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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Electron ptychography achieves atomic-resolution limits set by lattice vibrations

Transmission electron microscopes use electrons with wavelengths of a few picometers, potentially capable of imaging individual atoms in solids at a resolution ultimately set by the intrinsic size of an atom. However, owing to lens aberrations and multiple scattering of electrons in the sample, the image resolution is reduced by a factor of 3 to 10. By inversely solving the multiple scattering problem and overcoming the electron-probe aberrations using electron ptychography, we demonstrate an instrumental blurring of less than 20 picometers and a linear phase response in thick samples. The measured widths of atomic columns are limited by thermal fluctuations of the atoms. As a result, our method is also capable of locating embedded atomic dopant atoms in all three dimensions with subnanometer precision from only a single projection measurement.

42 ENGINEERING↗
DOE OSTI2025

Complex surface topographic changes from explosive experiments at the Dry Alluvium Geology site, southern Nevada, United States

Understanding the surface topographic change that results from underground explosions is important for global security. Current techniques to relate the surface change to underground explosion characteristics usually involve assuming the earth has homogenous properties, leading to highly variable interpretations. Here we use an unoccupied aerial platform and a digital single lens reflex camera along with 200+ ground control points surveyed with a real-time kinematic global navigation satellite system to measure the surface topographic change resulting from two underground explosions at the Dry Alluvium Geology site in Yucca Flat, Nevada National Security Site, southern Nevada, United States. We find areas of 5–7 cm of subsidence that are not directly above the explosion source but rather 200–300 m away. For experiment DAG2, this zone is located south and west of the explosion, while for DAG4, there is a zone of subsidence located northeast of the explosion. In addition, late-time measurements show as much as 5 cm of horizontal change without measurable associated vertical change in the weeks following DAG4 but not DAG2. These indicate that the deformation resulting from underground chemical explosions can be very complex and bear little to no resemblance to predictions using half-space models. It is likely the tectonic environment plays a significant role in controlling the surface change, but the details are not fully understood.

58 GEOSCIENCES↗
DOE OSTI2020

BPS spectra and 3-manifold invariants

We provide a physical definition of new homological invariants H a (M 3 ) of 3-manifolds (possibly, with knots) labeled by abelian flat connections. The physical system in question involves a 6d fivebrane theory on M 3 times a 2-disk, D 2 , whose Hilbert space of BPS states plays the role of a basic building block in categorification of various partition functions of 3d N = 2 theory T[M 3 ]: D 2 × S 1 half-index, S 2 × S 1 superconformal index, and S 2 × S 1 topologically twisted index. The first partition function is labeled by a choice of boundary condition and provides a refinement of Chern–Simons (WRT) invariant. A linear combination of them in the unrefined limit gives the analytically continued WRT invariant of M 3 . The last two can be factorized into the product of half-indices. Here, we show how this works explicitly for many examples, including Lens spaces, circle fibrations over Riemann surfaces, and plumbed 3-manifolds.

3-manifold↗
DOE OSTI2023

Rubisco Function, Evolution, and Engineering

Carbon fixation is the process by which CO 2 is converted from a gas into biomass. The Calvin–Benson–Bassham cycle (CBB) is the dominant carbon-consuming pathway on Earth, driving >99.5% of the ~120 billion tons of carbon that are converted to sugar by plants, algae, and cyanobacteria. The carboxylase enzyme in the CBB, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), fixes one CO 2 molecule per turn of the cycle into bioavailable sugars. Despite being critical to the assimilation of carbon, rubisco's kinetic rate is not very fast, limiting flux through the pathway. This bottleneck presents a paradox: Why has rubisco not evolved to be a better catalyst? Many hypothesize that the catalytic mechanism of rubisco is subject to one or more trade-offs and that rubisco variants have been optimized for their native physiological environment. Here, we review the evolution and biochemistry of rubisco through the lens of structure and mechanism in order to understand what trade-offs limit its improvement. We also review the many attempts to improve rubisco itself and thereby promote plant growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

FastrSHWFS Analysis

This code analyzes the reflection geometry of modified Shack-Hartmann Wavefront Sensor (SHWFS) masks, with a focus on the fastrSHWFS designs. It takes a height map of a reflective mask, divides it into sub apertures, removes the global focus term by referencing a central block, and fits local surface planes to each sub aperture. From these fits it computes reflection angles and propagates the corresponding rays downstream to determine spot positions and the overall reflected beam footprint as a function of distance. The implementation is parameterized in sub aperture size, number of sub apertures, focal length, and mask dimensions, so it can be adapted to different mask designs beyond the two current fastrSHWFS masks. The code: Converts mask bitmaps into physical height in microns and reconstructs a focus subtracted mask, divides the mask into a grid of sub apertures and assigns pixel and micron coordinates to each block, excludes user specified unused sub apertures from the analysis, fits a plane to each sub aperture to obtain local surface normals, propagates reflected rays to a range of z positions to compute ray spots and the full reflected beam width, computes the effective mask tilt angle with respect to the incoming beam as a function of propagation distance, and provides helper routines for plotting the grid over the mask and for visualizing the beam geometry. These tools are intended for iterating on fastrSHWFS mask designs and for planning downstream optical layouts, for example choosing lens positions and apertures that capture the reflected beam given known focal plane distances and beam widths.

Gerard, BenjaminL [Lawrence Livermore National Lab↗
DOE OSTI2026

lumicap v0.1

Automated HDR luminance imaging system designed for daylighting research and building science. It controls a fisheye-lens camera to capture time-lapse bracket sequences, merges them into calibrated HDR images, and runs a full post-processing pipeline — all unattended. Features: - Scheduled LDR bracket capture via gphoto2 - HDR merging with vignetting, ND filter, and fisheye projection corrections - Illuminance and luminance meter integration (Konica Minolta T-10A, LS-100/150) - Daylight glare probability (DGP) and solar position computation - Automated false-color rendering, JPEG thumbnails, and daily time-lapse video - CSV data logging per timestep Uses: - Long-term monitoring of daylight conditions in buildings - Glare analysis for occupant comfort research - Solar irradiance and sky luminance studies Advantages: - End-to-end automation — capture, calibration, analysis, and archiving run without manual intervention - Built on the proven Radiance toolchain, ensuring photometrically accurate HDR output - Hardware-agnostic meter support via serial auto-detection - Lightweight — no GUI overhead, deployable on a headless Raspberry Pi or similar embedded system

Wang, Taoning [Lawrence Berkeley National Laborato↗
DOE OSTI2022

Sex Determination and Ovarian Development in Reptiles and Amphibians: From Genetic Pathways to Environmental Influences

Background: Reptiles and amphibians provide untapped potential for discovering how a diversity of genetic pathways and environmental conditions are incorporated into developmental processes that can lead to similar functional outcomes. These groups display a multitude of reproductive strategies, and whereas many attributes are conserved within groups and even across vertebrates, several aspects of sexual development show considerable variation. Summary: Here, in this review, we focus our attention on the development of the reptilian and amphibian ovary. First, we review and describe the events leading to ovarian development, including sex determination and ovarian maturation, through a comparative lens. We then describe how these events are influenced by environmental factors, focusing on temperature and exposure to anthropogenic chemicals. Lastly, we identify critical knowledge gaps and future research directions that will be crucial to moving forward in our understanding of ovarian development and the influences of the environment in reptiles and amphibians. Key Messages: Reptiles and amphibians provide excellent models for understanding the diversity of sex determination strategies and reproductive development. However, a greater understanding of the basic biology of these systems is necessary for deciphering the adaptive and potentially disruptive implications of embryo-by-environment interactions in a rapidly changing world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Principal Component Analysis for Extremes and Application to U.S. Precipitation

Here, we propose a method for analyzing extremal behavior through the lens of a most efficient basis of vectors. The method is analogous to principal component analysis, but is based on methods from extreme value analysis. Specifically, rather than decomposing a covariance or correlation matrix, we obtain our basis vectors by performing an eigendecomposition of a matrix that describes pairwise extremal dependence. We apply the method to precipitation observations over the contiguous United States. We find that the time series of large coefficients associated with the leading eigenvector shows very strong evidence of a positive trend, and there is evidence that large coefficients of other eigenvectors have relationships with El Niño–Southern Oscillation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A Unified Interpretation of Variability in Precipitation Isotope Ratios

Abstract Several mechanisms have been proposed to explain why the isotope ratios of precipitation vary in space and time and why they correlate with other climate variables like temperature and precipitation. Here, we argue that this behavior is best understood through the lens of radiative transfer, which treats the depletion of atmospheric vapor transport by precipitation as analogous to the attenuation of light by absorption or scattering. Building on earlier work by Siler et al., we introduce a simple model that uses the equations of radiative transfer to approximate the two-dimensional pattern of the oxygen isotope composition of precipitation ( δ p ) from monthly mean hydrologic variables. The model accurately simulates the spatial and seasonal variability in δ p within a state-of-the-art climate model and permits a simple decomposition of δ p variability into contributions from gradients in evaporation and the length scale of vapor transport. Outside the tropics, δ p is mostly controlled by gradients in evaporation, whose dependence on temperature explains the positive correlation between δ p and temperature (i.e., the temperature effect). At low latitudes, δ p is mostly controlled by gradients in the transport length scale, whose inverse relationship with precipitation explains the negative correlation between δ p and precipitation (i.e., the amount effect). This suggests that the temperature and amount effects are both mostly explained by the variability in upstream rainout, but they reflect distinct mechanisms governing rainout at different latitudes. Significance Statement The isotopic composition of precipitation has long been used to make inferences about past climates based on its observed relationship with precipitation in the tropics and with temperature at higher latitudes. These relationships—known as the “amount effect” and “temperature effect,” respectively—have been attributed to many different mechanisms, most of which are thought to operate at either high or low latitudes but not both. Here, we present a unified framework for interpreting the isotope variability that can explain the latitude dependence of the temperature and amount effects despite making no distinction between high and low latitudes. Although our results are generally consistent with certain interpretations of the amount effect, they suggest that the temperature effect is widely misunderstood.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Understanding Uncertainties in Tropical Cyclone Rainfall Hazard Modeling Using Synthetic Storms

Tropical cyclone (TC) rainfall hazard assessment is subject to the bias in TC climatology estimation from climate simulations or synthetic downscaling. In this study, we investigate the uncertainty in TC rainfall hazard assessment induced by this bias using both rain gauge and radar observations and synthetic-storm-model-coupled TC rainfall simulations. We identify the storm’s maximum intensity, impact duration, and minimal distance to the site to be the three most important storm parameters for TC rainfall hazard, and the relationship between the important storm parameters and TC rainfall can be well captured by a physics-based TC rainfall model. The uncertainty in the synthetic rainfall hazard induced by the bias in TC climatology can be largely explained by the bias in the important storm parameters simulated by the synthetic storm model. Correcting the distribution of the most biased parameter may significantly improve rainfall hazard estimation. Bias correction based on the joint distribution of the important parameters may render more accurate rainfall hazard estimations; however, the general technical difficulties in resampling from high-dimensional joint probability distributions prevent more accurate estimations in some cases. The results of the study also support future investigation of the impact of climate change on TC rainfall hazards through the lens of future changes in the identified important storm parameters.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

Krinos, Arianna I. (ORCID:0000000197678392)↗
DOE OSTI2024

Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides

Abstract Background The oleaginous yeast Rhodotorula toruloides is a promising chassis organism for the biomanufacturing of value-added bioproducts. It can accumulate lipids at a high fraction of biomass. However, metabolic engineering efforts in this organism have progressed at a slower pace than those in more extensively studied yeasts. Few studies have investigated the lipid accumulation phenotype exhibited by R. toruloides under nitrogen limitation conditions. Consequently, there have been only a few studies exploiting the lipid metabolism for higher product titers. Results We performed a multi-omic investigation of the lipid accumulation phenotype under nitrogen limitation. Specifically, we performed comparative transcriptomic and lipidomic analysis of the oleaginous yeast under nitrogen-sufficient and nitrogen deficient conditions. Clustering analysis of transcriptomic data was used to identify the growth phase where nitrogen-deficient cultures diverged from the baseline conditions. Independently, lipidomic data was used to identify that lipid fractions shifted from mostly phospholipids to mostly storage lipids under the nitrogen-deficient phenotype. Through an integrative lens of transcriptomic and lipidomic analysis, we discovered that R. toruloides undergoes lipid remodeling during nitrogen limitation, wherein the pool of phospholipids gets remodeled to mostly storage lipids. We identify specific mRNAs and pathways that are strongly correlated with an increase in lipid levels, thus identifying putative targets for engineering greater lipid accumulation in R. toruloides . One surprising pathway identified was related to inositol phosphate metabolism, suggesting further inquiry into its role in lipid accumulation. Conclusions Integrative analysis identified the specific biosynthetic pathways that are differentially regulated during lipid remodeling. This insight into the mechanisms of lipid accumulation can lead to the success of future metabolic engineering strategies for overproduction of oleochemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Observing and modeling the effects of production infrastructure in electromagnetic surveys

Electromagnetic (EM) methods are among the original techniques for subsurface characterization in exploration geophysics because of their particular sensitivity to the earth electrical conductivity, a physical property of rocks distinct yet complementary to density, magnetization, and strength. However, this unique ability also makes them sensitive to metallic artifacts — infrastructure such as pipes, cables, and other forms of cultural clutter — the EM footprint of which often far exceeds their diminutive stature when compared to that of bulk rock itself. In the hunt for buried treasure or unexploded ordnance, this is an advantage; in the long-term monitoring of mature oil fields after decades of production, it is quite troublesome indeed. In this study we consider the latter through the lens of an evolving energy industry landscape in which the traditional methods of EM characterization for the exploration geophysicist are applied toward emergent problems in well-casing integrity, carbon capture and storage, and overall situational awareness in the oil field. We introduce case studies from these exemplars, showing how signals from metallic artifacts can dominate those from the target itself and impose significant burdens on the requisite simulation complexity. Furthermore, we show how recent advances in numerical methods mitigate the computational explosivity of infrastructure modeling, providing feasible and real-time analysis tools for the desktop geophysicist. Lastly, we demonstrate through comparison of field data and simulation results that incorporation of infrastructure into the analysis of such geophysical data is, in a growing number of cases, a requisite but now manageable step.

58 GEOSCIENCES↗
DOE OSTI2020

III/V silicon hybrid laser based on a resonant Bragg structure

We demonstrate a laser tunable in intensity with gigahertz tuning speed based on a III/V reflective semiconductor optical amplifier (RSOA) coupled to a silicon photonic chip. The silicon chip contains a Bragg-based Fabry–Perot resonator to form a passive bandpass filter within its stopband to enable single-mode operation of the laser. We observe a side mode suppression ratio of 43 dB, linewidth of 790 kHz, and an optical output power of 1.65 mW around 1530 nm. We also investigate using a micro-ball lens as an alternative coupling method between the RSOA and the silicon chip.

Davis, Jordan A. (ORCID:0000000343483295)↗
DOE OSTI2020

Generation and control of phase-locked Bessel beams with a persistent noninterfering region

We present, to the best of our knowledge, a novel method for the generation of multiple Bessel-like (Bessel–Gauss) beams with tilted wavefronts whose optical phases can be controlled independently. In the far field multiple field-free regions develop that are persistent to interference effects and the optical phase. The extent of these field-free regions can be controlled through the tilt angle of the wavefront with a theoretical maximum resolution of 0.1 mrad. Experimentally we employ a spatial light modulator, a lens, and an axicon, each suitable for narrow-band (continuous-wave) and broadband operation. Because of the simplicity in the optical elements, the number of noninterfering Bessel-like beams can be scaled on demand for applications that require multiple sources for coherent imaging or multiple intense beams over a controllable region with the added benefit of a field-free region for detection. Here, for reasons of clarity, we characterized two beams.

Rodnova, Zhanna↗
DOE OSTI2021

Low-threshold supercontinuum generation in polycrystalline media

Until recently, the generation of super-octave continua in bulk materials at full repetition rates of femtosecond (fs) oscillators has been limited to a few special cases of Kerr lens mode-locked Ti:sapphire lasers. In 2019, we described a 3.4-octave fs source with 50 nJ pulse energy at the repetition rate of 78 MHz based on polycrystalline Cr:ZnS [Vasilyev et al. , Optica 6 , 126 ( 2019 ) OPTIC8 2334-2536 10.1364/OPTICA.6.000126 ]. Here we explain the mechanism of fs supercontinuum generation in transition-metal doped polycrystalline II-VI semiconductors at relatively low (nJ-level) pulse energy. We demonstrate that this new supercontinuum regime is enabled by a complex, yet well-reproducible, interplay between the effects arising from the third-order nonlinearity, the quadratic nonlinearities, and thermal optical effects in the medium. We also demonstrate the control of fs pulse propagation in disordered χ <#comment/> ( 2 ) media via the control of the material microstructure.

Vasilyev, Sergey (ORCID:0000000225203547)↗
DOE OSTI2021

Higher-order harmonic generation and strong field ionization with Bessel–Gauss beams in a thin jet geometry

A promising alternative to Gaussian beams for use in strong field science is Bessel–Gauss (BG or Bessel-like) laser beams, as they are easily produced with readily available optics and provide more flexibility of the spot size and working distances. Here we use BG beams produced with a lens-axicon optical system for higher-order harmonic generation (HHG) in a thin gas jet. The finite size of the interaction region allows for scans of the HHG yield along the propagation axis. Further, by measuring the ionization yield in unison with the extreme ultraviolet (XUV), we are able to distinguish regions of maximum ionization from regions of optimum XUV generation. This distinction is of great importance for BG fields, as the generation of BG beams with axicons often leads to oscillations of the on-axis intensity, which can be exploited for extended phase-matching conditions. We observed such oscillations in the ionization and XUV flux along the propagation axis for the first time. As is the case for Gaussian modes, the harmonic yield is not maximum at the point of highest ionization. Finally, despite Bessel beams having a hole in the center in the far field, the XUV beam is well collimated, making BG modes a great alternative when spatial filtering of the fundamental is desired.

Davino, Michael↗
DOE OSTI2022

Spatiotemporal control of laser intensity through cross-phase modulation

Spatiotemporal pulse shaping provides control over the trajectory and range of an intensity peak. While this control can enhance laser-based applications, the optical configurations required for shaping the pulse can constrain the transverse or temporal profile, duration, or orbital angular momentum (OAM). Here we present a novel technique for spatiotemporal control that mitigates these constraints by using a "stencil" pulse to spatiotemporally structure a second, primary pulse through cross-phase modulation (XPM) in a Kerr lens. The temporally shaped stencil pulse induces a time-dependent focusing phase within the primary pulse. This technique, the "flying focus X," allows the primary pulse to have any profile or OAM, expanding the flexibility of spatiotemporal pulse shaping for laser-based applications. As an example, simulations show that the flying focus X can deliver an arbitrary-velocity, variable-duration intensity peak with OAM over distances much longer than a Rayleigh range.

47 OTHER INSTRUMENTATION↗