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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection

Abstract The emergence of the novel SARS-CoV-2 virus is the most important public-health issue of our time. Understanding the diverse clinical presentations of the ensuing disease, COVID-19, remains a critical unmet need. Here we present a comprehensive listing of the diverse clinical indications associated with COVID-19. We explore the theory that anti-SARS-CoV-2 antibodies could cross-react with endogenous human proteins driving some of the pathologies associated with COVID-19. We describe a novel computational approach to estimate structural homology between SARS-CoV-2 proteins and human proteins. Antibodies are more likely to interrogate 3D-structural epitopes than continuous linear epitopes. This computational workflow identified 346 human proteins containing a domain with high structural homology to a SARS-CoV-2 Wuhan strain protein. Of these, 102 proteins exhibit functions that could contribute to COVID-19 clinical pathologies. We present a testable hypothesis to delineate unexplained clinical observations vis-à-vis COVID-19 and a tool to evaluate the safety-risk profile of potential COVID-19 therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Quantifying the cooperative evolution of microphase segregation and nanostructural order in annealed polyurethanes of MDI-BDO-PTHF

Here, we quantify the relationship between microphase segregation and local structure development in thermoplastic polyurethanes. Samples were prepared with varying ratios of 4,40 -methylene diphenyl diisocyanate (MDI) and 1,4-butanediol (BDO) to polytetrahydrofuran (PTHF) and annealed at temperatures T a between RT–140 °C for 20 h each. Distinct populations of smaller and larger ordered domains are distinguished by pair distribution func tion analysis. The intermediate-range order of nanoscale hard domains in the paracrystalline state (form I) is directly extracted and characterized. The results suggest that form I of the MDI-BDO:PTHF system presents a conformational and packing order similar to the form III structure, typically obtained from stretching/annealing, but with limited spatial coherence of 3–7 nm. Heating above T g of the hard segments is necessary to achieve a substantial structural response from the annealing treatment. Increasing T a promotes purification of the soft phase via microphase segregation, coalescence of the hard blocks, and growth of paracrystalline phase, while a minority fraction of longer-range ordered domains left over from production remains relatively constant. We observe a composition-dependent decrease in the average nearest-neighbor dis tance that can be correlated with the greater number of C C, C N, and C O bonds with increased hard segment content. A non-linear deviation in the trend is observed to correlate with sample densification. The mechanical and thermal behavior of the samples is intimately tied to the segregation state.

processing-structure-properties↗
DOE OSTI2022

The root-zone soil moisture spectrum in a mediterranean ecosystem

Storage of water within soil pores of the root zone introduce memory effects in the dynamics of soil moisture that are considerably longer than the integral timescale of many atmospheric processes. Thus, hydro-climatic states can be “sustained” through land-surface heat and water vapor fluxes primarily because they can “feed off” on this long-term soil moisture memory. Root-zone soil moisture memory is only but one feature characterizing the spectrum of soil moisture dynamics, which is analyzed here using a combination of long-term measurements and models. In particular, the spectrum of root-zone soil moisture content in a Mediterranean ecosystem is examined using 14-years of half-hourly measurements. A distinguishing hydro-climatic feature in such ecosystems is that sources (mainly rainfall) and sinks (mainly evapotranspiration) of soil moisture are roughly out of phase with each other. For over 4 decades of time scales and 7 decades of energy, the canonical shape of the measured soil moisture spectrum is shown to be approximately Lorentzian determined by the soil moisture variance and its memory but with two exceptions: the occurrences of a peak at diurnal-to-daily time scales and a weaker peak at near annual time scales. Model calculations and spectral analysis demonstrate that diurnal and seasonal variations in hydroclimate forcing responsible for variability in evapotranspiration had minor impact on the normalized shape of the soil moisture spectrum. However, their impact was captured by adjustments in the temporal variance. These findings indicate that precipitation and not evapotranspiration variability dominates the multi-scaling properties of soil moisture variability consistent with prior climate model simulations. Furthermore, the soil moisture memory inferred by the annual peak of soil moisture (340 d) is consistent with climate model simulations, while the memory evaluated from the loss function of a linearized mass balance approach leads to a smaller value (50 d), highlighting the effect of weak non-stationarity on soil moisture variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Steric Modulation of Protein‐Mediated Nanoparticle Assembly: Controlling Cluster Size, Polydispersity, and FRET Responses by Rebalancing Short‐ and Long‐Range Interactions

Understanding and manipulating protein-nanoparticle interactions is of broad interest to fields ranging from nanomedicine to the biological fabrication of functional hierarchical materials. This study investigates how steric forces introduced by a pegylated derivative of superfolder green fluorescent protein (sfGFP) that is monofunctional for silica binding modulate the delicate interplay of long-range (electrostatic and van der Waals) and short-range (protein-mediated) interactions in pH-responsive silica nanoparticle (SiNP) assembly by bifunctional silica-binding sfGFP. Increasing the length of the PEG segment and pre-incubating SiNPs with increasing concentrations of pegylated proteins enables precise control over cluster size within the 800–1450 nm range with a sixfold decrease in polydispersity index to a remarkable 0.1 endpoint. Weakening short-range attractive interactions via mutagenesis extends this control to clusters in the 50–250 nm range and reveals that the Förster resonance energy transfer (FRET) efficiency of clusters scales linearly with cluster diameter below 230 nm but increases only by 15% as clusters grow to 1450 nm. Furthermore, these findings enable the development of a system that provides an optical readout to dynamic changes in solution conditions enacted by a combination of pH adjustment and ion charge screening.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

An effective description of charge diffusion and energy transport in a charged plasma from holography

We discuss the physics of sound propagation and charge diffusion in a plasma with non-vanishing charge density. Our analysis culminates the program initiated in to construct an open effective field theory of low-lying modes of the stress tensor and charge current in such plasmas. We model the plasma holographically as a Reissner-Nordström-AdS d+1 black hole, and study linearized fluctuations of longitudinally polarized scalar gravitons and photons in this background. We demonstrate that the perturbations can be decoupled and repackaged into the dynamics of two designer scalars, whose gravitational coupling is modulated by a non-trivial dilatonic factor. The holographic analysis allows us to isolate the phonon mode from the charge diffusion mode, and identify the combination of currents that corresponds to each of them. We use these results to obtain the real-time Gaussian effective action, which includes both the retarded response and the associated stochastic (Hawking) fluctuations, accurate to quartic order in gradients.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Determining Spatial Scales of Soil Moisture—Cloud Coupling Pathways Using Semi-Idealized Simulations

The spatial scales of land-atmosphere interactions over heterogeneous, realistic soil moisture patterns are critical to improve our understanding of land-atmosphere interactions. However, these scales are poorly quantified. We use high-resolution numerical experiments to quantify the spatial scales for a selected day during the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) campaign in Oklahoma. A semi-idealized approach (removing background winds and surface topography while retaining the real-world data for other boundary conditions) enables examination of the local influence from the surface. Simulations that apply uniform surface, variable land cover with uniform soil moisture, and variable land cover with variable soil moisture are then compared. Land cover variations, especially water and urban surfaces, create two variance peaks in the surface sensible heat flux in the scales >10 km (meso-β) and <6 km (meso-γ). Both peaks are enhanced by the observation-based soil moisture distribution that has most of its variance in the meso-β scale. Atmospheric response in the meso-β scale is hydrostatic with weak vertical motion. The land cover variations induce secondary circulations in the scales of 2.5–6 km. The additional soil moisture variability intensifies extreme circulations over dry soil patches and sharp sensible heat flux gradients, slightly extending the characteristic scales to 2.5–9 km. While their areal coverage is small, soil moisture variations on such “hotspots” lead to substantially larger convective cloud structure and domain-mean rainfall, calling for a consideration of their non-linear effect in large-scale models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Design and Assessment of a Novel Approach for Ecosystem Warming Experiments in High‐Energy Tidal Wetlands

Abstract Coastal salt marshes have an important role in climate change adaptation and mitigation. Direct and indirect responses to warming are expected to vary along the marsh elevation gradient, making ecosystem responses to warming at this marine‐terrestrial ecotone uncertain. The Marsh Ecosystem Response to Increased Temperatures (MERIT) experiment was established in 2018 on the North Sea coast of Germany. Experimental plots are evenly distributed over three elevational marsh zones (pioneer, low marsh, and high marsh) and include three temperature treatments (ambient, +1.5°C, +3.0°C). MERIT's novel design combines active warming (horizontal surface warming cables and vertical soil warming pins) with passive, partially covered domes. For performance assessment, temperature deltas between ambient and warmed plots were calculated and evaluated at seasonal, daily, and diurnal timescales. We used Linear Mixed Models with Residual Maximum Likelihood for evaluating warming treatment effects and constraining environmental factors. MERIT was effective at ecosystem warming in this high‐energy environment both above‐ and belowground. Mixed models show that warming treatment dominates temperature differences belowground and at the soil surface, along with factors such as wind speed, flooding duration, and solar radiation. Aboveground warming was lower than belowground warming, but the dome design minimized issues seen in other open‐top chamber experiments. The combination of passive aboveground warming with feedback‐controlled active surface and belowground heating provides a setup for understanding warming effects on tidal ecosystems without altering the natural impacts of wind, radiation, and tidal inundations at high‐energy coastlines. Our design creates opportunities to expand future warming experiments to remote locations and technically challenging environments.

Environmental Sciences & Ecology↗
DOE OSTI2021

Evolution of the superconducting properties from binary to ternary APC-Nb 3 Sn wires

We present a study conducted on binary Tube Type and ternary powder-in-tube Nb 3 Sn wires manufactured using the artificial pinning centres-internal oxidation method. All the specimens are doped with Zr: oxide nano-particles of this element are responsible for the pinning improvement, both by refining the A-15 grain-size and their own point-pinning contribution. Low-field J c magnetometry confirms that the hadron-hadron Future Circular Collider (FCC-hh) specifications are met by one ternary doped-sample. The differences in microstructure were assessed by scanning electron microscopy/transmission electron microscopy to clarify the reasons for the pinning improvement between the two generations. The deviations from the Dew Hughes model are also discussed, underlying some non-linear addition due to competition between the two pinning mechanisms. Finally, we show how the introduction of Ta as a ternary addition influences the A-15 phase by focusing on the radial inhomogeneities, evaluating the T c distribution and Sn composition gradients. The latter are used to model the currents, enabling us to evaluate the individual weights of the pinning mechanisms and their absolute contributions at the High Luminosity-Large Hadron Collider and FCC-hh dipoles operational points.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Large change of interlayer vibrational coupling with stacking in Mo 1-x W x Te 2

Stacking variations in quasi-two-dimensional materials can have an important influence on material properties, such as changing the topology of the band structure. Unfortunately, the weakness of van der Waals (vdW) interactions makes it difficult to compute the stacking dependence of properties, and even in a material as simple as graphite the stacking energetics remain unclear. Mo 1 - x W x Te 2 is a material in which three differently stacked phases are conveniently accessible by temperature changes: 1 T ' , T d * , and the reported Weyl semimetal phase T d . Additionally, the transitions proceed via layer sliding, and the corresponding interlayer shear mode (ISM) is relevant not just for the stacking energetics but also for understanding the relationship between Weyl physics and structural changes. However, the interlayer interactions of Mo 1 - x W x Te 2 are not well understood, with wide variation in computed properties. We report inelastic neutron scattering of the ISM in a Mo 0.91 W 0.09 Te 2 crystal. The ISM energies are generally consistent with the linear chain model, as expected given the weak interlayer interaction, though there are some discrepancies from predicted intensities. However, the interlayer force constants K x in the T d * and 1 T ' phases are substantially weaker than that of T d at 75(3) and 83(3)%, respectively. Considering that the relative positioning of atoms in neighboring layers is approximately the same regardless of overall stacking, our results suggest that longer-range influences, such as stacking-induced electronic band-structure changes, may be responsible for the substantial change in the interlayer vibrational coupling and thus the C 55 elastic constant. These findings should elucidate the stacking energetics of Mo 1 - x W x Te 2 and other vdW layered materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Tropical dry forest response to nutrient fertilization: a model validation and sensitivity analysis

Abstract. Soil nutrients, especially nitrogen (N) and phosphorus (P), regulate plant growth and hence influence carbon fluxes between the land surface and atmosphere. However, how forests adjust biomass partitioning to leaves, wood, and fine roots in response to N and/or P fertilization remains puzzling. Recent work in tropical forests suggests that trees increase fine root production under P fertilization, but it is unclear whether mechanistic models can reproduce this dynamic. In order to better understand mechanisms governing nutrient effects on plant allocation and improve models, we used the nutrient-enabled ED2 model to simulate a fertilization experiment being conducted in a secondary tropical dry forest in Costa Rica. We evaluated how different allocation parameterizations affected model performance. These parameterizations prescribed a linear relationship between relative allocation to fine roots and soil P concentrations. The slope of the linear relationship was allowed to be positive, negative, or zero. Some parameterizations realistically simulated leaf, wood, and fine root production, and these parameterizations all assumed a positive relationship between relative allocation to fine roots and soil P concentration. Model simulations of a 30-year timeframe indicated strong sensitivity to parameterization and fertilization treatment. Without P fertilization, the simulated aboveground biomass (AGB) accumulation was insensitive to the parameterization. With P fertilization, the model was highly sensitive to the parameterization and the greatest AGB accumulation occurred when relative allocation to fine roots was independent of soil P. Our study demonstrates the need for simultaneous measurements of leaf, wood, and fine root production in nutrient fertilization experiments and for longer-term experiments. Models that do not accurately represent allocation to fine roots may be highly biased in their simulations of AGB, especially on multi-decadal timescales.

Environmental Sciences & Ecology↗
DOE OSTI2024

Predicting transcription factor activity using prior biological information

Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Hugoniot states and optical response of soda lime glass shock compressed to 120 GPa

In contrast to relatively pure silica glass (fused silica-FS), commercial silica-rich glasses contain significant fractions of additional oxide components. In particular, soda-lime glass (SLG) consists of approximately 71% SiO 2 by weight, which raises the question: what is the effect of additional cations on the shock compression response of silica-rich glasses? To address this concern, plate impact experiments were conducted to determine the high-pressure Hugoniot states for shocked SLG (37 to 120 GPa) and compared with recently reported results on FS. Using laser interferometry, particle velocity profiles were measured at the impact surface and the SLG/LiF window interface. In all experiments, the transmitted profiles show a single shock wave, with no features indicative of a phase transformation. The Hugoniot states determined from the wave profiles are described well using a linear shock velocity–particle velocity relation. Interferometry measurements (using 1550-nm wavelength laser) at the impact surface show that SLG is transparent when shocked to 55 GPa, transparent for tens of nanoseconds after impact between 55 and 81 GPa, and opaque beyond 81 GPa. From impact surface measurements, a linear relationship between the apparent and true particle velocity was observed, resulting in a linear relationship between the refractive index (at 1550 nm) and density. At 120 GPa, the SLG density is nearly twice its ambient value, indicating that SLG can achieve highly dense amorphous states. When compared to FS, shocked SLG is much less compressible and likely does not transform to a crystalline phase. A plausible explanation for this difference is indicated.

58 GEOSCIENCES↗
DOE OSTI2025

Measured gain suppression in FBK LGADs with different active thicknesses

In recent years, the gain suppression mechanism has been studied for large localized charge deposits in Low-Gain Avalanche Detectors (LGADs). LGADs are a thin silicon detector with a highly doped gain layer that provides moderate internal signal amplification. Using the CENPA Tandem accelerator at the University of Washington, the response of LGADs with different thicknesses to MeV-range energy deposits from a proton beam were studied. Three LGAD prototypes of 50 μm, 100 μm, and 150 μm were characterized. The devices' gain was determined as a function of bias voltage, incidence beam angle, and proton energy. This study was conducted in the scope of the PIONEER experiment, an experiment proposed at the Paul Scherrer Institute to perform high-precision measurements of rare pion decays. LGADs are considered for the active target (ATAR), and energy linearity is an important property for particle ID capabilities.

Particle tracking detectors↗
DOE OSTI2020

Single Shot Characterization of High Transformer Ratio Wakefields in Nonlinear Plasma Acceleration

We report that plasma wakefields can enable very high accelerating gradients for frontier high energy particle accelerators, in excess of 10 GeV/m. To overcome limits on single stage acceleration, specially shaped drive beams can be used in both linear and nonlinear plasma wakefield accelerators (PWFA), to increase the transformer ratio, implying that the drive beam deceleration is minimized relative to acceleration obtained in the wake. In this Letter, we report the results of a nonlinear PWFA, high transformer ratio experiment using high-charge, longitudinally asymmetric drive beams in a plasma cell. An emittance exchange process is used to generate variable drive current profiles, in conjunction with a long (multiple plasma wavelength) witness beam. The witness beam is energy modulated by the wakefield, yielding a response that contains detailed spectral information in a single-shot measurement. Using these methods, we generate a variety of beam profiles and characterize the wakefields, directly observing transformer ratios up to R=7.8. Lastly, a spectrally based reconstruction technique, validated by 3D particle-in-cell simulations, is introduced to obtain the drive beam current profile from the decelerating wake data.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Soliton Generation in Negative Thermal Expansion Materials

Strain solitons have been observed statically in several 2D materials and dynamically in substrate materials using ultrafast laser pulses. The latter case relies on lattice relaxation in response to ultrafast heating in a light-absorbing transducer material, a process which is sensitive to the thermal expansion coefficient. Here we consider an unusual case where the sign of the thermal expansion coefficient is negative, a scenario which is experimentally feasible in light of rapid and recent advances in the discovery of negative thermal expansion materials. We present numerical solutions to a nonlinear differential equation which has been repeatedly demonstrated to quantitatively model experimental data and discuss the salient results using realistic parameters for material linear and nonlinear elasticity. The solitons that emerge from the initial value problem with negative and positive thermal expansion are qualitatively different in several ways. The new case of negative thermal expansion gives rise to a nearly-periodic soliton train with chirped profile and free of an isolated shock front. We suggest this unanticipated result may be realized experimentally and assess the potential for certain applications of this generic effect.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Does Regional Hydroclimate Change Scale Linearly With Global Warming?

Many aspects of climate change scale linearly with global warming. However, nonlinear changes are possible, especially in the context of hydroclimate, and under emissions scenarios with stabilized global temperature, as aspired to by current climate targets. In CMIP5 and 6, a progressively larger land area shows nonlinear changes as a function of global warming when considering precipitation, evaporation, and soil moisture, with the latter showing nonlinearity over ~50% of global land. Here, using ensemble simulations with the Community Earth System Model 1, in which individual forcing factors are held constant, we illustrate how nonadditive responses to anthropogenic greenhouse gases and industrial and fire-related aerosols can yield complex soil moisture changes in certain regions. This complexity contributes to uncertainty in regional soil moisture projections and suggests that the timing of, as well as model response uncertainty to, future aerosol reductions will have significant impacts on regional hydroclimate change as global temperatures stabilize.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Thermal Adaptation of Enzyme‐Mediated Processes Reduces Simulated Soil CO2 Fluxes Upon Soil Warming

Abstract Understanding factors influencing carbon effluxes from soils to the atmosphere is important in a world experiencing climatic change. Two important uncertainties related to soil organic carbon (SOC) stock responses to a changing climate are (a) whether soil microbial communities acclimate or adapt to changes in soil temperature and (b) how to represent this process in SOC models. To further explore these issues, we included thermal adaptation of enzyme‐mediated processes in a mechanistic SOC model (ReSOM) using the macromolecular rate theory. Thermal adaptation is defined here to encompass all potential responses of soil microbes and microbial communities following a change in temperature. To assess the effects of thermal adaptation of enzyme‐mediated processes on simulated SOC losses, ReSOM was applied to data collected from a 13‐year soil warming experiment. Results show that a model omitting thermal adaptation of enzyme‐mediated processes substantially overestimates observed CO 2 effluxes during the initial years of soil warming. The bias against observed CO 2 effluxes was lower for models including thermal adaptation of enzyme‐mediated processes. In addition, for a simulated linear 3°C soil warming over 100 years, models including thermal adaptation of enzyme‐mediated processes simulated SOC losses of a factor of three smaller than models omitting this process. As thermal adaptation of microbial community characteristics is generally not included in models simulating feedback between the soil, biosphere and atmosphere, we encourage future studies to assess the potential impact that microbial adaptation has on soil carbon – climate feedback representations in models. Plain Language Summary A major uncertainty in projecting how much soil organic carbon (SOC) will be converted to CO 2 as a consequence of climate change is related to how soil microbes may adapt to increasing soil temperatures. While this “microbial thermal adaptation” has been shown to occur in short‐term lab incubation experiments, its effect on SOC cycling on a decadal timescale is not clear. To address this knowledge gap, a mechanistic SOC model was used to simulate data collected from a 13‐year soil warming experiment, to assess how microbial thermal adaptation affects predicted SOC losses upon soil warming. The model results show that incorporating microbial thermal adaptation into the model led to reduced CO 2 effluxes from the soil to the atmosphere compared to the common approach of omitting this mechanism. Our results imply that projected SOC losses for the decades to come may be reduced when this mechanism is incorporated in land models. We therefore advocate for more research on the mechanisms controlling microbial thermal adaptation, and how to implement this mechanism in SOC models. Key Points A crucial aspect of soil organic carbon (SOC) models is the representation of soil microbes Predicted soil CO 2 fluxes upon soil warming are reduced when accounting for microbial thermal adaptation On a centennial time scale, this thermal adaptation results in up to a factor of three lower predicted SOC loss

Van de Broek, Marijn↗
DOE OSTI2025

Signatures of linearized gravity in atom interferometers: A simplified computational framework

We develop a general framework for calculating the leading-order, general relativistic contributions to the gravitational phase shift in single-photon atom interferometers within the context of linearized gravity. We show that the atom gradiometer observable, which only depends on the atom interferometer propagation phase, can be written in terms of three distinct contributions: the Doppler phase shift, which accounts for the tidal displacement of atoms along the baseline, the Shapiro phase shift, which accounts for the delay in the arrival time of photons at atom-light interaction points, and the Einstein phase shift, which accounts for the gravitational redshift measured by the atoms. For specific atom gradiometer configurations, we derive the signal and response functions for two physically motivated scenarios: (i) transient gravitational waves in the transverse-traceless gauge and, for the first time, in the proper detector frame, and (ii) transient massive objects sourcing weak and slow-varying Newtonian potentials. Here, we find that the Doppler contribution of realistic Newtonian noise sources (e.g., a freight truck or a piece of space debris) at proposed atom gradiometer experiments, such as AION, MAGIS, and AEDGE, can exceed the shot noise level and thus affect physics searches if not properly subtracted. Note: 44 pages including appendices, 4 figures; v2: different formatting, fixed typos, 28 pages including appendices, 5 figures, agrees with published version

Atom interferometry↗