods can be time consuming, inefficient, and computationally expensive for high-dimensional problems. In this paper, we present an accurate and robust method to calibrate the SWAT model (i.e., 20 parameters) using scalable deep learning (DL). We developed inverse models based on convolutional neural networks (CNN) to assimilate observed streamflow data and estimate the SWAT model parameters. Scalable hyperparameter tuning is performed using high-performance computing resources to identify the top 50 optimal neural network architectures. We used ensemble SWAT simulations to train, validate, and test the CNN models. We estimated the parameters of the SWAT model using observed streamflow data and assessed the impact of measurement errors on SWAT model calibration. We tested and validated the proposed scalable DL methodology on the American River Watershed, located in the Pacific Northwest-based Yakima River basin. Our results show that the CNN-based calibration is better than two popular parameter estimation methods (i.e., the generalized likelihood uncertainty estimation [GLUE] and the dynamically dimensioned search [DDS], which is a global optimization algorithm). For the set of parameters that are sensitive to the observations, our proposed method yields narrower ranges than the GLUE method but broader ranges than values produced using the DDS method within the sampling range even under high relative observational errors. The SWAT model calibration performance using the CNNs, GLUE, and DDS methods are compared using R 2 and a set of efficiency metrics, including Nash-Sutcliffe, logarithmic Nash-Sutcliffe, Kling-Gupta, modified Kling-Gupta, and non-parametric Kling-Gupta scores, computed on the observed and simulated watershed responses. The best CNN-based calibrated set has scores of 0.71, 0.75, 0.85, 0.85, 0.86, and 0.91. The best DDS-based calibrated set has scores of 0.62, 0.69, 0.8, 0.77, 0.79, and 0.82. The best GLUE-based calibrated set has scores of 0.56, 0.58, 0.71, 0.7, 0.71, and 0.8. The scores above show that the CNN-based calibration leads to more accurate low and high streamflow predictions than the GLUE and DDS sets. Our research demonstrates that the proposed method has high potential to improve our current practice in calibrating large-scale integrated hydrologic models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Resonance Scattering Treatment with the Windowed Multipole Formalism

A new method for directly sampling the resonance upscattering effect is presented. Alternatives have relied on inefficient rejection sampling techniques or large tabular storage of relative velocities. None of these approaches, which require pointwise energy data, are particularly well suited to the windowed multipole cross-section representation. The new method, called multipole analytic resonance scattering, overcomes these limitations by inverse transform sampling from the target relative velocity distribution where the cross section is expressed in the multipole formalism. The closed-form relative speed distribution contains a novel special function we deem the incomplete Faddeeva function, and we present the first results on its efficient numerical evaluation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

A new method for quantifying 64 Cu in nuclear debris samples

Quantifying 64 Cu in post-detonation nuclear debris samples can provide important diagnostic information regarding the structural materials used within a nuclear device. However, this task is challenging due to the weak gamma emissions associated with the decay of 64 Cu, its short half-life (12.701 h), and the presence of interfering fission product radioisotopes. Large quantities of debris sample are generally needed to accurately quantify 64 Cu, which can be problematic in sample-limited scenarios where other radiometric analyses are required. Herein, we present a new method for the separation of 64 Cu from solutions of mixed fission products and demonstrate the quantification of its activity through use of gas-flow proportional beta counting. Here, the new method was validated through a series of rigorous tests and was shown to improve the detection limit of 64 Cu by over two orders of magnitude, from 2.5 × 10 6 to 1.3 × 10 4 atoms/sample for 100 min measurements.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗
DOE OSTI2022

Adaptive-in-temperature method for fast on-the-fly sampling of thermal neutron scattering data in MCNP6 [Slides]

The project objective and motivation is to develop thermal data libraries for selected isotopes in MCNP6 to support on-the-fly S(alpha, beta) sampling for temperature ranges applicable to nuclear criticality safety, thereby enhancing the physics treatment in MCNP6 so that it can perform fast on-the-fly sampling of S(alpha, beta) data at arbitrary temperature.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Further, our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Efficient Optimization of Plasma Radiation Detector Configurations using Imperfect Inference Models

The configurations of instruments fielded on an experiment affect the amount of information captured and the quality of subsequent inference. Here, we investigate the problem of optimizing plasma x-ray radiation detectors in a magneto-inertial fusion experiment at Sandia National Laboratories. It is impossible to directly measure properties such as the temperature of the thermonuclear fusion plasma produced in these experiments because of the extreme environment and destructive nature of the experiment. Among other diagnostics, several detectors are placed with significant standoff from the fusion target to capture the x-rays emitted by the fusion plasma, which can be used to infer some of its properties. To optimize the configuration of these detectors, a high-fidelity model (HFM) is used for simulating outputs and a low-fidelity model (LFM) is used for inference. We develop methods based on A- and L-optimality criteria that are efficient to compute while explicitly accounting for the discrepancy between the HFM and the LFM. The method allows us to find detector configurations that perform similarly to or better than the configuration obtained using an existing sampling-based optimization method while decreasing computational time by a factor of 50. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Bayesian optimization↗