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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.

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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

Infiltration of Agrobacterium tumefaciens into Nicotiana benthamiana has become a foundational technique in plant biology, enabling efficient delivery of transgenes in planta with technical ease, robust signal, and relatively high throughput. Despite transient expression’s prevalence in disciplines such as synthetic biology, little work has been done to describe and address the variability inherent in this system, a concern for experiments that rely on highly quantitative readouts. In a comprehensive analysis of N. benthamiana agroinfiltration experiments, we model sources of variability that affect transient expression. Our findings emphasize the need to validate normalization methods under the specific conditions of each study, as distinct normalization schemes do not always reduce variation either within or between experiments. Using a dataset of 1915 plants collected over three years, we develop a model of variation in N. benthamiana transient expression, using power analysis to determine the number of individual plants required for a given effect size. Drawing on our longitudinal data, these findings inform practical guidelines for minimizing variability through strategic experimental design and power analysis, providing a foundation for more robust and reproducible use of N. benthamiana in quantitative plant biology and synthetic biology applications.

Tang, Sophia N. [Joint BioEnergy Institute (JBEI),↗
DOE OSTI2021

Computation-guided optimization of split protein systems

Splitting bioactive proteins into conditionally reconstituting fragments is a powerful strategy for building tools to study and control biological systems. However, split proteins often exhibit a high propensity to reconstitute, even without the conditional trigger, limiting their utility. Current approaches for tuning reconstitution propensity are laborious, context-specific or often ineffective. Here, we report a computational design strategy grounded in fundamental protein biophysics to guide experimental evaluation of a sparse set of mutants to identify an optimal functional window. We hypothesized that testing a limited set of mutants would direct subsequent mutagenesis efforts by predicting desirable mutant combinations from a vast mutational landscape. This strategy varies the degree of interfacial destabilization while preserving stability and catalytic activity. We validate our method by solving two distinct split protein design challenges, generating both design and mechanistic insights. Furthermore, this new technology will streamline the generation and use of split protein systems for diverse applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure

A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational changes during the chemical reaction of macromolecules. Individual-particle electron tomography (IPET) is an approach for obtaining a snap-shot 3D structure of an individual macromolecule particle by aligning the tilt series of electron tomographic (ET) images of a targeted particle through a focused iterative 3D reconstruction method. The method can reduce the influence on the 3D reconstruction from large-scale image distortion and deformation. Due to the mechanical tilt limitation, 3D reconstruction often contains missing-wedge artifacts, presented as elongation and an anisotropic resolution. Here, we report a post-processing method to correct the missing-wedge artifact. This low-tilt tomographic reconstruction (LoTToR) method contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Comprehensive single-shot biophysical cytometry using simultaneous quantitative phase imaging and Brillouin spectroscopy

Abstract Single-cell analysis, or cytometry, is a ubiquitous tool in the biomedical sciences. Whereas most cytometers use fluorescent probes to ascertain the presence or absence of targeted molecules, biophysical parameters such as the cell density, refractive index, and viscosity are difficult to obtain. In this work, we combine two complementary techniques—quantitative phase imaging and Brillouin spectroscopy—into a label-free image cytometry platform capable of measuring more than a dozen biophysical properties of individual cells simultaneously. Using a geometric simplification linked to freshly plated cells, we can acquire the cellular diameter, volume, refractive index, mass density, non-aqueous mass, fluid volume, dry volume, the fractional water content of cells, both by mass and by volume, the Brillouin shift, Brillouin linewidth, longitudinal modulus, longitudinal viscosity, the loss modulus, and the loss tangent, all from a single acquisition, and with no assumptions of underlying parameters. Our methods are validated across three cell populations, including a control population of CHO-K1 cells, cells exposed to tubulin-disrupting nocodazole, and cells under hypoosmotic shock. Our system will unlock new avenues of research in biophysics, cell biology, and medicine.

Steelman, Zachary A.↗
DOE OSTI2026

A human-in-the-loop explanation framework for morphologically transparent AI predictions from whole-slide images

Deep learning models enable the prediction of clinical endpoints from whole-slide images (WSIs), but many such models function as “black boxes”, lacking transparency about whether and which histomorphological patterns drive their predictions, hindering interpretability and clinical adoption. Here we propose a human-in-the-loop explanation framework, MorphoXAI, which provides both local and global interpretability for deep learning models by incorporating human-expert interpretations. At the global level, it reveals the histomorphological patterns on which the model consistently relies to distinguish between classes of WSIs, as well as the patterns associated with confusion between classes. At the local level, it indicates which of these patterns are used in the prediction of an individual WSI and which regions within the slide correspond to such patterns. We validated our method across multiple deep learning–based WSI analysis tasks spanning different tissue types. The results show that our framework generates explanations that accurately reflect the histomorphology underlying the model’s predictions at both global and local levels. For interpretability and clinical utility in diagnostic contexts, human evaluation results showed that our explanations were easy to interpret, rich in diagnostic features, and directly helpful for diagnostic decision-making, thereby enhancing pathologist-AI collaboration. Our work highlights that unifying global and local explanations and grounding them in expert-interpreted morphology enhances the interpretability and verifiability of deep learning models, thereby facilitating the transparent deployment of such models in clinical practice.

Lou, Peiliang↗
DOE OSTI2024

Question-answering system extracts information on injection drug use from clinical notes

Background. Injection drug use (IDU) can increase mortality and morbidity. Therefore, identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no other structured data available, such as International Classification of Disease (ICD) codes, and IDU is most often documented in unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods. Here, to address this gap in clinical information, we design a question-answering (QA) framework to extract information on IDU from clinical notes for use in clinical operations. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We use 2323 clinical notes of 1145 patients curated from the US Department of Veterans Affairs (VA) Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information from temporally out-of-distribution data. Results. Here, we show that for a strict match between gold-standard and predicted answers, the QA model achieves a 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains a 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions. Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Effects of nanoconfinement and surface charge on iron adsorption on mesoporous silica

Here, we present a combined molecular dynamics (MD) simulation and X-ray absorption fine structure (XAFS) spectroscopic investigation of aqueous iron adsorption on nanoconfined amorphous silica surfaces. The simulation models examine the effects of pore size, pH (surface charge), iron valency, and counter-ion (chloride or hydroxide). The simulation methods were validated by comparing the coordination environment of adsorbed iron with coordination numbers and bond lengths derived from XAFS. In the MD models, nanoconfinement effects on local iron coordination were investigated by comparing results for unconfined silica surfaces and in confined domains within 2 nm, 4 nm, and 8 nm pores. Experimentally, coordination environments of iron adsorbed onto mesoporous silica with 4 nm and 8 nm pores at pH 7.5 were investigated. The effect of pH in the MD models was included by simulating Fe(II) adsorption onto negatively charged SiO 2 surfaces and Fe(III) adsorption on neutral surfaces. The simulation results show that iron adsorption depends significantly on silica surface charge, as expected based on electrostatic interactions. Adsorption on a negatively charged surface is an order of magnitude greater than on the neutral surface, and simulated surface coverages are consistent with experimental results. Pore size effects from the MD simulations were most notable in the adsorption of Fe(II) at deprotonated surface sites (SiO - ), but adsorption trends varied with concentration and aqueous Fe speciation. The coordination environment of adsorbed iron varied significantly with the type of anion. Considerable ion pairing with hydroxide anions led to the formation of oligomeric surface complexes and aqueous species, resulting in larger iron hydroxide clusters at higher surface loadings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A Mixed integer linear programming‐based distributed energy management for networked microgrids considering network operational objectives and constraints

Abstract Mixed integer linear programming (MILP)–based distributed energy management for networked microgrids embedded modern distribution systems is proposed. Considering the diverse ownership of microgrids, distributed energy resources (DERs) that interface directly with utilities and responsive loads, an alternating direction method of multipliers–based distributed framework was formulated for the scheduling of networked microgrids embedded modern distribution systems by adjusting nodal price signals iteratively. In addition, to make the formulated optimization problems resolvable through more accessible and popular MILP solvers, different linearisation techniques were employed to transform the nonlinear terms into linear or mixed integer linear formats. The proposed MILP‐based distributed method preserves all participants' autonomy (e.g., microgrids, DERs that interface directly with utilities and responsive loads), while incentivising them to actively participate in the distribution system operation with price signals. The proposed method is validated with results of numerical simulation using a modern distribution system consisting of multiple networked microgrids, DERs that interface directly with utilities, as well as responsive loads.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Quantification of storage required for preserving frequency security in wind‐integrated systems

Abstract The penetration of wind power generation into the power grid has been accelerated in recent times due to the aggressive emission targets set by governments and other regulatory authorities. Although wind power has the advantage of being environment‐friendly, wind as a resource is intermittent in nature. In addition, wind power contributes little inertia to the system as most wind turbines are connected to the grid via power electronic converters. These negative aspects of wind power pose serious challenges to the frequency security of power systems as penetration increases. In this work, an approach is proposed where an energy storage system (ESS) is used to mitigate frequency security issues of wind‐integrated systems. ESSs are well equipped to supply virtual inertia to the grid due to their fast‐acting nature, thus replenishing some of the energy storage capability of displaced inertial generation. In this work, a probabilistic approach is proposed to estimate the amount of inertia required by a system to ensure frequency security. Reduction in total system inertia due to the displacement of conventional synchronous generation by wind power generation is considered in this approach, while also taking into account the loss of inertia due to forced outages of conventional units. Monte Carlo simulation is employed for implementing the probabilistic estimation of system inertia. An ESS is then sized appropriately, using the system swing equation, to compensate for the lost inertia. The uncertainty associated with wind energy is modeled into the framework using an autoregressive moving average technique. Effects of increasing the system peak load and changing the wind profile on the expected system inertia are studied to illustrate various factors that might affect system frequency security. The proposed method is validated using the IEEE 39‐bus test system.

17 WIND ENERGY↗
DOE OSTI2018

Efficient Full-Field Vibration Measurements and Operational Modal Analysis Using Neuromorphic Event-Based Imaging

Traditional vibration measurement typically requires physically attached sensors, such as accelerometers and strain gauges. However, these discrete-point sensors provide only low spatial resolution vibration measurements, potentially foregoing valuable structural information such as localized damage. Noncontact optical measurement methods such as laser vibrometers can achieve high spatial resolution vibration measurements but only through time-consuming sequential measurements and are not cost-effective. As an alternative to traditional vibration measurement methods, digital video cameras are relatively low-cost, agile, and offer noncontact, simultaneous high spatial resolution measurements where every pixel on the structure becomes a measurement point. However, regular digital video cameras are frame-based where each pixel simultaneously performs temporally uniform (synchronous) measurements containing large amounts of redundant (background) data, which consumes considerable resources for video data measurement, management, and processing. To alleviate such a challenge, this work explores the use of event-based neuromorphic imagers, specifically silicon retinas, an efficient alternative to traditional frame-based video cameras, to perform full-field vibration measurements and operational modal analysis. By imitating biological vision, each silicon retina pixel independently and asynchronously records only intensity change events that contain structural motion information while excluding redundant (background) information. Such an asynchronous event-based data measurement mechanism allows for structural motion to be captured on the microsecond scale in an extremely data-efficient manner, which could benefit real-time vibration measurement and control applications. This study takes the first step toward these applications by formulating an existing video frame-based full-field operational modal analysis technique in the event-based, asynchronous silicon retina measurement framework. Specifically, local phase-based motion extraction and blind source separation are used to automatically and efficiently extract full-field vibration and dynamics parameters from silicon retina measurements. The developed method is validated by laboratory experiments on a bench-scale cantilever beam.

42 ENGINEERING↗
DOE OSTI2015

Acoustic scattering of a cylindrical quasi-Gaussian beam with arbitrary incidence focused on a rigid elliptical cylinder

Using the partial-wave series expansion method in cylindrical coordinates, a formal analytical solution for the acoustical scattering of a 2D cylindrical quasi-Gaussian beam with an arbitrary angle of incidence θ{sub i}, focused on a rigid elliptical cylinder in a non-viscous fluid, is developed. The cylindrical focused beam expression is an exact solution of the Helmholtz equation. The scattering coefficients for the elliptical cylinder are determined by forcing the expression of the total (incident + scattered) field to satisfy the Neumann boundary condition for a rigid immovable surface, and performing the product of matrices involving an inversion procedure. Computations for the matrices elements require a single numerical integration procedure for each partial-wave mode. Numerical results are performed with particular emphasis on the focusing properties of the incident beam and its angle of incidence with respect to the major axis a of the ellipse as well as the aspect ratio a/b where b is the minor axis (assuming a > b). The method is validated and verified against previous results obtained via the T-matrix for plane waves. The present analysis is the first to consider an acoustical beam on an elliptic cylinder of variable cross-section as opposed to plane waves of infinite extent. Other 2D non-spherical and Chebyshev surfaces are mentioned that may be examined throughout this analytical formalism assuming a small deformation parameter ε.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Inertia-driven particle migration and mixing in a wall-bounded laminar suspension flow

Laminar pressure-driven suspension flows are studied in the situation of neutrally buoyant particles at finite Reynolds number. The numerical method is validated for homogeneous particle distribution (no lateral migration across the channel): the increase of particle slip velocities and particle stress with inertia and concentration is in agreement with former works in the literature. In the case of a two-phase channel flow with freely moving particles, migration towards the channel walls due to the Segré-Silberberg effect is observed, leading to the development of a non-uniform concentration profile in the wall-normal direction (the concentration peaks in the wall region and tends towards zero in the channel core). The particle accumulation in the region of highest shear favors the shear-induced particle interactions and agitation, the profile of which appears to be correlated to the concentration profile. A 1D model predicting particle agitation, based on the kinetic theory of granular flows in the quenched state regime when Stokes number St = O(1) and from numerical simulations when St < 1, fails to reproduce the agitation profile in the wall normal direction. Instead, the existence of secondary flows is clearly evidenced by long time simulations. These are composed of a succession of contra-rotating structures, correlated with the development of concentration waves in the transverse direction. The mechanism proposed to explain the onset of this transverse instability is based on the development of a lift force induced by spanwise gradient of the axial velocity fluctuations. The establishment of the concentration profile in the wall-normal direction therefore results from the combination of the mean flow Segré-Silberberg induced migration, which tends to stratify the suspension and secondary flows which tend to mix the particles over the channel cross section.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

An X-band waveguide measurement technique for the accurate characterization of materials with low dielectric loss permittivity

In this work, we present a new X-band waveguide (WR90) measurement method that permits the broadband characterization of the complex permittivity for low dielectric loss tangent material specimens with improved accuracy. An electrically long polypropylene specimen that partially fills the cross-section is inserted into the waveguide and the transmitted scattering parameter (S{sub 21}) is measured. The extraction method relies on computational electromagnetic simulations, coupled with a genetic algorithm, to match the experimental S{sub 21} measurement. The sensitivity of the technique to sample length was explored by simulating specimen lengths from 2.54 to 15.24 cm, in 2.54 cm increments. Analysis of our simulated data predicts the technique will have the sensitivity to measure loss tangent values on the order of 10{sup −3} for materials such as polymers with relatively low real permittivity values. The ability to accurately characterize low-loss dielectric material specimens of polypropylene is demonstrated experimentally. The method was validated by excellent agreement with a free-space focused-beam system measurement of a polypropylene sheet. This technique provides the material measurement community with the ability to accurately extract material properties of low-loss material specimen over the entire X-band range. This technique could easily be extended to other frequency bands.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Calculations of non-adiabatic couplings within equation-of-motion coupled-cluster framework: Theory, implementation, and validation against multi-reference methods

In this work, we report an implementation of non-adiabatic coupling (NAC) forces within the equation-of-motion coupled-cluster with single and double excitations (EOM-CCSD) framework via the summed-state approach. Using illustrative examples, we compare NAC forces computed with EOM-CCSD and multi-reference (MR) wave functions (for selected cases, we also consider configuration interaction singles). In addition to the magnitude of the NAC vectors, we analyze their direction, which is important for the calculations of the rate of non-adiabatic transitions. Our benchmark set comprises three doublet radical-cations (hexatriene, cyclohexadiene, and uracil), neutral uracil, and sodium-doped ammonia clusters. When the characters of the states agree among different methods, we observe good agreement between the respective NAC vectors, both in the Franck-Condon region and away. In the cases of large discrepancies between the methods, the disagreement can be attributed to the difference in the states’ character, which, in some cases, is very sensitive to electron correlation, both within single-reference and multi-reference frameworks. Finally, the numeric results confirm that the accuracy of NAC vectors depends critically on the quality of the underlying wave functions. Within their domain of applicability, EOM-CC methods provide a viable alternative to MR approaches.

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

Absolute photoluminescence intensity in thin film solar cells

A calculation is presented for the direct conversion of a measured luminescence signal to the implied open circuit voltage. The effects of re-absorption, spectral dependence, and interference with front and back interfaces are all included, so long as the optical properties of the structure are known. The method is validated through a comparison of the terminal open-circuit voltage with the photoluminescence intensity of Cu(In,Ga)Se 2 solar cells, each as a function of illumination intensity.

14 SOLAR ENERGY↗
DOE OSTI2020

Density determination of the thermonuclear fuel region in inertial confinement fusion implosions

Understanding of the thermonuclear burn in an inertial confinement fusion implosion requires knowledge of the local deuterium–tritium (DT) fuel density. Neutron imaging of the core now provides this previously unavailable information. Two types of neutron images are required. The first is an image of the primary 14-MeV neutrons produced by the D +T fusion reaction. The second is an image of the 14-MeV neutrons that leave the implosion hot spot and are downscattered to lower energy by elastic and inelastic collisions in the fuel. These neutrons are measured by gating the detector to record the 6–12 MeV neutrons. Using the reconstructed primary image as a nonuniform source, a set of linear equations is derived that describes the contribution of each voxel of the DT fuel region to a pixel in the downscattered image. Using the measured intensity of the 14-MeV neutrons and downscattered images, the set of equations is solved for the density distribution in the fuel region. The method is validated against test problems and simulations of high-yield implosions. The calculated DT density distribution from one experiment is presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Statistically elucidated responses from low-signal contrast mechanisms in ultrafast electron microscopy

The emergence of ultrafast electron microscopy (UEM) has enabled the discovery of strongly correlated dynamic mechanisms, including electron–phonon coupling, structural phase transitions, thermal transport, and electromagnetic deflection. Most UEM systems operate stroboscopically, meaning that the technique is susceptible to artifacts, mistakes, and misinterpretation of the data due to extensive experimental effort. In contrast to the ultrafast designation, data acquisition is extraordinarily slow because the electron beam has significantly reduced signal compared to traditional transmission electron microscopy due to pulsing the electron beam. Consequently, the sample may drift, tilt, or undergo irreversible structural changes that are independent of the time-resolved dynamics throughout the experimental time frame. Furthermore, these datasets require significant user interpretation that can be problematic when proper controls are not implemented thoroughly. Here, we demonstrate a new algorithm designed to separate ultrafast structural dynamics from long-term artifacts using a LiNbO 3 sample experiencing electrically driven surface acoustic wave propagation. Additionally, we provide examples of the impact of user bias when analyzing the data and provide a methodology, which enables the extraction of time-resolved responses when the image signal is extraordinarily low. Overall, the goal of this publication is to provide methods that validate the experimental results and reduce researcher biases during UEM data interpretation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗