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At least 595 records · Page 33

Dynamic enhancer landscapes in human craniofacial development

The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.

60 APPLIED LIFE SCIENCES↗

Three-dimensional simulation of the University of Hawai‘i FEL oscillator with cavity desynchronization

In this paper, we present three-dimensional, time-dependent simulations of the University of Hawai‘i (UH) at Mānoa free-electron laser (FEL) oscillator. Using beam parameters from the UH facility, we study the pass-by-pass evolution of the radiation field, including its temporal, spectral, and transverse properties. At nominal bunch length, the radiation pulse develops temporal spiking near saturation, together with sideband formation and increased sensitivity to machine timing jitter. Our results show that modest cavity desynchronization can enhance the radiation energy by 63%. Large cavity desynchronization, on the other hand, can effectively suppress the spiking instabilities and improve robustness to timing fluctuations. Finally, we simulate a short-bunch operational mode with a bunch length comparable to the slippage length, which accelerates saturation and further amplifies the FEL power. Overall, these results provide a quantitative foundation for pulse control studies in the UH FEL oscillator and a critical benchmark for future experimental validation and machine optimization.

free-electron lasers↗

Reduced global plant respiration due to the acclimation of leaf dark respiration coupled with photosynthesis

Summary Leaf dark respiration ( R d ) acclimates to environmental changes. However, the magnitude, controls and time scales of acclimation remain unclear and are inconsistently treated in ecosystem models. We hypothesized that R d and Rubisco carboxylation capacity ( V cmax ) at 25°C ( R d,25 , V cmax,25 ) are coordinated so that R d,25 variations support V cmax,25 at a level allowing full light use, with V cmax,25 reflecting daytime conditions (for photosynthesis), and R d,25 / V cmax,25 reflecting night‐time conditions (for starch degradation and sucrose export). We tested this hypothesis temporally using a 5‐yr warming experiment, and spatially using an extensive field‐measurement data set. We compared the results to three published alternatives: R d,25 declines linearly with daily average prior temperature; R d at average prior night temperatures tends towards a constant value; and R d,25 / V cmax,25 is constant. Our hypothesis accounted for more variation in observed R d,25 over time ( R 2 = 0.74) and space ( R 2 = 0.68) than the alternatives. Night‐time temperature dominated the seasonal time‐course of R d , with an apparent response time scale of c. 2 wk. V cmax dominated the spatial patterns. Our acclimation hypothesis results in a smaller increase in global R d in response to rising CO 2 and warming than is projected by the two of three alternative hypotheses, and by current models.

Plant Sciences↗

Parallel Time Integration for Constrained Optimization

The number of transistors in an average processor continues to increase, but individual clock speeds have plateaued. Those transistors are instead going into additional cores, increasing the number of different things that a processor can do at once and placing an emphasis on parallel computation. Many problems in scientific computing follow a time-evolution model, and it can be difficult to solve such problems in parallel across the temporal domain. The Multi-Grid Reduction In Time (MGRIT) algorithm, developed at Lawrence Livermore National Laboratory (LLNL), solves differential equations with a method designed specifically to take advantage of extreme numbers of processors by parallelizing across time. The Tri-diagonal MGRIT (TriMGRIT) algorithm, also developed at LLNL, is a generalization of MGRIT which enables parallel-in-time solving of a greater number of problems. Constrained optimization problems, in particular, may be solved in parallel using TriMGRIT. These consist of choosing a control function such that an objective functional is minimized, constrained by a differential-equation. We consider two such problems: applying torque to a pendulum to bring it to a gentle stop and moving a crowd of people from one distribution into another. We also perform some miscellaneous theoretical and practical research, including investigating the use of a line-search subroutine to refine intermediate TriMGRIT results and preliminary work on strategies for choosing operators for TriMGRIT to use.

97 MATHEMATICS AND COMPUTING↗

Calibration, measurement, and characterization of soil moisture dynamics in a central Amazonian tropical forest

Soil moisture plays a key role in hydrological, biogeochemical, and energy budgets of terrestrial ecosystems. Accurate soil moisture measurements in remote ecosystems such as the Amazon are difficult and limited because of logistical constraints. Time domain reflectometry (TDR) sensors are widely used to monitor soil moisture and require calibration to convert the TDR's dielectric permittivity measurement (K a ) to volumetric water content (θ v ). In this study, our objectives were to develop a field-based calibration of TDR sensors in an old-growth upland forest in the central Amazon, to evaluate the performance of the calibration, and then to apply the calibration to determine the dynamics of soil moisture content within a 14.2 -m-deep vertical soil profile. Depth-specific TDR calibration using local soils in a controlled laboratory setting yielded a novel K a –θ v third-degree polynomial calibration. The sensors were later installed to their specific calibration depth in a 14.2-m pit. The widely used K a –θ v relationship (Topp model) underestimated the site-specific θ v by 22–42%, indicating significant error in the model when applied to these well-structured, clay-rich tropical forest soils. The calibrated wet- and dry-season θ v data showed a variety of depth and temporal variations highlighting the importance of soil textural differentiation, root uptake depths, as well as event to seasonal precipitation effects. Data such as these are greatly needed for improving our understanding of ecohydrological processes within tropical forests and for improving models of these systems in the face of changing environmental conditions.

54 ENVIRONMENTAL SCIENCES↗

Increasing phosphorus loss despite widespread concentration decline in US rivers

The loss of phosphorous (P) from the land to aquatic systems has polluted waters and threatened food production worldwide. Systematic trend analysis of P, a nonrenewable resource, has been challenging, primarily due to sparse and inconsistent historical data. Here, we leveraged intensive hydrometeorological data and the recent renaissance of deep learning approaches to fill data gaps and reconstruct temporal trends. We trained a multitask long short-term memory model for total P (TP) using data from 430 rivers across the contiguous United States (CONUS). Trend analysis of reconstructed daily records (1980–2019) shows widespread decline in concentrations, with declining, increasing, and insignificantly changing trends in 60%, 28%, and 12% of the rivers, respectively. Concentrations in urban rivers have declined the most despite rising urban population in the past decades; concentrations in agricultural rivers however have mostly increased, suggesting not-as-effective controls of nonpoint sources in agriculture lands compared to point sources in cities. TP loss, calculated as fluxes by multiplying concentration and discharge, however exhibited an overall increasing rate of 6.5% per decade at the CONUS scale over the past 40 y, largely due to increasing river discharge. Results highlight the challenge of reducing TP loss that is complicated by changing river discharge in a warming climate.

Science & Technology - Other Topics↗

Degradation of temporal contrast from post-pedestal interference with a chirped pulse in an optical parametric amplifier

Pre-pedestal generation is observed in a 0.35-PW laser front end coming from a post-pedestal via instantaneous gain and pump depletion in an optical parametric amplifier during chirped-pulse amplification. Generalized simulations show how this effect arises from gain nonlinearity and applies to all optical parametric chirped-pulse–amplification systems with a post-pedestal. An experiment minimizing the effect of B -integral is used to isolate and study the newly observed conversion of a continuous post-pedestal into a continuous pre-pedestal. Matching numerical simulations confirm experimental results and additionally reveal how third-order dispersion largely controls the slope of the generated pre-pedestal.

47 OTHER INSTRUMENTATION↗

Multiscale Patterning from Competing Interactions and Length Scales

We live in an era of complexity marked by impressive new tools powering the scientific method to accelerate discovery, prediction, and control of increasingly complex systems. In common with many disciplines and societal challenges and opportunities, materials and condensed matter sciences are beneficiaries. The volume and fidelity of experimental, computational, and visualization data available, and tools to rapidly interpret them, are remarkable. Conceptual frameworks, including multiscale, multiphysics modeling of this complexity, are fueled by the data and, in turn, guide directions for future experimental and computational strategies. In this spirit, we discuss the importance of competing interactions, length scales, and constraints as pervasive sources of spatio-temporal complexity. We use representative examples drawn from materials and condensed matter, including the important role of elasticity in some technologically important quantum materials.

36 MATERIALS SCIENCE↗

Pore-Scale Dynamics of Liquid CO2–Water Displacement in 2D Axisymmetric Porous Micromodels Under Strong Drainage and Weak Imbibition Conditions: High-Speed μPIV Measurements

Resolving pore-scale transient flow dynamics is crucial to understanding the physics underlying multiphase flow in porous media and informing large-scale predictive models. Surface properties of the porous matrix play an important role in controlling such physics, yet interfacial mechanisms remain poorly understood, in part due to a lack of direct observations. This study reports on an experimental investigation of the pore-scale flow dynamics of liquid CO 2 and water in two-dimensional (2D) circular porous micromodels with different surface characteristics employing high-speed microscopic particle image velocimetry (μPIV). The design of the micromodel minimized side boundary effects due to the limited size of the domain. The high-speed μPIV technique resolved the spatial and temporal dynamics of multiphase flow of CO 2 and water under reservoir-relevant conditions, for both drainage and imbibition scenarios. When CO 2 displaced water in a hydrophilic micromodel (i.e., drainage), unstable capillary fingering occurred and the pore flow was dominated by successive pore-scale burst events (i.e., Haines jumps). When the same experiment was repeated in a nearly neutral wetting micromodel (i.e., weak imbibition), flow instability and fluctuations were virtually eliminated, leading to a more compact displacement pattern. Energy balance analysis indicates that the conversion efficiency between surface energy and external work is less than 30%, and that kinetic energy is a disproportionately smaller contributor to the energy budget. This is true even during a Haines jump event, which induces velocities typically two orders of magnitude higher than the bulk velocity. These novel measurements further enabled direct observations of the meniscus displacement, revealing a significant alteration of the pore filling mechanisms during drainage and imbibition. While the former typically featured burst events, which often occur only at one of the several throats connecting a pore, the latter is typically dominated by a cooperative filling mechanism involving simultaneous invasion of a pore from multiple throats. This cooperative filling mechanism leads to merging of two interfaces and releases surface energy, causing instantaneous high-speed events that are similar, yet fundamentally different from, burst events. Finally, pore-scale velocity fields were statistically analyzed to provide a quantitative measure of the role of capillary effects in these pore flows.

Li, Yaofa↗

Physics-Informed Graph Neural Networks for Collaborative Dynamic Reconfiguration and Voltage Regulation in Unbalanced Distribution Systems

Network reconfiguration has long been employed as a strategic approach to minimize power distribution system losses and effectively regulate voltage levels. Tap-changing voltage regulators are also critical for controlling bus voltages, especially in accommodating the increasing integration of distributed energy resources (DERs) with intermittent outputs. This paper introduces novel methodologies to address the challenges of dynamic reconfiguration and optimal tap setting in unbalanced three-phase distribution systems. We propose an approximated mixed-integer quadratically constrained program (MIQCP) to model dynamic reconfiguration, along with a pioneering formulation for voltage regulator (VR) tap-setting based on Special Ordered Set type 1 (SOS1). To mitigate computational complexity, we propose a physics-informed spatial-temporal graph convolutional network (STGCN) with an integrated link classifier. The proposed approach enables efficient solution generation by fixing specific variables in the MIQCP instance and solving the simplified sub-MIP using an MIP solver. Numerical studies demonstrate the superior prediction accuracy of our STGCN model compared to baseline neural network models, resulting in reduced DER curtailment and voltage deviation with shorter computation time.

dynamic reconfiguration↗

Investigation of Superluminescent Diodes for Smart Lighting Systems. Final Report

The solid-state lighting ecosystem has evolved very rapidly over the last few years, with significant improvements in the technical performance of light-emitting diodes (LEDs) and the commoditization of LED-based lighting fixtures. As the performance of conventional lighting products begins to saturate, there is growing market interest in “Lighting as a Service” applications that will leverage advanced systems to impart new functionalities to lighting and improve energy efficiency, human health, and productivity. These “Smart Lighting” systems will include high-performance light sources, specialized sensors, and dynamic controls to deliver high quality, energy efficient, color tunable lighting with customized spatial light delivery and integrated visible light communication capability. To achieve these capabilities, smart lighting systems will place greater demands on the performance of light sources. Highly efficient sources with additional functionalities compared to conventional LEDs, such as small form factor, large modulation bandwidth, and spatially coherent output beams, will be required. While laser diodes have been proposed as potential sources for smart lighting systems, they also exhibit several properties that pose challenges, such as temporal coherence, extremely high spatial coherence, and ultra-narrow linewidths. To address these issues, we propose an investigation of an alternative device architecture known as a superluminescent diode (SLD). SLDs are similar in form to ridge laser diodes and share many of the same characteristics, such as stimulated emission operation, spatially coherent output, small form factor, and the potential for large modulation bandwidth. However, the operating principle for SLDs is distinct from laser diodes in that SLDs lack a strong cavity feedback mechanism, resulting in spatially coherent but temporally incoherent light output. Thus, SLDs may address the issues with laser diodes for lighting, while simultaneously maintaining some of the desirable characteristics of both laser diodes and LEDs. The objectives of this proposal are to design, grow, and fabricate blue (450 nm) SLDs on polar c-plane and nonpolar m-plane free-standing GaN substrates, and to evaluate their potential as sources in smart lighting systems through basic device characterization and detailed investigations of their efficiency droop and modulation bandwidth. The primary scientific aims of this work are to understand the fundamental role of optical gain in the superluminescent (non-lasing) regime on efficiency droop and modulation bandwidth in III-nitride emitters and to understand the effects of higher optical gain on SLD performance by comparing polar c-plane and nonpolar m-plane SLDs. The University of New Mexico (UNM) will collaborate with Sandia National Laboratories (SNL) and the Center for Integrated Nanotechnologies to design, fabricate, grow, and characterize the SLDs. UNM will perform the design and epitaxial growth, while SNL will focus on the fabrication and device characterization. The novelty of the proposed work includes the first comprehensive theoretical and experimental investigations of efficiency droop and the first investigation of modulation bandwidth in GaN-based emitters operating in the superluminescent regime. Moreover, the comparison of c-plane and m-plane SLDs will enable the first analysis of the effects of higher optical gain on the device performance. The development of high-performance GaN-based SLDs may enable efficiency gains and improved functionality in next-generation smart lighting systems.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Conceptual Model Update of Mercury Sources and Flux at Y-12 and Upper East Fork Poplar Creek, Oak Ridge,Tennessee

The interactions between the key processes that control the fate and transport of mercury (Hg) in the sediments, groundwater, and stream water within the Y-12 National Security Complex (Y-12) in Oak Ridge, Tennessee are complex, and many aspects are not well understood. In contaminated environments such as Y-12, conceptual models are frequently developed to aid in visualizing and understanding the dynamic nature of the hydrologic, geochemical, and physical environment. These conceptual models integrate data in an internally consistent manner to understand processes that control the fate and transport of contaminants. Over the past few decades of environmental investigation at Y-12, a number of conceptual models have been developed to identify and define various technical processes at various scales. The main purpose of the activities described in this report is to update the 2011 conceptual model for Upper East Fork Poplar Creek using the most recent Hg concentration and flux data and informed scientific interpretation. Emphasis was placed on improving the previous model by implementing a more detailed spatial and temporal approach to visualize transport pathways in the watershed and trends in flux and concentration over time, and to compare baseflow and stormflow system dynamics. Detailed descriptions of historical and current Hg sources and transport pathways are also provided for the east and west ends of the facility. This conceptual model will allow the US Department of Energy to evaluate past and present remedial activities and provide a strong technical basis for prioritizing and optimizing remedial responses in a cost-effective and efficient manner. Twenty years ago, Hg flux from Outfall (OF) 200 at the headwaters of East Fork Poplar Creek represented approximately 20% of the overall flux leaving Y-12. By the time of the 2011 conceptual model report, that percentage had increased to 70%–80%. Flux estimates compiled for this report using data from 2009 to 2018 show that OF200 accounted for roughly 60% of the flux leaving Y-12. The relative role of the four storm drain conduits to OF200 appeared similar to 2011, with OF163 being the greatest contributor to downstream flux. An increase in Hg concentrations and flux occurred throughout and downstream of west end storm drains in 2011 in response to a storm drain cleanout. Leading up to the 2011 storm drain cleanout, annual baseflow flux was higher at OF200A6 than at Station 17. From 2011 to 2018, the trend reversed with concentrations and flux being higher at Station 17 than at OF200A6. A spike in concentrations occurred in July 2018, potentially due to a one-time influx of Hg that occurred during COLEX decontamination and decommissioning activities at Y-12. This report includes recommendations for improving our conceptual understanding of Hg sources, transport pathways, and flux at Y-12. Important recommendations include further evaluation of transport pathways, concurrent measurement of Hg concentration and flux under baseflow and stormflow conditions at multiple sites, and research to understand the connections among periphyton and methylmercury concentration, bioavailability, and bioaccumulation. Ongoing facility decontamination and decommissioning efforts, site characterization, remedial actions, and research are facilitating the collection of new Hg data at Y-12. The conceptual model update provided herein takes advantage of the extensive recent Hg sampling to provide an updated assessment of Hg mass balance and support a refined understanding of Hg behavior at or near Y-12. This assessment should assist in future environmental management decisions and in mitigating the impacts of Hg on the surrounding environment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Machine learning analysis of perovskite oxides grown by molecular beam epitaxy

Reflection high-energy electron diffraction (RHEED) is a ubiquitous in situ molecular beam epitaxial (MBE) characterization tool. Although RHEED can be a powerful means for crystal surface structure determination, it is often used as a static qualitative surface characterization method at discrete intervals during a growth. A full analysis of RHEED data collected during the entirety of MBE growths is made possible using principle component analysis (PCA) and $\textit{k}$-means clustering to examine significant boundaries that occur in the temporal clusters grouped from RHEED data and identify statistically significant patterns. This process is applied to data from homoepitaxial SrTiO 3 growths, heteroepitaxial SrTiO 3 grown on scandate substrates, BaSnO 3 films grown on SrTiO 3 substrates, and LaNiO 3 films grown on SrTiO 3 substrates. We report this analysis may provide additional insights into the surface evolution and transitions in growth modes at precise times and depths during growth, and that video archival of an entire RHEED image sequence may be able to provide more insight and control overgrowth processes and film quality.

36 MATERIALS SCIENCE↗

ORBITAL ANGULAR MOMENTUM BEAMS RESEARCH USING A FREE-ELECTRON LASER OSCILLATOR

Orbital angular momentum (OAM) photon beams are excellent tools for non-contact optical manipulation of mat- ter in a broad photon energy range. A free-electron laser (FEL) oscillator is well-suited for studying OAM beams with various features including a wide spectral coverage, wavelength tunability, two-color lasing, polarization control, etc. Here, we report the first experimental demonstration of superposed OAM beams from an oscillator FEL. Lasing at around 458 nm, we have generated superposed OAM beams up to the fourth order as a superposition of two pure OAM modes with opposite helicities. These generated beams have a good beam quality, a high degree of circular polarization, and high power. Using external rf modulation with frequen- cies from 1 to 30 Hz, we also developed a pulsed mode operation of the OAM beams with a highly reproducible temporal structure. FEL operation showcased in this work can be extended to higher photon energies, e.g. using a future x-ray FEL oscillator. The operation of such an OAM FEL also paves the way for the generation of OAM gamma-ray beams via Compton scattering.

Liu, P.↗

Evaluation of smart charging for electric vehicle-to-building integration: A case study

Higher electric vehicle (EV) adoption will stress the importance of demand flexibility to achieve more economic, efficient, and reliable grid operation. Charging technologies will be paramount in shifting temporally to better fit the variable generation of wind and solar. As such, analysis is warranted on the benefits of EV charge scheduling with respect to installation cost, operation cost, difficulty of implementation, and grid flexibility. We tackle this by analyzing the cost savings of implementing an EV charge scheduling infrastructure to reduce demand charges and installation costs. In this paper, we analyze a case study for operation of 16 level 2 chargers and 1 fast charger for two different building types. We then evaluate various test phases for controlling building and charging loads using an adaptive charging network (ACN) algorithm to characterize the ACN’s potential to reduce overall project cost.

30 DIRECT ENERGY CONVERSION↗

Tunable momentum pair creation of spin excitations in dipolar bilayers

Here we study the temporal growth and spatial propagation of quantum correlations in a two-dimensional bilayer realizing a spin-1/2 quantum XXZ model with couplings mediated by long-range and anisotropic dipolar interactions. Starting with an initial state consisting of spins with opposite magnetization in each of the layers, we predict a dynamic instability that results, at short times, in the creation of correlated pairs of excitations at specific momenta at exponentially fast rates and entanglement between spatially separated modes. The momentum structure of the created pairs can be controlled via the dipolar orientation, the layer separation, or the dipolar couplings. The predicted behavior remains observable at very low filling fractions, making it accessible in state-of-the-art experiments with Rydberg atoms, magnetic atoms, and polar molecule arrays.

74 ATOMIC AND MOLECULAR PHYSICS↗

Phase Transition Dynamics in a Complex Oxide Heterostructure

Understanding the behavior of defects in the complex oxides is key to controlling myriad ionic and electronic properties in these multifunctional materials. The observation of defect dynamics, however, requires a unique probe-one sensitive to the configuration of defects as well as its time evolution. Here, we present measurements of oxygen vacancy ordering in epitaxial thin films of SrCoO x and the brownmillerite-perovskite phase transition employing x-ray photon correlation spectroscopy. These and associated synchrotron measurements and theory calculations reveal the close interaction between the kinetics and the dynamics of the phase transition, showing how spatial and temporal fluctuations of heterointerface evolve during the transformation process. The energetics of the transition are correlated with the behavior of oxygen vacancies, and the dimensionality of the transformation is shown to depend strongly on whether the phase is undergoing oxidation or reduction. Finally, the experimental and theoretical methods described here are broadly applicable to in situ measurements of dynamic phase behavior and demonstrate how coherence may be employed for novel studies of the complex oxides as enabled by the arrival of fourth-generation hard x-ray coherent light sources.

36 MATERIALS SCIENCE↗

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗