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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The case for data science in experimental chemistry: examples and recommendations

The physical sciences community is increasingly taking advantage of the possibilities offered by modern data science to solve problems in experimental chemistry and potentially to change the way we design, conduct and understand results from experiments. Successfully exploiting these opportunities involves considerable challenges. In this Expert Recommendation, we focus on experimental co-design and its importance to experimental chemistry. We provide examples of how data science is changing the way we conduct experiments, and we outline opportunities for further integration of data science and experimental chemistry to advance these fields. Our recommendations include establishing stronger links between chemists and data scientists; developing chemistry-specific data science methods; integrating algorithms, software and hardware to ‘co-design’ chemistry experiments from inception; and combining diverse and disparate data sources into a data network for chemistry research.

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

Improved AlphaFold modeling with implicit experimental information

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

Abstract Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these predictions vary, however, and they do not take into account ligands, covalent modifications or other environmental factors. Here, we evaluate how well AlphaFold predictions can be expected to describe the structure of a protein by comparing predictions directly with experimental crystallographic maps. In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses. We further suggest that it is important to consider the confidence in prediction when interpreting AlphaFold predictions and to carry out experimental structure determination to verify structural details, particularly those that involve interactions not included in the prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Experimental and computational investigation of the bond energy of thorium dicarbonyl cation and theoretical elucidation of its isomerization mechanism to the thermodynamically most stable isomer, thorium oxide ketenylidene cation, OTh + CCO

Collision-induced dissociation (CID) of [Th,2C,2O] + with Xe is performed using a guided ion beam tandem mass spectrometer (GIBMS). The only products observed are ThCO + and Th + by sequential loss of CO ligands. The experimental findings and theoretical calculations support that the structure of [Th,2C,2O] + is the bent homoleptic thorium dicarbonyl cation, Th + (CO) 2 , having quartet spin, which is both thermodynamically and kinetically stable enough in the gas phase to be observed in our GIBMS instrument. Analysis of the kinetic energy-dependent cross sections for this CID reaction yields the first experimental determination of the bond dissociation energy (BDE) of (CO)Th + –CO at 0 K as 1.05 ± 0.09 eV. A theoretical BDE calculated at the CCSD(T) level with cc-pVXZ (X = T and Q) basis sets and a complete basis set (CBS) extrapolation is in very good agreement with the experimental result. Although the doublet spin bent thorium oxide ketenylidene cation, OTh + CCO, is calculated to be the most thermodynamically stable structure, it is not observed in our experiment where [Th,2C,2O] + is formed by association of Th + and CO in a direct current discharge flow tube (DC/FT) ion source. Potential energy profiles of both quartet and doublet spin are constructed to elucidate the isomerization mechanism of Th + (CO) 2 to OTh + CCO. The failure to observe OTh + CCO is attributed to a barrier associated with C–C bond formation, which makes OTh + CCO kinetically inaccessible under our experimental conditions. Furthermore, chemical bonding patterns in low-lying states of linear and bent Th + (CO) 2 and OTh + CCO isomers are also investigated.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Development of the Marble experimental platform at the National Ignition Facility

The Marble experimental platform at the National Ignition Facility (NIF) was developed to quantify the influence of heterogeneous mix on fusion burn. The platform utilizes a plastic capsule filled with a deuterated plastic foam of controlled coarseness, with tritium gas filling the voids in the foam. The capsule implosion is driven with x rays generated in an NIF Hohlraum in which the time-dependent symmetry of the implosion can be controlled via dynamic beam phasing. Importantly, the Hohlraum drive conditions can be understood via integrated 2D radiation-hydrodynamic simulations, and capsule implosions can be reliably calculated. After several years of development and experimentation, the NIF Marble platform has become successful and has produced important experimental results. Here, the experimental results, which will be presented in a future publication by the LANL Marble team, provide the first definitive examination of the influence of heterogeneous mix on thermonuclear burn.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Mining experimental magnetized liner inertial fusion data: Trends in stagnation morphology

In magnetized liner inertial fusion (MagLIF), a cylindrical liner filled with fusion fuel is imploded with the goal of producing a one-dimensional plasma column at thermonuclear conditions. However, structures attributed to three-dimensional effects are observed in self-emission x-ray images. Despite this, the impact of many experimental inputs on the column morphology has not been characterized. We demonstrate the use of a linear regression analysis to explore correlations between morphology and a wide variety of experimental inputs across 57 MagLIF experiments. Results indicate the possibility of several unexplored effects. For example, we demonstrate that increasing the initial magnetic field correlates with improved stability. Although intuitively expected, this has never been quantitatively assessed in integrated MagLIF experiments. We also demonstrate that azimuthal drive asymmetries resulting from the geometry of the “current return can” appear to measurably impact the morphology. In conjunction with several counterintuitive null results, we expect the observed correlations will encourage further experimental, theoretical, and simulation-based studies. Finally, we note that the method used in this work is general and may be applied to explore not only correlations between input conditions and morphology but also with other experimentally measured quantities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Experimental validation of a collision-radiation dataset for molecular hydrogen in plasmas

Quantitative spectroscopy of molecular hydrogen has generated substantial demand, leading to the accumulation of diverse elementary process data encompassing radiative transitions, electron-impact transitions, predissociations, and quenching. However, their rates currently available are still sparse, and there are inconsistencies among those proposed by different authors. In this study, we demonstrate an experimental validation of such a molecular dataset by composing a collisional-radiative model (CRM) for molecular hydrogen and comparing experimentally obtained vibronic populations across multiple levels. From the population kinetics of molecular hydrogen, the importance of each elementary process in various parameter space is studied. In low-density plasmas (electron density ne≲1017 m−3) the excitation rates from the ground states and radiative decay rates, both of which have been reported previously, determine the excited state population. The inconsistency in the excitation rates affects the population distribution the most significantly in this parameter space. However, in higher density plasmas (ne≳1018 m−3), the excitation rates from excited states become important, which have never been reported in the literature, and may need to be approximated in some way. In order to validate these molecular datasets and approximated rates, we carried out experimental observations for two different hydrogen plasmas; a low-density radio frequency heated plasma (ne≈1016 m−3) and the Large Helical Device (LHD) divertor plasma (ne≳1018 m−3). The visible emission lines from EF1Σg+, HH¯1Σg+, D1Πu±, GK1Σg+, I1Πg±, J1Δg±, h3Σg+, e3Σu+, d3Πu±,g3Σg+, i3Πg±, and j3Δg± states were observed simultaneously and their population distributions were obtained from their intensities. We compared the observed population distributions with the CRM prediction, in particular the CRM with the rates compiled by Janev et al., Miles et al., and those calculated with the molecular convergent close-coupling (MCCC) method. The MCCC prediction gives the best agreement with the experiment, particularly for the emission from the low-density plasma. However, the population distribution in the LHD divertor shows a worse agreement with the CRM than those from low-density plasma, indicating the necessity of the precise excitation rates from excited states. We also found that the rates for the electron attachment is inconsistent with experimental results. This requires further investigation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

An experimental and computational study of thin-layer Rayleigh–Taylor instability development during deceleration with and without an externally applied magnetic field

The importance of mitigating the Rayleigh–Taylor instability (RTI) in inertial confinement fusion (ICF) is critical to successfully achieve high gain fusion yield. Consequently, understanding the seed mechanisms of RTI and the potential evolution of RTI in ICF relevant conditions is crucial. Single feature perturbations consistently demonstrate non-linear RTI evolution, for which an experimental platform on OMEGA-EP is developed. Manufacturing defects introduced into the target design require exploration of unanticipated changes to RTI development and an identification of targets that will still render quantifiable physics results. Consequently, it is presented that the inherent 3D nature of experimental targets necessitates 3D modeling for accurate design work and predictive modeling of experimental targets, especially when high resolution imaging diagnostics, like Fresnel Zone Plates, are utilized. A study of the morphology of the RTI evolution due to changing initial conditions and the presence of an externally applied magnetic field are also explored. Experimental data show thin-layer RTI morphology comparable to resistive magneto hydrodynamic 3D results. A discussion on the impacts of an externally applied magnetic field makes the case for continued efforts to observe a magnetic field's impact on RTI morphology.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Development and preliminary results of 270 GHz microwave forward scattering diagnostic system on the experimental advanced superconducting tokamak (EAST)

To measure localized (intermediate, high) poloidal wavenumber electron density fluctuations, a tangential millimeter-wave collective scattering system has been designed and successfully developed on the experimental advanced superconducting tokamak (EAST). This innovative system employs a 270 GHz mm-wave probe beam, emitted from the mid-plane of Port K and directed towards Port P after passing through a combination of two in-vessel mirrors. Here these two ports are located on the EAST device’s midplane and are 110° apart. The downward scattered signals pass through two in-vessel mirrors, and exit through the P window. The received multi-channel separated scattering signals are arranged along the poloidal direction. This optical arrangement makes the monitored turbulent wave number is poloidal dominant and up to 40 cm −1 . The tangential microwave scattering scheme enables this diagnostic to monitor local density fluctuations, with typically a radial spatial resolution △ R = 5 cm, and a wavenumber resolution of △ k = 0.4 cm −1 . The scattering system underwent comprehensive laboratory testing in 2023, with installation finalized in 2024. The system features steerable launch and receiver optics, allowing remote control to position the scattering volume from normalized radius ρ –0 to the pedestal region on a shot-by-shot basis. Effective experimental data, characterized by distinct off-center spectral peaks, have been successfully obtained in neutral beam-heated plasmas on EAST. The beam tracing forward modeling has been employed for experimental data interpretation. The advanced millimeter-wave scattering system provides fluctuation measurement capability from ion temperature gradient to electron temperature gradient scale on low field side. Preliminary experimental density fluctuation data have been successfully obtained in neutral beam-heated plasmas on EAST. The localized measurement will be used for kinetic turbulence transport numerical simulation validation.

high-k collective scattering↗
DOE OSTI2025

Experimental parameters for plasma wakefield acceleration in a narrow plasma column

Recent theoretical advancements propose multiple positron acceleration schemes in plasma wakefield acceleration (PWFA). One of the most promising ideas involves the creation of an electron-driven blowout wake within a finite-radius pre-ionized plasma column. This leads to the formation of an elongated region of sheath electrons at the closing of the first wake period capable of accelerating positrons while simultaneously providing a transverse focusing force. Additionally, the proposed scheme has shown to be a potential means of suppressing instabilities. We present an experimental opportunity to explore the narrow column PWFA at the Facility for Advanced Accelerator Experimental Tests II (FACET-II): the E333 experiment. As a pivotal first step towards achieving positron acceleration in PWFA, we have planned a precursor experiment utilizing the currently available single-bunch electron beam to study the physics of the narrow plasma PWFA scheme. We outline the feasible experimental parameters, including beam and ionization laser parameters, along with the required laser optics for the experiment. The primary observable signatures for this stage of the experiment are the final energy spectrum and transverse position of the electron bunch, anticipating reduced energy loss and enhanced beam guidance in the narrow plasma column compared to the nominal PWFA. Comprehensive simulations are used to detail our experimental plan.

Lee, Valentina [University of Colorado, Boulder, C↗
DOE OSTI2021

Experimental investigation of abnormal transverse flow enhancement of α particles in heavy-ion collisions

The mass dependence of the transverse flow for Z = 1–5 fragments from the collisions of 40 Ar + 27 Al, 40 Ar + 48 Ti, and 40 Ar + 58 Ni at 47 MeV/nucleon is investigated experimentally in this article. The transverse flow values are determined using the in-plane components of the fragment transverse momenta, where three conventional methods, i.e., the kinetic flow tensor method, the transverse momentum analysis method, and the azimuthal correlation method, are applied to reconstruct the reaction plane in an event-by-event basis. It is demonstrated from the comparison of the present experimental mass dependent flow measurements and the model simulations using an improved antisymmetrized molecular dynamics model that the experimentally observed abnormal α transverse flow enhancement is closely related to the reaction plane reconstruction procedure in the flow extraction. We further investigate the physical existence of the abnormal α flow behavior using a two-particle azimuthal correlation method, which allows us to provide the relative flow magnitude information with an identification of fragment charge number without the knowledge of the reaction plane differing from the three conventional methods. It is found that the relative flow magnitudes deduced from the two-particle azimuthal correlation functions with an identification of Z, with the correction for the recoil effect imposed by the momentum conservation, show a monotonically increasing trend as a function of fragment charge number, with no exception of the α flow enhancement. These results, in addition to those from the improved antisymmetrized molecular dynamics model simulations, definitely provide experimental evidences for the inexistence of the abnormal α flow behavior in the heavy-ion collisions at the present incident energy region in nature.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Experimental and Computational Heat Transfer Study of sCO 2 Single-Jet Impingement

This study experimentally and computationally investigates the heat transfer capability of supercritical carbon dioxide (sCO 2 ) single jet impingement. The evaluated jet Reynolds number range is between 80,000 and 600,000, with a nondimensional jet-to-target surface spacing of 2.8. CO 2 -impinging jet stagnation conditions were maintained at approximately 200 bar and a temperature of ∼400 °C for most experiments. The goal is to understand how changes in the aforementioned parameters influence heat transfer between the working fluid and the heated surface. Additionally, due to the elevated Reynolds numbers and difference in thermodynamic properties between air and CO 2 , air-derived impingement correlations may not be appropriate for CO 2 impingement; these correlations will be evaluated against experimental sCO 2 impingement data. At the time of this study, no sCO 2 impingement data was available relevant to sCO 2 power cycles. The target surface is a 1.5-in. diameter copper block centered on the 3 mm jet orifice. A mica heating element bolted to the bottom of the copper block provides a uniform heat flux. Thermocouples embedded in the copper block are used to determine the surface temperature. Nusselt numbers obtained from experimental sCO 2 test data are compared to area-averaged Nusselt numbers from air-derived correlations. The comparisons showed that air correlations drastically underpredict the heat transfer when sCO 2 is used as the working fluid. A modified sCO 2 correlation using experimental data at discussed conditions is derived based on an existing air correlation. A CFD study is also performed to further investigate sCO 2 heat transfer characteristics, and assess the numerical model applicability to this problem type.

42 ENGINEERING↗
DOE OSTI2021

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study

Abstract Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

AmeriFlux FLUXNET-1F US-xSR NEON Santa Rita Experimental Range (SRER)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xSR NEON Santa Rita Experimental Range (SRER). This is the FLUXNET version of the carbon flux data for the site US-xSR NEON Santa Rita Experimental Range (SRER) produced by applying the standard ONEFlux (1F) software. Site Description - Santa Rita Experimental Range encompasses 21,000 hectares of upland Sonoran Desert, approximately 32 km south of Tucson, Arizona. Santa Rita Experimental Range was founded in 1903. It is the longest continuously active rangeland research facility and among the five oldest biological field stations in the United States. The site is broken into distinct pastures, through which cattle graze throughout the year in various densities and durations.

Network), NEON (National Ecological Observatory↗
DOE OSTI2023

AmeriFlux FLUXNET-1F US-xSJ NEON San Joaquin Experimental Range (SJER)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xSJ NEON San Joaquin Experimental Range (SJER). This is the FLUXNET version of the carbon flux data for the site US-xSJ NEON San Joaquin Experimental Range (SJER) produced by applying the standard ONEFlux (1F) software. Site Description - Located at The San Joaquin Experimental Range, in the western foothills of the Sierra Nevada, this 18.2 kilometer terrestrial field site is a mix of open woodlands, shrubs and grasslands with low density cattle grazing. SJER is an ecosystem research experimental area. It was originally conceived as a cooperative interdisciplinary research center to identify cost-effect methods of commercial livestock production in the annual grass-oak pine woodlands, while maintaining the integrity of the ecosystem. More recently, research objectives have expanded and diversified to include research projects making contributions to our knowledge of the patterns and processes working in this ecosystem.

Network), NEON (National Ecological Observatory↗
DOE OSTI2025

AmeriFlux FLUXNET-1F PR-xLA NEON Lajas Experimental Station (LAJA)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site PR-xLA NEON Lajas Experimental Station (LAJA). This is the FLUXNET version of the carbon flux data for the site PR-xLA NEON Lajas Experimental Station (LAJA) produced by applying the standard ONEFlux (1F) software. Site Description - The NEON Lajas Experimental Station (LAJA) site is located on the southwest corner of the main island of Puerto Rico in a experimental range. This is a grassland site that is periodically grazed by cattle.

Network), NEON (National Ecological Observatory [N↗
DOE OSTI2026

AmeriFlux FLUXNET-1F US-MEF Manitou Experimental Forest

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-MEF Manitou Experimental Forest. This is the FLUXNET version of the carbon flux data for the site US-MEF Manitou Experimental Forest produced by applying the standard ONEFlux (1F) software. Site Description - This site was established on an existing 30-m tower structure at the Forest Service's Manitou Experimental Forest, Colorado. Manitou Experimental Forest is located approximately 38 km northwest of Colorado Springs, within the Pike National Forest. The tower was constructed and used between 2008 and 2013 by NCAR for the BEACHON project and has line power and internet connections. The tower is located in approximately 12 km^2 of ponderosa pine forest and savannah with a land use history of thinning and prescribed burning, though these disturbances have not occurred for many years. The tower is situated in a broad, flat valley that drains to the north. Early research at the site was focused mainly on grazing, while more recently it has turned broadly to the ecology and management of ponderosa pine ecosystems. In 2002, the Hayman Fire burned approximately 56,000 ha to the west and northwest of the tower location.

Frank, John [US Forest Service, Rocky Mountain Res↗