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DOE OSTI2023

Standardized Data to Improve Understanding and Modeling of Soil Nitrogen at Continental Scale

Abstract Nitrogen (N) is a key limiting nutrient in terrestrial ecosystems, but there remain critical gaps in our ability to predict and model controls on soil N cycling. This may be in part due to lack of standardized sampling across broad spatial–temporal scales. Here, we introduce a continentally distributed, publicly available data set collected by the National Ecological Observatory Network (NEON) that can help fill these gaps. First, we detail the sampling design and methods used to collect and analyze soil inorganic N pool and net flux rate data from 47 terrestrial sites. We address methodological challenges in generating a standardized data set, even for a network using uniform protocols. Then, we evaluate sources of variation within the sampling design and compare measured net N mineralization to simulated fluxes from the Community Earth System Model 2 (CESM2). We observed wide spatiotemporal variation in inorganic N pool sizes and net transformation rates. Site explained the most variation in NEON’s stratified sampling design, followed by plots within sites. Organic horizons had larger pools and net N transformation rates than mineral horizons on a sample weight basis. The majority of sites showed some degree of seasonality in N dynamics, but overall these temporal patterns were not matched by CESM2, leading to poor correspondence between observed and modeled data. Looking forward, these data can reveal new insights into controls on soil N cycling, especially in the context of other environmental data sets provided by NEON, and should be leveraged to improve predictive modeling of the soil N cycle.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting

Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. Here, we introduce nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells via RNA sequencing and mass spectrometry-based proteomics, respectively. Benchmarking of nanoSPLITS demonstrates high measurement precision with deep proteomic and transcriptomic profiling of single-cells. We apply nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing insights into cell cycle regulation. We extend nanoSPLITS to primary cells isolated from human pancreatic islets, introducing an efficient approach for facile identification of unknown cell types and their protein markers by mapping transcriptomic data to existing large-scale single-cell RNA sequencing reference databases. Accordingly, we establish nanoSPLITS as a multiomic technology incorporating global proteomics and anticipate the approach will be critical to furthering our understanding of biological systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Combined computational and experimental investigation of high temperature thermodynamics and structure of cubic ZrO 2 and HfO 2

Structure and thermodynamics of pure cubic ZrO 2 and HfO 2 were studied computationally and experimentally from their tetragonal to cubic transition temperatures (2311 and 2530 degrees C) to their melting points (2710 and 2800 degrees C). Computations were performed using automated ab initio molecular dynamics techniques. High temperature synchrotron X-ray diffraction on laser heated aerodynamically levitated samples provided experimental data on volume change during tetragonal-to-cubic phase transformation (0.55 +/- 0.09% for ZrO 2 and 0.87 +/- 0.08% for HfO 2 ), density and thermal expansion. Fusion enthalpies were measured using drop and catch calorimetry on laser heated levitated samples as 55 +/- 7 kJ/mol for ZrO 2 and 61 +/- 10 kJ/mol for HfO 2 , compared with 54 +/- 2 and 52 +/- 2 kJ/mol from computation. Volumetric thermal expansion for cubic ZrO 2 and HfO 2 are similar and reach (4 +/- 1).10 -5 /K from experiment and (5 +/- 1).10 -5 /K from computation. Finally, an agreement with experiment renders confidence in values obtained exclusively from computation: namely heat capacity of cubic HfO 2 and ZrO 2 , volume change on melting, and thermal expansion of the liquid to 3127 degrees C. Computed oxygen diffusion coefficients indicate that above 2400 degrees C pure ZrO 2 is an excellent oxygen conductor, perhaps even better than YSZ.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Quantum many-body physics from a gravitational lens

The past two decades have seen the emergence of remarkable interconnections among previously remotely related disciplines, such as condensed matter, nuclear physics, gravity and quantum information, fuelled both by experimental advances and by the new powerful theoretical methods offered by holographic duality. In this Review, we sample some recent developments in holographic duality in connection with quantum many-body dynamics. These include insights into strongly correlated phases without quasiparticles and their transport properties, quantum many-body chaos and the scrambling of quantum information. We also discuss recent progress in understanding the structure of holographic duality itself using quantum information, including a ‘local’ version of the duality, as well as the quantum error-correction interpretation of quantum many-body states with a gravity dual, and how such notions help to demonstrate the unitarity of black hole evaporation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Efficient learning of accurate surrogates for simulations of complex systems

Machine learning methods are increasingly deployed to construct surrogate models for complex physical systems at a reduced computational cost. However, the predictive capability of these surrogates degrades in the presence of noisy, sparse or dynamic data. Here, we introduce an online learning method empowered by optimizer-driven sampling that has two advantages over current approaches: it ensures that all local extrema (including endpoints) of the model response surface are included in the training data, and it employs a continuous validation and update process in which surrogates undergo retraining when their performance falls below a validity threshold. We find, using benchmark functions, that optimizer-directed sampling generally outperforms traditional sampling methods in terms of accuracy around local extrema even when the scoring metric is biased towards assessing overall accuracy. Finally, the application to dense nuclear matter demonstrates that highly accurate surrogates for a nuclear equation-of-state model can be reliably autogenerated from expensive calculations using few model evaluations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap

Using temperature replica-exchange molecular dynamics, we characterize a globule-to-coil transition for a softwood-like lignin biopolymer in a tetrahydrofuran (THF)-water cosolvent system at temperatures at which the cosolvent undergoes a de-mixing transition. The lignin is found to be in a coil state, similar to that in the high-temperature miscible region. Analysis of the transition kinetics indicates that THF acts in a surfactant-like fashion. In conclusion, the present study thus suggests that THF-water based pretreatments may efficiently remove lignin from biomass even at relatively low (non-water boiling) temperatures.

09 BIOMASS FUELS↗

DOE OSTI2016

Static and dynamic properties of vortex pairs in asymmetric nanomagnets

Stacked spin-vortex pairs in magnetic multilayered nanopillars, with vertical separation between the vortices small compared to the vortex core size and pure magnetostatic coupling, exhibit spin dynamics absent in individual vortices. This dynamics is nonlinear and is due to the strong direct core-core coupling in the system, dominating energetically for small-signal excitation. We observe and explain the appearance of spin resonance modes, forbidden within linear dynamics, and discuss how they depend on the magnetic and morphological asymmetries in the samples.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Wobbly discs – corrugations seen in the dust lanes of edge-on galaxies

ABSTRACT We report the detection of small-scale bending waves, also known as corrugations, in the dust lanes of five nearby edge-on disc galaxies. This phenomenon, where the disc mid-plane bends to become wavy, just as in warps but on a smaller scale, is seen here for the first time, in the dust lanes running across the discs. Because they are seen in absorption, this feature must be present in the dust disc in the outskirts of these galaxies. We enhance the visibility of these features using unsharp masking, trace the dust mid-plane across the disc, measure the corrugation amplitude by eye and the corrugation wavelength using Fourier analysis. The corrugation amplitude is found to be in the range of 70–300pc and the wavelengths lie between 1 and 5 kpc. In this limited sample, we find that the amplitude of the corrugations tends to be larger for lower mass galaxies, whereas the wavelength of corrugation does not seem to depend on the mass of host galaxies. Linear stability analysis is performed to find out the dynamical state of these dust discs. Based on WKB analysis, we find that the dust corrugations in about half of our sample are stable. Further analysis, on a larger sample would be useful to strengthen the above results.

Narayan, Chaitra A.↗

DOE OSTI2020

Broadening of the drumhead-mode spectrum due to in-plane thermal fluctuations of two-dimensional trapped ion crystals in a Penning trap

Two-dimensional crystals of ions stored in Penning traps are a leading platform for quantum simulation and sensing experiments. For small amplitudes, the out-of-plane motion of such crystals can be described by a discrete set of normal modes called the drumhead modes, which can be used to implement a range of quantum information protocols. However, experimental observations of crystals with Doppler-cooled and even nearground- state-cooled drumhead modes reveal an unresolved drumhead-mode spectrum. In this work, we establish in-plane thermal fluctuations in ion positions as a major contributor to the broadening of the drumhead-mode spectrum. In the process, we demonstrate how the confining magnetic field leads to unconventional in-plane normal modes, whose average potential and kinetic energies are not equal. This property, in turn, has implications for the sampling procedure required to choose the in-plane initial conditions for molecular-dynamics simulations. Further, for current operating conditions of the NIST Penning trap, our study suggests that the two-dimensional crystals produced in this trap undergo in-plane potential-energy fluctuations of the order of 10mK. Our study therefore motivates the need for designing improved techniques to cool the in-plane degrees of freedom.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Comparative Visualization of Vector Field Ensembles Based on Longest Common Subsequence

We propose a longest common subsequence (LCS) based approach to compute the distance among vector field ensembles. By measuring how many common blocks the ensemble pathlines passing through, the LCS distance defines the similarity among vector field ensembles by counting the number of sharing domain data blocks. Compared to the traditional methods (e.g. point-wise Euclidean distance or dynamic time warping distance), the proposed approach is robust to outlier, data missing, and sampling rate of pathline timestep. Taking the advantages of smaller and reusable intermediate output, visualization based on the proposed LCS approach revealing temporal trends in the data at low storage cost, and avoiding tracing pathlines repeatedly. Finally, we evaluate our method on both synthetic data and simulation data, which demonstrate the robustness of the proposed approach.

Liu, Richen↗

DOE OSTI2019

Application of Plasmonic nanoprobes for SERS sensing and imaging of biotargets in plant systems

The knowledge over gene expression dynamics and location in plants is crucial for applications ranging from basic biological research to agricultural biotechnology (e.g., biofuel development). However, current methods cannot provide in vivo dynamic detection of genomic targets in plants. This limitation is due to the complex sample preparation needed by current methods for nucleic acids detection, which disrupt spatial and temporal resolution. We report the development of a unique multimodal method based on plasmonics-active nanoprobes, referred to inverse molecular sensitnels capable of in vivo imaging and biosensing of microRNA biotargets within whole plant using surface-enhanced Raman scattering (SERS) detection. This work lays the foundations for in vivo functional imaging of RNA biotargets in plants with previously unmet spatial and temporal resolution for many applications ranging from agricultural biotechnology to biofuel research.

biofuel↗

DOE OSTI2020

Investigating Liquid Water Transport in Different Pore Structure of Gas Diffusion Layers for PEMFC Using Lattice Boltzmann Method

Proton exchange membrane fuel cells (PEMFC) require a gas diffusion layer (GDL) to aid in the transport of liquid fuel to the catalyst layer. In this work, direct modeling using the Lattice Boltzmann Method (LBM) was applied to X-ray CT scans of four different carbon gas diffusion layers to understand the mass transport properties through the samples. Three injection orientations were used to study local saturation levels, water evolution through the sample, and mass transport behavior at breakthrough conditions. The LBM, combined with computational fluid dynamic modeling techniques, can accurately predict liquid saturation at the macro and micro scale, which provides more insight into the mass transport phenomena through the GDL. The change of pore structure and orientation in both the in-plane and through-plane determines the path that liquid water must take, which could aid or impact PEMFC performance. The outcomes from this work will also benefit any research that needs knowledge of internal mass transport qualities of gas diffusion media.

Sepe, M.↗

DOE OSTI2023

AL-ASMR: Active Learning of Atomistic Surrogate Models for Rare Events

Atomistic simulation with artificial intelligence (AI) is an emerging tool for understanding materials' properties and behaviors and predicting novel materials with optimized/targeted properties. Neural network potentials (NNPs) are outstanding in this field as they have shown a comparable accuracy to ab initio electronic structure calculations for reproducing potential energy surfaces while being several orders of magnitude faster. However, such NNPs can perform poorly outside of their training domain and typically fail catastrophically in the prediction of rare events in molecular dynamics (MD) simulations. For effective AL loops to distinguish the informative data from enhanced sampled configurations, we developed a decision engine by configurational similarity and uncertainty quantification (UQ) with data augmentation.

Jung, Gang Seob↗

DOE OSTI2024

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers

Chronic infection with hepatitis B virus (HBV) is caused by the persistence of closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Despite available therapeutic anti-HBV agents, eliminating the cccDNA remains challenging. Thus, quantifying and understanding the dynamics of cccDNA are essential for developing effective treatment strategies and new drugs. However, such study requires repeated liver biopsy to measure the intrahepatic cccDNA, which is basically not accepted because liver biopsy is potentially morbid and not common during hepatitis B treatment. We here aimed to develop a noninvasive method for quantifying cccDNA in the liver using surrogate markers in peripheral blood. We constructed a multiscale mathematical model that explicitly incorporates both intracellular and intercellular HBV infection processes. The model, based on age-structured partial differential equations, integrates experimental data from in vitro and in vivo investigations. By applying this model, we roughly predicted the amount and dynamics of intrahepatic cccDNA within a certain range using specific viral markers in serum samples, including HBV DNA, HBsAg, HBeAg, and HBcrAg. Our study represents a significant step towards advancing the understanding of chronic HBV infection. The noninvasive quantification of cccDNA using our proposed method holds promise for improving clinical analyses and treatment strategies. By comprehensively describing the interactions of all components involved in HBV infection, our multiscale mathematical model provides a valuable framework for further research and the development of targeted interventions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Current measurements in the intermittent-contact mode of atomic force microscopy using the Fourier method: a feasibility analysis

Atomic force microscopy (AFM) is an important tool for measuring a variety of nanoscale surface properties, such as topography, viscoelasticity, electrical potential and conductivity. Some of these properties are measured using contact methods (static contact or intermittent contact), while others are measured using noncontact methods. Some properties can be measured using different approaches. Conductivity, in particular, is mapped using the contact-mode method. However, this modality can be destructive to delicate samples, since it involves continuously dragging the cantilever tip on the surface during the raster scan, while a constant tip–sample force is applied. In this paper we discuss a possible approach to develop an intermittent-contact conductive AFM mode based on Fourier analysis, whereby the measured current response consists of higher harmonics of the cantilever oscillation frequency. Such an approach may enable the characterization of soft samples with less damage than contact-mode imaging. To explore its feasibility, we derive the analytical form of the tip–sample current that would be obtained for attractive (noncontact) and repulsive (intermittent-contact) dynamic AFM characterization, and compare it with results obtained from numerical simulations. Although significant instrumentation challenges are anticipated, the modelling results are promising and suggest that Fourier-based higher-harmonics current measurement may enable the development of a reliable intermittent-contact conductive AFM method.

14 SOLAR ENERGY↗

DOE OSTI2016

CLASH-VLT: DISSECTING THE FRONTIER FIELDS GALAXY CLUSTER MACS J0416.1-2403 WITH ∼800 SPECTRA OF MEMBER GALAXIES

We present VIMOS-Very Large Telescope (VLT) spectroscopy of the Frontier Fields cluster MACS J0416.1-2403 ( z = 0.397). Taken as part of the CLASH-VLT survey, the large spectroscopic campaign provided more than 4000 reliable redshifts over ∼600 arcmin{sup 2}, including ∼800 cluster member galaxies. The unprecedented sample of cluster members at this redshift allows us to perform a highly detailed dynamical and structural analysis of the cluster out to ∼2.2 r {sub 200} (∼4 Mpc). Our analysis of substructures reveals a complex system composed of a main massive cluster ( M {sub 200} ∼ 0.9 × 10{sup 15} M {sub ⊙} and σ{sub V,r200} ∼ 1000 km s{sup −1}) presenting two major features: (i) a bimodal velocity distribution, showing two central peaks separated by Δ V {sub rf} ∼ 1100 km s{sup −1} with comparable galaxy content and velocity dispersion, and (ii) a projected elongation of the main substructures along the NE–SW direction, with a prominent sub-clump ∼600 kpc SW of the center and an isolated BCG approximately halfway between the center and the SW clump. We also detect a low-mass structure at z ∼ 0.390, ∼10′ south of the cluster center, projected at ∼3 Mpc, with a relative line-of-sight velocity of Δ V{sub rf} ∼ −1700 km s{sup −1}. The cluster mass profile that we obtain through our dynamical analysis deviates significantly from the “universal” NFW, being best fit by a Softened Isothermal Sphere model instead. The mass profile measured from the galaxy dynamics is found to be in relatively good agreement with those obtained from strong and weak lensing, as well as with that from the X-rays, despite the clearly unrelaxed nature of the cluster. Our results reveal an overall complex dynamical state of this massive cluster and support the hypothesis that the two main subclusters are being observed in a pre-collisional phase, in agreement with recent findings from radio and deep X-ray data. In this article, we also release the entire redshift catalog of 4386 sources in the field of this cluster, which includes 60 identified Chandra X-ray sources and 105 JVLA radio sources.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1975

Design of an optical fiber cable link for lightning instrumentation

A lightning instrumentation system was designed to record current magnitudes of lightning strikes that hit a launch pad service structure at NASA's Kennedy Space Center. The instrumentation system consists of a lightning ground rod with a current sensor coil, an optical transmitter, an optical fiber cable link, a detector receiver, and a recording system. The transmitter is a wideband pulse transformer driving an IR LED emitter. The transmitter operates linearly as a transducer. A low loss fiber bundle provides isolation of the recorder system from the electromagnetic field of the lightning strike. The output of an optical detector receiver module is sampled and recorded in digital format. The significant factors considered in the design were dynamic range, linearity, mechanical configuration, electromagnetic isolation, and temperature compensation.

Grove, C. H.↗

NASA NTRS1985

Semi-2-interpenetrating polymer networks of high temperature systems

A semi-interpenetrating (semi-IPN) polymer system of the semi-2-IPN type is described in which a polymer of acetylene-terminated imidesulfone (ATPISO2) is cross linked in the presence of polyimidesulfone (PISO2). Six different formulations obtained by mixing of either ATPISO2-1n or ATPISO2-3n with PISO2 in three different proportions were characterized in terms of glass transition temperature, thermooxidative stability, inherent viscosity, and dynamic mechanical properties. Adhesive (lap shear) strength was tested at elevated temperatures on aged samples of adhesive scrim cloth prepared from each resin. Woven graphite (Celion 1000)/polyimide composites were tested for flexural strength, flexural modulus, and shear strength. The network polymers have properties intermediate between those of the component polymers alone, have greatly improved processability over either polyimide, and are able to form good adhesive bonds and composites, making the semi-2-IPN systems superior materials for aerospace structures.

Hanky, A. O.↗