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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effects of Livestock Exclusion on Stream Habitat and Aquatic Biota: A Review and Recommendations for Implementation and Monitoring

Abstract To inform riparian restoration, research, and monitoring and to provide management recommendations, we reviewed published studies evaluating the physical and biological effectiveness of livestock exclusion and grazing reduction on various metrics in riparian and aquatic areas. We identified 95 North American studies that reported the effects of livestock grazing reduction on physical habitat (channel morphology, mesohabitats, substrate, and bank stability), biological assemblages (riparian vegetation, macroinvertebrates, fish, and birds), and water quality metrics (temperature, nitrates, phosphorus, and turbidity). Most studies reported that methods to reduce or exclude livestock decreased channel width, width-to-depth ratio, bank erosion, soil bulk density, bare ground, water temperature, nitrogen, and phosphorus and increased riparian vegetation (cover, height, productivity, biomass, and abundance), riparian bird abundance, and young-of-the-year fishes. Results for channel depth, instream substrate, mesohabitats, water depth, juvenile and adult fishes, and macroinvertebrates showed no consistent response to exclusion. Project success was influenced by the time since exclusion; whether there was complete exclusion or continued grazing; and local climate, geology, and soils. Apart from bank erosion and stability, most of the physical and biological metrics took more than a decade to respond to livestock exclusion. However, coupling exclusion with planting and other restoration measures decreased the recovery time. Complete exclusion of livestock produced more consistent improvements in riparian condition and other metrics than rest–rotation or other grazing management strategies. Understanding how physical and biological metrics respond to livestock exclusion will require (1) focused, long-term studies using before–after or before–after, control–impact designs; and (2) monitoring of metrics that most consistently respond to exclusion. Ultimately, the design of exclusions should be driven by local climate, geology, biophysical conditions, and management history. Our results highlight the need for watershed-scale approaches to excluding livestock from broad areas and the need for implementation monitoring to ensure that fencing and other exclusion measures continue to exclude livestock and produce the desired responses.

Krall, Michelle↗
DOE OSTI2021

Science & Technology Review March 2021

At Lawrence Livermore National Laboratory, we focus on science and technology research to ensure our nation’s security. We also apply that expertise to solve other important national problems in energy, bioscience, and the environment. Science & Technology Review is published eight times a year to communicate, to a broad audience, the Laboratory’s scientific and technological accomplishments in fulfilling its primary missions. The publication’s goal is to help readers understand these accomplishments and appreciate their value to the individual citizen, the nation, and the world.

08 HYDROGEN↗
DOE OSTI2021

Groundwater Inflows to the Columbia River Along the Hanford Reach and Associated Nitrate Concentrations

Healthy river ecosystems require the interaction of many physical and biological processes to maintain their status. One physical process supporting biogeochemical cycling is hydrologic exchange (i.e., hydrologic exchange flows, HEFs) between relatively fast-flowing channel waters and slower-flowing surface and subsurface waters (lateral and vertical). Land uses adjacent to rivers have the potential to alter the water quality of off-channel surface and subsurface waters, and HEFs therefore have the potential to deliver solutes associated with river-adjacent land uses to rivers. HEFs can be nonpoint, diffuse sources of pollution, making the ultimate pollution source difficult to identify, especially in large rivers. Here, we seek to identify HEFs in the Columbia River near Richland, WA by looking for anomalies in temperature and electrical conductivity (EC) along the bed of the river in February, June, July, August, and November 2018. These are ultimately the “ends” of HEFs as they are locations of subsurface inflow to the river. We found these anomalies to be a combination of warmer or colder and higher (but not lower) EC than river water. We identified a majority of warm anomalies in February and July 2018, and majority cold anomalies in June, August, and November 2018. High-EC anomalies were found mostly in February, August, and November. Combined, we observe a shift from warm, high EC anomalies dominating in February to equivalent EC, warm anomalies in June, to equivalent EC, cool anomalies dominating July. In August, we also measured dissolved nitrate ($NO^-_3$) in-situ to determine whether anomalies were associated with increased $NO^-_3$ loading to the river, especially along the eastern shoreline, which is dominated by agricultural land use. Inflows along the eastern shoreline have greater concentrations of nitrate than river water (up to 10 mg $N–NO^-_3$/L). This research demonstrates that HEFs are temporally and spatially dynamic transferring heat and solutes to rivers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Deep-Learning Electron Diffractive Imaging

Here, we report the development of deep-learning coherent electron diffractive imaging at subangstrom resolution using convolutional neural networks (CNNs) trained with only simulated data. We experimentally demonstrate this method by applying the trained CNNs to recover the phase images from electron diffraction patterns of twisted hexagonal boron nitride, monolayer graphene, and a gold nanoparticle with comparable quality to those reconstructed by a conventional ptychographic algorithm. Fourier ring correlation between the CNN and ptychographic images indicates the achievement of a resolution in the range of 0.70 and 0.55 Å. We further develop CNNs to recover the probe function from the experimental data. The ability to replace iterative algorithms with CNNs and perform real-time atomic imaging from coherent diffraction patterns is expected to find applications in the physical and biological sciences.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Physical, resource supply, and biological controls on nutrient processing along the river continuum

Nutrient impairment has led to damages to US surface and groundwater systems in excess of 100 billion dollars per year. Therefore, there is a strong need to develop methods to predict the transport, uptake, and export of nutrients along fluvial networks. We present results that are based on a data-driven mechanistic understanding of three factors that largely control nutrient uptake and export: 1) interactions between transport-related processes (mass transfer to metabolically active zones), 2) resource supply dynamics (nutrient concentration, stoichiometric constraints, etc.), and 3) biological controls (microbial community structure and function). Our results were generated from column experiments conducted along the Jemez River-Rio Grande continuum, which spans four orders of magnitude in mean annual discharge, more than 2000 m in altitude, and more than 500 km of stream longitude. Two resource supply injections were performed on each of the columns, i.e., a nitrate only addition, followed by a stoichiometrically ‘balanced’ 106Carbon:16Nitrogen:1Phosphorus addition. We quantified NO3-N uptake kinetics while constraining three variables: stream order, sediment type and type of injection (N vs stoichiometrically ‘balanced’ C:N:P). Following the laboratory nutrient uptake experiments, the columns were destructively sampled and the contents were homogenized to collect subsamples for DNA sequencing. Amplicon analysis was carried out as described by the Earth Microbiome Protocol for 16s and ITS sequencing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Predictability of Seawater DMS During the North Atlantic Aerosol and Marine Ecosystem Study (NAAMES)

This work presents an overview of a unique set of surface ocean dimethylsulfide (DMS) measurements from four shipboard field campaigns conducted during the North Atlantic Aerosol and Marine Ecosystem Study (NAAMES) project. Variations in surface seawater DMS are discussed in relation to biological and physical observations. Results are considered at a range of timescales (seasons to days) and spatial scales (regional to sub-mesoscale). Elevated DMS concentrations are generally associated with greater biological productivity, although chlorophyll a (Chl) only explains a small fraction of the DMS variability (15%). Physical factors that determine the location of oceanic temperature fronts and depth of vertical mixing have an important influence on seawater DMS concentrations during all seasons. The interplay of biomass and physics influences DMS concentrations at regional/seasonal scales and at smaller spatial and shorter temporal scales. Seawater DMS measurements are compared with the global seawater DMS climatology and predictions made using a recently published algorithm and by a neural network model. The climatology is successful at capturing the seasonal progression in average seawater DMS, but does not reproduce the shorter spatial/temporal scale variability. The input terms common to the algorithm and neural network approaches are biological (Chl) and physical (mixed layer depth, photosynthetically active radiation, seawater temperature). Both models predict the seasonal North Atlantic average seawater DMS trends better than the climatology. However, DMS concentrations tend to be under-predicted and the episodic occurrence of higher DMS concentrations is poorly predicted. The choice of climatological seawater DMS product makes a substantial impact on the estimated DMS flux into the North Atlantic atmosphere. These results suggest that additional input terms are needed to improve the predictive capability of current state-of-the-art approaches to estimating seawater DMS.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Excitonic structure and charge separation in the heliobacterial reaction center probed by multispectral multidimensional spectroscopy

Photochemical reaction centers are the engines that drive photosynthesis. The reaction center from heliobacteria (HbRC) has been proposed to most closely resemble the common ancestor of photosynthetic reaction centers, motivating a detailed understanding of its structure-function relationship. The recent elucidation of the HbRC crystal structure motivates advanced spectroscopic studies of its excitonic structure and charge separation mechanism. We perform multispectral two-dimensional electronic spectroscopy of the HbRC and corresponding numerical simulations, resolving the electronic structure and testing and refining recent excitonic models. Through extensive examination of the kinetic data by lifetime density analysis and global target analysis, we reveal that charge separation proceeds via a single pathway in which the distinct A 0 chlorophyll a pigment is the primary electron acceptor. In addition, we find strong delocalization of the charge separation intermediate. Our findings have general implications for the understanding of photosynthetic charge separation mechanisms, and how they might be tuned to achieve different functional goals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Using neural network ensembles to separate ocean biogeochemical and physical drivers of phytoplankton biogeography in Earth system models

Abstract. Earth system models (ESMs) are useful tools for predicting and understanding past and future aspects of the climate system. However, the biological and physical parameters used in ESMs can have wide variations in their estimates. Even small changes in these parameters can yield unexpected results without a clear explanation of how a particular outcome was reached. The standard method for estimating ESM sensitivity is to compare spatiotemporal distributions of variables from different runs of a single ESM. However, a potential pitfall of this method is that ESM output could match observational patterns because of compensating errors. For example, if a model predicts overly weak upwelling and low nutrient concentrations, it might compensate for this by allowing phytoplankton to have a high sensitivity to nutrients. Recently, we demonstrated that neural network ensembles (NNEs) are capable of extracting relationships between predictor and target variables within ocean biogeochemical models. Being able to view the relationships between variables, along with spatiotemporal distributions, allows for a more mechanistically based examination of ESM outputs. Here, we investigated whether we could apply NNEs to help us determine why different ESMs produce different spatiotemporal distributions of phytoplankton biomass. We tested this using three cases. The first and second case used different runs of the same ESM, except that the physical circulations differed between them in the first case, while the biological equations differed between them in the second. Our results indicated that the NNEs were capable of extracting the relationships between variables for different runs of a single ESM, allowing us to distinguish between differences due to changes in circulation (which do not change relationships) from changes in biogeochemical formulation (which do change relationships). In the third case, we applied NNEs to two different ESMs. The results of the third case highlighted the capability of NNEs to contrast the apparent relationships of different ESMs and some of the challenges it presents. Although applied specifically to the ocean components of an ESM, our study demonstrates that Earth system modelers can use NNEs to separate the contributions of different components of ESMs. Specifically, this allows modelers to compare the apparent relationships across different ESMs and observational datasets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Accelerator Technologies and Science: Progress and Outlook

For over half a century, high-energy particle accelerators play a key role and shape modern nuclear and particle physics, they are also the instruments at the forefront of research for material science and biology. The physics needs continuously push us to invent novel ways to increase energy and improve the performance of accelerators, reduce their cost and make them more power-efficient. Here we briefly overview the most notable accelerator facilities which recently became operational and are now employed for research in nuclear physics, basic energy sciences, neutrinos, high energy particle frontier. We also present upcoming and planned future facilities and outline their main goals, challenges, and required R&D. Focus will be given to the core accelerator technologies such as magnets, RF acceleration, and targets as we as leading beam physics developments such as beam cooling, colliding beams and plasma acceleration.

Shiltsev, Vladimir D.↗
DOE OSTI2022

Mechanism of endosomal escape by p H -responsive nucleic-acid vectors

Successful intracellular delivery of nucleic acids (NAs) hinges on many factors, one of them being NAs’ efficacious escape from endosomes. As competent NA vectors, pH-responsive gemini surfactants (GSs) might achieve high efficacy by facilitating endosomal escape. However, how the GSs assist the escape remains debated as many proposed mechanisms still lack experimental support, which hinders replication and further improvement of the efficient delivery. Here, via UV, fluorescence spectroscopy, and small-angle neutron scattering (SANS), we examined a pH-responsive GS's and a pH-unresponsive GS's capabilities to compact DNA and withstand binding competition, and their interactions with model endosomal and lysosomal membranes, at varied pHs. Acidification-driven enhancement of DNA-compaction capability and of stability against binding competition were found specific to the pH-responsive GS. Alongside the pH-responsive GS's structural perturbation to the membranes as observed with SANS, the features suggest that pH-responsive GSs facilitate endosomal escape by releasing excess GS molecules from DNA-GS complexes upon acidification in endosome maturation, with the released GS molecules disrupting endosomal and lysosomal membranes and thereby assisting the escape. Here a general design principle for NA vectors is proposed on the basis of this experimental finding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

40th Eastern Regional Photosynthesis Conference

Photosynthesis has shaped global biochemistry and geochemistry in its production of almost all atmospheric oxygen, and almost every electron that supports the processes of life on Earth was extracted from water by the light-dependent reactions, many of which were then used to fix carbon in the dark reactions. To humans, that fixed carbon is the originator of all fossil fuels and a critical step in conversion of solar photons to human-usable energy. The Eastern Regional Photosynthesis Conference (ERPC) serves as a forum for advancement of science in this field. As a regional-level conference, it specializes in providing developmental opportunities for early-career researchers from undergraduates to pre-tenure professors, as well as broadening the field in terms of participating scholars and research approaches to produce new interdisciplinary collaborations. Funding from the Department of Energy is used to mitigate registration and attendance costs for junior (non-PI) researchers. The ERPC is one of the three regional conferences in the field of photosynthesis research in the United States, alongside the Western Photosynthesis Conference (currently in California) and the Midwestern Photosynthesis Conference (Turkey Run, Indiana). A longstanding incubator for scientific discourse, discovery, and collaborations, this conference has spawned many collaborations which led to Department of Energy-funded projects and brought two full generations of scientists into the field. In 2023 the landmark 40th such conference was held at the Woods Hole Marine Biological Laboratory in Massachusetts. The conference was held April 14th-16th, 2023. The majority of the total attendees are traditionally undergraduates, graduate students, and postdoctoral researchers, whose scientific development greatly benefits from conferences like these. Almost all talks besides the ones given by invited speakers were given by young scientists who benefited from this award. Many posters presented at this conference were also the work of junior scientists. This conference is many young scientists' first exposure to the photosynthesis research community and its primary goal is to provide a positive atmosphere for those attendees, as exemplified by the three poster sessions and dedicated interactions between senior and junior scientists. Additionally, this was the first year of a successful equitable outreach and speaker recruitment plan to provide fair representation at the conference in line with Department of Energy policies and mission. The central focus of the ERPC is the understanding of energy flow from photons to usable chemical products in both natural and artificial photosynthesis. We support the DOE-BES aim of understanding of the biochemical/biophysical processes of photosynthesis to inform new technology development and field applications. This year’s theme, “Photosynthesis Across Scales,” reflected the scope of work being done from the individual exciton to the crop scale. This research encompasses applied biology, chemistry, physics, and materials engineering. The aim of this conference is to present new discoveries, techniques, and questions which can be sourced from any of these disciplines and provide an audience which is broadly qualified to use or respond to these developments.

08 HYDROGEN↗
DOE OSTI2022

Simulation of high-frequency dissolved oxygen dynamics in a shallow estuary, the Corsica River, Chesapeake Bay

Understanding shallow water biogeochemical dynamics is a challenge in coastal regions, due to the presence of highly variable land-water interface fluxes, tight coupling with sediment processes, tidal dynamics, and diurnal variability in biogeochemical processes. While the deployment of continuous monitoring devices has improved our understanding of high-frequency (12 - 24 hours) variability and spatial heterogeneity in shallow regions, mechanistic modeling of these dynamics has lagged behind conceptual and empirical models. The inherent complexity of shallow water systems is represented in the Corsica River estuary, a small basin within the Chesapeake Bay ecosystem, where abundant monitoring data have been collected from long-term monitoring stations, continuous monitoring sensors, synoptic sensor surveys, and measurements of sediment-water fluxes. A state-of-the-art modeling system, the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), was applied to the Corsica domain with a high-resolution grid and nutrient loads from the most recent version of the Chesapeake Bay watershed model. The Corsica SCHISM model reproduced observed high-frequency variability in dissolved oxygen, as well as seasonal variability in chlorophyll-a and sediment-water fluxes. Time-series signal analyses using Empirical Model Decomposition and spectral analysis revealed that the diurnal and M2 tide frequencies are the dominant high-frequency modes and physical transport contributes a larger share to dissolved oxygen budgets than biogeochemical processes on an hourly time scale. Heterogeneity and patchiness in dissolved oxygen resulting from phytoplankton distributions and geometry-driven eddies amplify the physical transport effect, and on longer time scales oxygen is controlled more by photosynthesis and respiration. Our simulation demonstrates that interactions among physical and biological dynamics generate complex high-frequency variability in water quality and non-linear reposes to nutrient loading and environmental forcing in shallow water systems.

54 ENVIRONMENTAL SCIENCES↗