Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Reproducibility”

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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Synthetic antibacterial minerals: harnessing a natural geochemical reaction to combat antibiotic resistance

The overuse of antibiotics in clinical and livestock settings is accelerating the selection of multidrug resistant bacterial pathogens. Antibiotic resistant bacteria result in increased mortality and financial strain on the health care and livestock industry. The development of new antibiotics has stalled, and novel strategies are needed as we enter the age of antibiotic resistance. Certain naturally occurring clays have been shown to have antimicrobial properties and kill antibiotic resistant bacteria. Harnessing the activity of compounds within these clays that harbor antibiotic properties offers new therapeutic opportunities for fighting the potentially devastating effects of the post antibiotic era. However, natural samples are highly heterogenous and exhibit variable antibacterial effectiveness, therefore synthesizing minerals of high purity with reproducible antibacterial activity is needed. Here we describe for the first time synthetic smectite clay minerals and Fe-sulfide microspheres that reproduce the geochemical antibacterial properties observed in natural occurring clays. We show that these mineral formulations are effective at killing the ESKAPE pathogens ( Enterococcus sp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter sp., Pseudomonas aeruginosa and Enterobacter sp.) by maintaining Fe 2+ solubility and reactive oxygen species (ROS) production while buffering solution pH, unlike the application of metals alone. Our results represent the first step in utilizing a geochemical process to treat antibiotic resistant topical or gastrointestinal infections in the age of antibiotic resistance.

58 GEOSCIENCES↗
DOE OSTI2023

Single-shot X-ray absorption spectroscopy at X-ray free electron lasers

X-ray Absorption Spectroscopy (XAS) is a widely used X-ray diagnostic method for studying electronic and structural properties of matter. At first glance, the relatively narrow bandwidth and the highly fluctuating spectral structure of X-ray Free Electron Lasers (XFEL) sources seem to require accumulation over many shots to achieve high data quality. To date the best approach to implementing XAS at XFEL facilities has been using monochromators to scan the photon energy across the desired spectral range. While this is possible for easily reproducible samples such as liquids, it is incompatible with many important systems. Here, we demonstrate collection of single-shot XAS spectra over 10s of eV using an XFEL source, with error bars of only a few percent. We additionally show how to extend this technique over wider spectral ranges towards Extended X-ray Absorption Fine Structure measurements, by concatenating a few tens of single-shot measurements. Our results pave the way for future XAS studies at XFELs, in particular those in the femtosecond regime. This advance is envisioned to be especially important for many transient processes that can only be initiated at lower repetition rates, for difficult to reproduce excitation conditions, or for rare samples, such as those encountered in high-energy density physics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Decadal predictability of North Atlantic blocking and the NAO

Can multi-annual variations in the frequency of North Atlantic atmospheric blocking and mid-latitude circulation regimes be skilfully predicted? Recent advances in seasonal forecasting have shown that mid-latitude climate variability does exhibit significant predictability. However, atmospheric predictability has generally been found to be quite limited on multi-annual timescales. New decadal prediction experiments from NCAR are found to exhibit remarkable skill in reproducing the observed multi-annual variations of wintertime blocking frequency over the North Atlantic and of the North Atlantic Oscillation (NAO) itself. This is partly due to the large ensemble size that allows the predictable component of the atmospheric variability to emerge from the background chaotic component. The predictable atmospheric anomalies represent a forced response to oceanic low-frequency variability that strongly resembles the Atlantic Multi-decadal Variability (AMV), correctly reproduced in the decadal hindcasts thanks to realistic ocean initialization and ocean dynamics. The occurrence of blocking in certain areas of the Euro-Atlantic domain determines the concurrent circulation regime and the phase of known teleconnections, such as the NAO, consequently affecting the stormtrack and the frequency and intensity of extreme weather events. Therefore, skilfully predicting the decadal fluctuations of blocking frequency and the NAO may be used in statistical predictions of near-term climate anomalies, and it provides a strong indication that impactful climate anomalies may also be predictable with improved dynamical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Optical analogues to the equatorial Kerr–Newman black hole

Optical analogues to black holes allow the investigation of general relativity in a laboratory setting. Previous works have considered analogues to Schwarzschild black holes in an isotropic coordinate system; the major drawback is that required material properties diverge at the horizon. We present the dielectric permittivity and permeability tensors that exactly reproduce the equatorial Kerr–Newman metric, as well as the gradient-index material that reproduces equatorial Kerr–Newman null geodesics. Importantly, the radial profile of the scalar refractive index is finite along all trajectories except at the point of rotation reversal for counter-rotating geodesics. Construction of these analogues is feasible with available ordinary materials. A finite-difference frequency-domain solver of Maxwell’s equations is used to simulate light trajectories around a variety of Kerr–Newman black holes. For reasonably sized experimental systems, ray tracing confirms that null geodesics can be well-approximated in the lab, even when allowing for imperfect construction and experimental error.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Photocatalytic water splitting

With the goal of achieving large-scale H 2 production from renewable resources, water splitting into H 2 and O 2 using semiconductor photocatalysts (sometimes called artificial photosynthesis) has been studied for five decades. Unfortunately, the lack of rigour and reproducibility in the data collection and analysis of experimental results has hindered progress in the field. This Primer provides a comprehensive overview of proper characterization and evaluation of photocatalysts for overall water splitting. In particular, the Primer covers various pitfalls in photocatalysis research, best practices for reproducibility and reliable methods for conducting rigorous experiments. As a result, the recommendations are intended to reduce false positives in the literature and to promote progress towards a practical technology for producing H 2 from water by using sunlight.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Quantifying the hydration structure of sodium and potassium ions: taking additional steps on Jacob's Ladder

The ability to reproduce the experimental structure of water around the sodium and potassium ions is a key test of the quality of interaction potentials due to the central importance of these ions in a wide range of important phenomena. In this study, we simulate the Na + and K + ions in bulk water using three density functional theory functionals: (1) the generalized gradient approximation (GGA) based dispersion corrected revised Perdew, Burke, and Ernzerhof functional (revPBE-D3) (2) the recently developed strongly constrained and appropriately normed (SCAN) functional (3) the random phase approximation (RPA) functional for potassium. We compare with experimental X-ray diffraction (XRD) and X-ray absorption fine structure (EXAFS) measurements to demonstrate that SCAN accurately reproduces key structural details of the hydration structure around the sodium and potassium cations, whereas revPBE-D3 fails to do so. However, we show that SCAN provides a worse description of pure water in comparison with revPBE-D3. RPA also shows an improvement for K + , but slow convergence prevents rigorous comparison. Finally, we analyse cluster energetics to show SCAN and RPA have smaller fluctuations of the mean error of ion–water cluster binding energies compared with revPBE-D3.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Chicken fat for catalysis: a scaffold is as important for molecular complexes for energy transformations as it is for enzymes in catalytic function

Metalloenzymes are remarkably active, specific, and efficient catalysts.Mimicking the active sites with organometallic complexes based on crystal structures has been a focus for many synthetic chemists. These surrogates have provided significant mechanistic insight into both the molecular complexes as well as the enzymes, however, one of the principle findings has been that just reproducing the active site is not adequate in reproducing the catalytic function. Specifically, the scaffold surrounding the active site plays a critical role in many aspects of catalysis, from positioning reactants optimally to positioning functional groups for reaction to creating the ideal environment for catalysis. Each of these can be controlled with both static positioning as well as small and large dynamics that can activate or control a specific part of the reaction. In this review, we will discuss the effect of organic/peptidic scaffolds, along with medium as an extension of the scaffold, and their varying impacts on catalytic reactivity.

Laureanti, Joseph A.↗
DOE OSTI2021

Transfer learning of memory kernels for transferable coarse-graining of polymer dynamics

The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of polymer solutions. The CG model is based on the generalized Langevin equation, where the memory kernel plays the critical role in determining the dynamics in all time scales. Thus, we propose methods for transfer learning of memory kernels. The key ingredient of our methods is Gaussian process regression. By integration with the model order reduction via proper orthogonal decomposition and the active learning technique, the transfer learning can be practically efficient and requires minimum training data. Through two example polymer solution systems, we demonstrate the accuracy and efficiency of the proposed transfer learning methods in the construction of transferable memory kernels. The transferability allows for out-of-sample predictions, even in the extrapolated domain of parameters. Built on the transferable memory kernels, the CG models can reproduce the dynamic properties of polymers in all time scales at different thermodynamic conditions (such as temperature and solvent viscosity) and for different systems with varying concentrations and lengths of polymers.

Ma, Zhan↗
DOE OSTI2021

Are you using the right probe molecules for assessing the textural properties of metal–organic frameworks?

Textural properties—such as the surface area, pore size distribution, and pore volume—are at the forefront of characterization for porous materials. Therefore, it is essential to accurately and reproducibly report a material's textural properties as they could ultimately dictate its applicability. This work aims to provide insightful and comprehensive studies of textural properties for a set of metal–organic frameworks (MOFs), a class of porous materials, using various gases to equip researchers in the field with a helpful guide and reference. Here, we selected a series of nine MOFs with different surface areas, pore sizes, shapes, and chemical environments to represent a wide range of materials. We probed the textural properties of these MOFs using traditional and distinctive gases: N 2 , Kr and O 2 at 77 K, Ar at 87 K, and CO 2 at 195 and 273 K. With regard to surface area, we discuss the validity and challenges associated with the current BET method, the importance of utilizing the Rouquerol et al. consistency criteria to ensure accuracy and reproducibility, and the recommended gas probes for certain materials. For pore size distribution, we discuss the efficacy of each probe for determining the pore sizes within a porous material relative to the calculated distribution from its crystal structure, the limitations of current computational kernels used to calculate pore size distributions, and the need for advanced kernels to envelope the diversity of porous materials. Finally, for pore volume, we discuss the use of the Gurvich rule to obtain the total pore volume in comparison with calculated values from crystal structures and its consistency as a metric for porous materials. Ultimately, we hope that this article will aid researchers in characterizing the textural properties of porous materials and encourage the development of new kernels capable of encompassing the complexity of MOFs and other porous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Ultra-high SERS detection of consumable coloring agents using plasmonic gold nanostars with high aspect-ratio spikes

Solution-based SERS detection by using a portable Raman instrument has emerged as an important tool due to its simplicity, and flexibility for rapid and on-site screening of analyte molecules. However, this method has several shortcomings, including poor sensitivity especially for weak-affinity analyte molecules, where there is no close contact between the plasmonic metal surface and analyte molecule. Examples of weak-affinity molecules include pigment molecules that are commonly used as a consumable coloring agent, such as allura red (AR), and sunset yellow (SY). As high consumption of colorant agents has been shown to cause adverse effects on human health, there is a strong need to develop a simple and practical sensing system with high sensitivity for these agents. Here we present a novel, highly sensitive solution-based SERS detection method for AR, and SY by using CTAC capped gold nanostars (GNS) having different aspect ratios (GNS-2, GNS-4, and GNS-5) without utilizing any aggregating agents which can enhance SERS signal however it reduces batch to batch reproducibility. The influence of the aspect ratio of GNS on SERS properties was investigated. We have achieved a limit of detection (LOD) of AR and SY as low as 0.5 and 1 ppb, respectively by using GNS-5 with the advantages of minimal sample preparation by just mixing the analyte solution into a well plate containing GNS solution. In addition, excellent colloidal stability and reproducibility have further enhanced the applicability in real-world samples. Altogether, our results evidence that the solution-based SERS detection platform using high aspect-ratio GNS can be applied for practical application to detect pigment molecules in real samples with satisfactory results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Simulation of the photodetachment spectra of the nitrate anion (NO 3 ₋ ) in the B ~ 2 E' energy range and non-adiabatic electronic population dynamics of NO 3

The photodetachment spectrum of the nitrate anion (NO 3 ₋ ) in the energy range of the NO 3 second excited state is simulated from first principles using quantum wave packet dynamics. The prediction at 10 K and 435 K relies on the use of an accurate full-dimensional fully coupled five state diabatic potential model utilizing an artificial neural network. The ability of this model to reproduce experimental spectra was demonstrated recently for the lower energy range. Analysis of the spectra indicates a weaker Jahn–Teller coupling compared to the first excited state. The detailed non-adiabatic dynamics is studied by computing the population dynamics. An ultra-fast non-statistical radiationless decay is found only among the Jahn–Teller components, which is followed by a slow statistical non-radiative decay among the different state manifolds. The latter is reproduced perfectly by a simple first order kinetics model. The dynamics in the second excited state is not affected by the presence of a conical intersection with the first excited state manifold.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Compositional and structural control in LLZO solid electrolytes

Garnet-based solid-state electrolytes (SSEs) represent a promising class of materials for next-generation batteries with improved safety and performance. However, lack of control over the composition and crystal structure of the well-known Li 7 La 3 Zr 2 O 12 (LLZO) garnet material has led to poor reproducibility with a wide range of ionic conductivities reported in the literature. In this study, the role of precursor homogeneity in controlling the compositional and structural evolution of Al-doped LLZO is explored. A novel solution-based synthesis approach is employed to demonstrate enhanced atomic-scale mixing of the starting materials in comparison to conventional solid-state preparation methods. Through this technique, it is shown that the stability and formation temperature of the highly conductive cubic phase is directly impacted by the spatial distribution of the doping element and reactant species in the precursor mixture. Precursor homogeneity was also an important factor in mitigating the formation of unwanted secondary impurities. These findings can be used to guide the synthesis of SSEs with reproducible material characteristics and enhanced electrolytic performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Controlling the spacing of the linked graphene oxide system with dithiol linkers under confinement

2D nanoscale confined systems exhibit behavior that is markedly different from that observed at the macroscale. Confinement can be tuned by controlling the interlayer spacing between confining layers using organic dithiol linkers. Adjusting spacing and selective intercalation have important impacts for catalysis, superconductivity, spin engineering, sodium ion batteries, 2D magnets, optoelectronics, and many other applications. In this study, we report how reaction conditions and organic linkers can be used to create variable, reproducible spacings between graphene oxide to provide confinement systems. We determined the conditions under which the spacing can be variably adjusted by the type of linker used, the concentration of the linker, and the reaction conditions. Employing dithiol linkers of different lengths, such as three (TPDT) and four (QPDT) aromatic rings, we can adjust the spacing between graphene oxide layers under varied reaction conditions. Here, we show that by varying dithiol linker length and using different reaction conditions, we can reproducibly control the spacing between graphene oxide layers from 0.37 nm to over 0.50 nm.

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

Relationship between microporous structure and light gas transport through glassy polymeric membranes revealed by molecular simulations

Microporous glassy polymers are attractive materials for gas separation membranes, due to their high permeability and tailorable selectivity, provided physical aging can be delayed. The archetypal microporous glassy polymer, PTMSP, can be blended with a hyper-crosslinked isatin–triptycene porous polymer network (PPN) to delay physical aging. However, while PPN is effective at reducing physical aging, it also affects the permeability of light gases through PTMSP. Molecular dynamics simulations were used here to shed fundamental light on the mechanisms responsible for these effects. Atomistic models are developed that satisfactorily reproduce experimental observations such as matrix density and cavity size distributions for neat PTMSP as well as for PTMSP–PPN blends. Analysis of the simulation results suggests that physical aging is delayed because the PPN inclusions slow down PTMSP relaxation while reducing the connectivity between free volume pockets. To understand how PPN inclusions affect light gas permeability, the atomistic models developed are used to probe CO 2 and CH 4 diffusion and sorption. These simulations are conducted for PTMSP matrices exhibiting varying density, towards reproducing experimental permeability data. Interrogating the simulation trajectories, it is discovered that while CH 4 travels preferentially through the free volume cavities, CO 2 preferentially interacts with the available surfaces, especially in the presence of PPN. These differences help interpret experimental observations. The transport of C 2 H 6 and H 2 S through PTMSP matrices was also investigated. These gases, and in particular H 2 S, were found to absorb within PTMSP, yielding very low diffusion coefficients. The ability to predict differences in diffusion pathways for various natural gas components unveils the possibility of engineering membranes to control permeability and selectivity towards large-scale applications.

Bao Le, Tran Thi [Univ. of Oklahoma, Norman, OK (U↗
DOE OSTI2021

Well-balanced treatment of gravity in astrophysical fluid dynamics simulations at low Mach numbers

We report accurate simulations of flows in stellar interiors are crucial to improving our understanding of stellar structure and evolution. Because the typically slow flows are merely tiny perturbations on top of a close balance between gravity and the pressure gradient, such simulations place heavy demands on numerical hydrodynamics schemes. We demonstrate how discretization errors on grids of reasonable size can lead to spurious flows orders of magnitude faster than the physical flow. Well-balanced numerical schemes can deal with this problem. Three such schemes were applied in the implicit, finite-volume SEVEN-LEAGUE HYDRO code in combination with a low-Mach-number numerical flux function. We compare how the schemes perform in four numerical experiments addressing some of the challenges imposed by typical problems in stellar hydrodynamics. We find that the α-β and deviation well-balancing methods can accurately maintain hydrostatic solutions provided that gravitational potential energy is included in the total energy balance. They accurately conserve minuscule entropy fluctuations advected in an isentropic stratification, which enables the methods to reproduce the expected scaling of convective flow speed with the heating rate. The deviation method also substantially increases accuracy of maintaining stationary orbital motions in a Keplerian disk on long timescales. The Cargo–LeRoux method fares substantially worse in our tests, although its simplicity may still offer some merits in certain situations. Overall, we find the well-balanced treatment of gravity in combination with low Mach number flux functions essential to reproducing correct physical solutions to challenging stellar slow-flow problems on affordable collocated grids.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Dark Energy Survey Year 3 Results: Galaxy mock catalogs for BAO analysis

The calibration and validation of scientific analysis in simulations is a fundamental tool to ensure unbiased and robust results in observational cosmology. In particular, mock galaxy catalogs are a crucial resource to achieve these goals in the measurement of baryon acoustic oscillation (BAO) in the clustering of galaxies. Here we present a set of 1952 galaxy mock catalogs designed to mimic the Dark Energy Survey Year 3 BAO sample over its full photometric redshift range 0.6 < zphoto < 1.1. The mocks are based upon 488 ICE-COLA fast N-body simulations of full-sky light cones and were created by populating halos with galaxies, using a hybrid halo occupation distribution – halo abundance matching model. This model has ten free parameters, which were determined, for the first time, using an automatic likelihood minimization procedure. We also introduced a novel technique to assign photometric redshift for simulated galaxies, following a two-dimensional probability distribution with VIMOS Public Extragalactic Redshift Survey data. The calibration was designed to match the observed abundance of galaxies as a function of photometric redshift, the distribution of photometric redshift errors, and the clustering amplitude on scales smaller than those used for BAO measurements. An exhaustive analysis was done to ensure that the mocks reproduce the input properties. Finally, mocks were tested by comparing the angular correlation function w(θ), angular power spectrum Cℓ, and projected clustering ξp(r⊥) to theoretical predictions and data. The impact of volume replication in the estimate of the covariance is also investigated. The success in accurately reproducing the photometric redshift uncertainties and the galaxy clustering as a function of redshift render this mock creation pipeline as a benchmark for future analyses of photometric galaxy surveys.Key words: catalogs / large-scale structure of Universe / galaxies: distances and redshifts / Galaxy: halo / methods: numerical

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Disc dichotomy signature in the vertical distribution of [Mg/Fe] and the delayed gas infall scenario

Context. Analysis of the Apache Point Observatory Galactic Evolution Experiment project (APOGEE) data suggests the existence of a clear distinction between two sequences of disc stars in the [α/Fe] versus [Fe/H] abundance ratio space, known as the high- and low-α sequence, respectively. This dichotomy also emerges from an analysis of the vertical distribution of the [α/Fe] abundance ratio. Aims. We aim to test whether the revised two-infall chemical evolution models designed to reproduce the low- and high-α sequences in the [α/Fe] versus [Fe/H] ratios in the solar neighbourhood are also capable of predicting the disc bimodality observed in the vertical distribution of [Mg/Fe] in APOGEE DR16 data. Methods. Along with the chemical composition of the simple stellar populations born at different Galactic times predicted by our reference chemical evolution models in the solar vicinity, we provide their maximum vertical height above the Galactic plane |zmax| computed assuming the relation between the vertical action and stellar age in APOGEE thin-disc stars. Result. The vertical distribution of the [Mg/Fe] abundance ratio predicted by the reference chemical evolution models is in agreement with that observed when combining the APOGEE DR16 data (chemical abundances) with the astroNN catalogue (stellar ages, orbital parameters) for stars younger than 8 Gyr (only low-α sequence stars). Including the high-α disc component, the dichotomy in the vertical [Mg/Fe] abundance distribution is reproduced considering the observational cut in the Galactic height of |z|< 2 kpc. However, our model predicts an overly flat (almost constant) growth of the maximum vertical height |zmax| quantity as a function of [Mg/Fe] for high-α objects in contrast with the median values from APOGEE data. Possible explanations for such a tension are that: (i) the APOGEE sample with |z|< 2 kpc is more likely than ours to be contaminated by halo stars, causing the median values to be kinematically hotter, and (ii) external perturbations – such as minor mergers – that the Milky Way experienced in the past could have heated up the disc, and the heating of the orbits cannot be modeled by only scattering processes. Assuming a disc dissection based on chemistry for APOGEE-DR16 stars (|z|< 2 kpc), the observed |zmax| distributions for high-α and low-α sequences are in good agreement with our model predictions if we consider the errors in the vertical action estimates in the calculation. Moreover, a better agreement between predicted and observed stellar distributions at different Galactic vertical heights is achieved if asteroseismic ages are included as a constraint in the best-fit model calculations. Conclusions. The signature of a delayed gas infall episode, which gives rise to a hiatus in the star formation history of the Galaxy, are imprinted both in the [Mg/Fe] versus [Fe/H] relation and in vertical distribution of [Mg/Fe] abundances in the solar vicinity.

79 ASTRONOMY AND ASTROPHYSICS↗