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At least 811 records · Page 45

Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology

Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca 2+ -permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca 2+ ) homeostasis. The resultant up-regulation of intracellular Ca 2+ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca 2+ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca 2+ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. The fluorescence time-series data from individual pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. As a result, we demonstrate the up-regulation of gating of various Ca 2+ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca 2+ permeability transition into those with high open probability and Ca 2+ permeability.

59 BASIC BIOLOGICAL SCIENCES↗

Methane and CO2 chamber fluxes and porewater concentrations US-OWC Ameriflux wetland site, 2015-2018

The data measurements of CH4 and CO2 at different patch types (classified by dominant macrophyte vegetation or hydrological state). CH4 and CO2 data include 3 types of measurements: 1) Surface flux measurements from chamber measurements. 2) Leaf flux measurements from plant chambers, providing the rate per leaf area of methane flow through three species of macropyte aerenchemous plants (Water Lily, American Lotus, and Cattail) with the corresponding flux of CO2 at the same leaves. 3) Pore water concentrations of dissolved CO2 and CH4 concentrations. These are measured along vertical profiles at varying depths from the soil-water interface using in-situ porewater dialysis profiles (peepers). Observations of 1 and 3 are available monthly for most months of the growing season (May-September) of 2015, 2016 and 2018. Leaf flux measurements (plant chambers) are available only in June, July and August of 2018. We also included the patch type classification maps during 2015, 2017 and 2018 the relative water elevation map (bathymetry) for the site.In 8/23/2020 we added the data file ChamberFluxes_2018_Separated_Diffusive_Ebullitive_Fluxes.xlsx with observation related to chamber measurements in OWC during September 2018. In these observations, we partitioned the methane flux to its diffusive and ebullitive components, using an analysis approach we describe in section 5 of the methods "Ebullition and diffusion partitioning".

54 ENVIRONMENTAL SCIENCES↗

NGEE Arctic 2019 Alder Ground Truth Survey, Seward Peninsula AK

In July 2019 we made traveled the road system outside of Nome, AK and detailed the GPS coordinates of alder shrublands for the purpose of ground-truthing alder maps of the region. Both visual and ground-based observations were made for patches of alder shrublands greater 5x5m and larger, ideally 10x10m. Visual observations were made from the car and GPS coordinates are approximate, placed by dropping pins on georeferenced pdfs using the Avenza app. Visual observations included positive identified alder shrublands as well as thickets of non-alder shrubs. Ground Observations were made at a subset of locations where we were able to hike to alders shrubland areas. Ground observations include GPS points (made with Garmin InReach) as well as relevant features of a centrally located, representative alder shrub in the patch (max height, basal diameter of all ramets, soil depth). Aboveground biomass (weight dry mass) of the surveyed shrub was calculated based on alder-specific allometric equations in Berner et al 2015 which our team checked for accuracy for the Seward Peninsula as part of Salmon et al 2019. This dataset contains three data files, three data dictionaries, and one file-level metadata file all in*.csv format plus one *.txt README file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Post-fire soil respiration in late growing season (2023 and 2024), Kougarok Fire Complex, Seward Peninsula, Alaska

Field soil respiration data collected in 2023 and 2024 from burned and unburned tussock tundra sites in the Kougarok Fire Complex, near Nome, on the Seward Peninsula of Alaska. Specifically, we measured soil properties and late-growing season CO2 fluxes in patches of unique plant functional types (forbs, shrubs, and graminoids) across two years in tundra recovering from repeated wildfires over the decade. The goal was to identify the main drivers of soil respiration in Arctic tundra underlain by discontinuous permafrost that is recovering from two recent, repeated wildfires that differed in fire age and number of times burned, thereby resulting in different levels of vegetation and subsurface property changes (i.e., successional trajectories). There are five files in *.csv format with one data file and four data description files including data, dictionary, methods, terminology, and file-level metadata. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), is a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic Phase 3 project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

Santos, Fernanda [ORNL] (ORCID:0000000191555623)↗

AmeriFlux US-An2 Anaktuvuk River Moderate Burn

This is the AmeriFlux version of the carbon flux data for the site US-An2 Anaktuvuk River Moderate Burn. Site Description - The Anaktuvuk River fire on the North Slope of Alaska started on July 16, 2007 by lightning. It continued until the end of September when nearby lakes had already frozen over and burned >256,000 acres, creating a mosaic of patches that differed in burn severity. The Anaktuvuk River Severe Burn, Moderate Burn, and Unburned sites are 40 km to the west of the nearest road and were selected in late May 2008 to determine the effects of the fire on carbon, water, and energy exchanges during the growing season. Because the fire had burned through September of the previous year, initial deployment of flux towers occurred prior to any significant vegetative regrowth, and our sampling campaign captured the full growing season in 2008. The Moderate Burn site consisted of a large area with small patches of completely and partially burned tundra intermixed across the landscape.

Rocha, Adrian↗

AmeriFlux MX-Aog Alamos Old-Growth tropical dry forest

This is the AmeriFlux version of the carbon flux data for the site MX-Aog Alamos Old-Growth tropical dry forest. Site Description - This tower is located at a patch of remnant old growth tropical dry forest where the dominant vegetation are leguminous trees and a notorious presence of the genus Brusera. The site is at about 18 km from the municipality of Alamos Sonora Mexico within a private ranch managed by the NGO Nature Culture International. The area is also within a federally protected land named “Area de Proteccion de Flora y Fauna Sierra de Alamos Rio-Cuchijaqui" in the catalog of the “Comision Nacional de Areas Naturales Protegidas (CONANP-Mexico)”. The preserved ranch is surrounded by a mosaic of forest patches with different successional stages of tropical dry forest, and some places that are used for local agriculture and livestock. This ecosystem lies in a highly seasonal region under the influence of the North American Monsoon that brings about 70% of the rains from July to September.

Yepez, Enrico A.↗

AmeriFlux FLUXNET-1F MX-Aog Alamos Old-Growth tropical dry forest

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site MX-Aog Alamos Old-Growth tropical dry forest. This is the FLUXNET version of the carbon flux data for the site MX-Aog Alamos Old-Growth tropical dry forest produced by applying the standard ONEFlux (1F) software. Site Description - This tower is located at a patch of remnant old growth tropical dry forest where the dominant vegetation are leguminous trees and a notorious presence of the genus Brusera. The site is at about 18 km from the municipality of Alamos Sonora Mexico within a private ranch managed by the NGO Nature Culture International. The area is also within a federally protected land named “Area de Proteccion de Flora y Fauna Sierra de Alamos Rio-Cuchijaqui" in the catalog of the “Comision Nacional de Areas Naturales Protegidas (CONANP-Mexico)”. The preserved ranch is surrounded by a mosaic of forest patches with different successional stages of tropical dry forest, and some places that are used for local agriculture and livestock. This ecosystem lies in a highly seasonal region under the influence of the North American Monsoon that brings about 70% of the rains from July to September.

Yepez, Enrico A. [Instituto Tecnologico de Sonora]↗

Refinements to the Graves–Pitarka Kinematic Rupture Generator, Including a Dynamically Consistent Slip-Rate Function, Applied to the 2019 Mw 7.1 Ridgecrest Earthquake

The main objective of this study is to develop physics–based constraints on the spatiotemporal variation of the slip–rate function using a simplified dynamic rupture model. First, we performed dynamic rupture modeling of the 2019 M w 7.1 Ridgecrest, California, earthquake, to analyze the effects of depth–dependent stress and material friction on slip rate. Then, we used our modeling results to guide refinements to the slip–rate function that were implemented in the Graves–Pitarka kinematic rupture generation technique. The dynamic ruptures were computed on a surface–rupturing, planar strike–slip fault that includes a weak (negative to low–stress–drop) zone in the upper 4 km of the crust. Below the weak zone, we placed high–stress–drop patches designed to mirror the large–slip areas seen in various rupture model inversions of the event. The locations of the high–stress–drop patches and the hypocenter were varied in multiple realizations to investigate how changing the dynamic conditions affected the resulting rupture kinematics, in particular, the slip rate. From these simulations, we observed a systematic change in the shape of the slip–rate function from Kostrov type below the weak zone to a predominantly symmetric shape within the weak zone, along with a depth–dependent reduction of peak slip rate. We generalized these shallow rupture features into a depth–dependent parametric variation of the slip–rate function and implemented it in the Graves–Pitarka kinematic rupture model generator. The performance of the updated kinematic approach was then verified in 0–4 Hz simulations of the M w 7.1 Ridgecrest earthquake, which showed that incorporating the depth–dependent variation in the shape of the slip–rate function improves the fit to the observed near–fault ground motions in the 0.5–3 s period range.

58 GEOSCIENCES↗

Landscape corridors can increase invasion by an exotic species and reduce diversity of native species.

Abstract. Landscape corridors are commonly used to mitigate negative effects of habitat fragmentation, but concerns persist that they may facilitate the spread of invasive species. In a replicated landscape experiment of open habitat, we measured effects of corridors on the invasive fire ant, Solenopsis invicta, and native ants. Fire ants have two social forms: polygyne, which tend to disperse poorly but establish at high densities, and monogyne, which disperse widely but establish at lower densities. In landscapes dominated by polygyne fire ants, fire ant abundance was higher and native ant diversity was lower in habitat patches connected by corridors than in unconnected patches. Conversely, in landscapes dominated by monogyne fire ants, connectivity had no influence on fire ant abundance and native ant diversity. Polygyne fire ants dominated recently created landscapes, suggesting that these corridor effects may be transient. Our results suggest that corridors can facilitate invasion and they highlight the importance of considering species’ traits when assessing corridor utility.

Solenopsis invicta↗

A feasibility study for experimentally determining dynamic force distribution in a lap joint

Developing constitutive models of the physics in mechanical joints is currently stymied by inability to measure forces and displacements within the joint. The current state of the art estimates whole joint stiffness and energy loss per cycle from external measured force input and one or two acceleration responses. To validate constitutive models beyond this state requires a measurement of the distributed forces and displacements at the joint interface. Unfortunately, introducing measurement devices at the interface completely disrupts the desired physics. A feasibility study is presented for a non-intrusive method of solving for the interface dynamic forces from an inverse problem using full field measured responses. The responses come from the viewable surface of a beam. The noise levels associated with digital image correlation and continuous scanning laser Doppler velocimetry are evaluated from typical beam experiments. Two inverse problems are simulated. One utilizes the extended Sum of Weighted Accelerations Technique (SWAT). The second is a new approach dubbed the method of truncated orthogonal forces. These methods are much more robust if the contact patch geometry is well identified. Various approaches to identifying the contact patch are investigated, including ion marker tracking, Prussian blue and ultrasonic measurements. A typical experiment is conceived for a beam which has a lap joint at one end with a single bolt connecting it to another identical beam. In a virtual test using the beam finite element analysis, it appears that the SWAT inverse method requires evaluation of too many coefficients to adequately identify the force distribution to be viable. However, the method of truncated orthogonal forces appears viable with current digital image correlation (and probably other) imaging techniques.

47 OTHER INSTRUMENTATION↗

Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units

Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.

97 MATHEMATICS AND COMPUTING↗

Integrity Levels: A New Paradigm for Protecting Computing Systems

As the field of determined and increasingly sophisticated adversaries multiplies, the risk to integrity of deployed computing devices magnifies. Given the ubiquitous connectivity, substantial storage, and accessibility, the increased reliance on computer platforms make them a significant target for attackers. Over the past decade, malware has transitioned from attacking a single program to subverting the operating system (OS) kernel by means of what is commonly known as a rootkit. While computer systems require patches to fix newly discovered vulnerabilities, undiscovered vulnerabilities remain Furthermore, typical solutions utilize mechanisms that operate within the OS. If the OS becomes compromised, these mechanisms may be vulnerable to being disabled or upon detection of the potential compromise, being "shut down" until patched or otherwise mitigated. We propose an innovative approach to designing computer systems that allows the behavior or functionality of the computer system to change based on the integrity of the system. Instead of attempting to prevent or detect all malware attacks, our proposed approach allows possible graceful degradation of functionality according to the security policy specification as anomalies of security concern are detected. We believe this innovative paradigm can determine the "integrity lever of the system. Based on the integrity level, the computer system may behave differently or limit access to data.

97 MATHEMATICS AND COMPUTING↗

INGRID: An interactive grid generator for 2D edge plasma modeling

A fusion boundary-plasma domain is defined by axisymmetric magnetic surfaces where the geometry is often complicated by the presence of one or more X-points; and modeling boundary plasmas usually relies on computational grids that account for the magnetic field geometry. The new grid generator INGRID (Interactive Grid Generator) presented here is a Python-based code for calculating grids for fusion boundary plasma modeling, for a variety of configurations with one or two X-points in the domain. INGRID first performs partitioning over the domain consisting of a small number of patches conforming to the magnetic field and wall geometry; then it generates a subgrid on each of the patches and joins them into a global grid. This domain partitioning strategy makes possible a uniform treatment of various configurations with one or two X-points in the domain. This includes single-null, double-null, and other configurations with two X-points in the domain. The INGRID design allows generating grids either interactively, via a parameterfile driven GUI, or using a non-interactive script-controlled workflow. Results of testing demonstrate that INGRID is a flexible, robust, and user-friendly grid-generation tool for fusion boundary-plasma modeling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

MCNP6.3: A Year in Review [Slides]

This presentation discusses the past year and the many accomplishments of the MCNP6.3 team. It states that the MCNP6.3 release is imminent and that the approved, final documents have been making their way to the website. The code executables and source are already packaged up for distribution and the new installer is being finalized and tested now, for all platforms. The package will be sent to RSICC before the end of October 2022. Additionally, the presentation discusses some things to think about as MCNP6.3 is requested and/or used. For example, many of the recent efforts have been focused on making development, updates, and distribution of the code and documents more robust and streamlined. They will be revising/updating documents more frequently than ever before and they will be exploring avenues to distribute official patches to MCNP6.3. As they explain, this allows them to be more responsive to bugs and issues that are identified. In conclusion, the application of a patch to MCNP6.3 will require having the source code.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Functional-type modeling approach and data-driven parameterization of methane emissions in wetlands (Final Technical Science Report)

Our goals are to improve understanding and quantitative representation of the multiple processes that affect methane emissions at a high (patch level, vertically detailed) spatial resolution, and translate this understanding to improved modeling capability of coastal wetland fluxes using the E3SM Land Model (ELM v1) wetland CH4 biogeochemistry module. We propose an experimental approach to identify and parameterize uncertainties in ELM. Understanding of methane emissions can be improved along three conceptual axes: (i) horizontal (ecohydrological patch resolution), (ii) vertical (through the depth of the soil column), and (iii) process level (e.g., resolving microbial pathways, vegetation specific transport pathways). Along each of the three axes, we will characterize, quantify, and model, the key ecological, hydrological, and meteorological controls of methane (CH4) flux heterogeneity in four model coastal wetlands.

54 ENVIRONMENTAL SCIENCES↗

Quantum Gauge Networks: A New Kind of Tensor Network

Although tensor networks are powerful tools for simulating low-dimensional quantum physics, tensor network algorithms are very computationally costly in higher spatial dimensions. We introduce quantum gauge networks: a different kind of tensor network ansatz for which the computation cost of simulations does not explicitly increase for larger spatial dimensions. We take inspiration from the gauge picture of quantum dynamics, which consists of a local wavefunction for each patch of space, with neighboring patches related by unitary connections. A quantum gauge network (QGN) has a similar structure, except the Hilbert space dimensions of the local wavefunctions and connections are truncated. We describe how a QGN can be obtained from a generic wavefunction or matrix product state (MPS). All 2k-point correlation functions of any wavefunction for M many operators can be encoded exactly by a QGN with bond dimension O(M k ). In comparison, for just k = 1, an exponentially larger bond dimension of 2 M/6 is generically required for an MPS of qubits. We provide a simple QGN algorithm for approximate simulations of quantum dynamics in any spatial dimension. The approximate dynamics can achieve exact energy conservation for time-independent Hamiltonians, and spatial symmetries can also be maintained exactly. We benchmark the algorithm by simulating the quantum quench of fermionic Hamiltonians in up to three spatial dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SPRUCE High-Resolution Minirhizotrons in an Experimentally-Warmed Peatland Provide an Unprecedented Glimpse at Fine Roots and their Fungal Partners: Supporting Data

Images were collected using first of their kind, non-destructive, high-resolution automated minirhizotrons (RhizoSystems, LLC) to assess the response of plant fine-root and fungal mycelium dynamics to elevated temperatures after 4-6 years of whole-ecosystem warming and exposure to elevated carbon dioxide concentrations (e[CO2]) in a peat bog where the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment is located. We focused on two SPRUCE experimental plots: Plot 10 has elevated temperature (+9°C) and plot 19 is a control (+0°C). Both have elevated carbon dioxide (e[CO2]). Changes in root and fungal abundance with warming were estimated from a timeseries of landscape-level mosaiced images for each plot by measuring the proportional abundance of five belowground classes: fine roots of vascular plants, ectomycorrhizas, fungal hyphae, fungal rhizomorphs, and fungal sporocarps. To examine root and fungal phenology responses to warming, the length per individual root or fungal structure (except fungal hyphae that did not grow linearly but rather increased in areal coverage) were measured per image area of a set of timeseries patch-level mosaiced images for each plot. The experimental work was conducted in a Picea mariana [black spruce] – Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). This ecosystem, which is located at the southern margin of the boreal forest, is considered especially vulnerable to climate change and anticipated to be near its tipping point. These data were used in analyses published in Defrenne et al (2021). This dataset contains 5 data files in comma-separate values (*.csv) format and a compressed folder (*.zip) containing 383 JPEG (*.jpg) images. Data files contain landscape-level assessment of belowground class abundance, patch-level growth phenology, and environmental variables (originally published in Hanson et al., 2016 and Hanson et al 2020). Images were collected with automated minirhizotrons and analyzed for phenology. Additional metadata are provided: 5 data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗

Evaluating Basin-Scale Forest Adaptation Scenarios: Wildfire, Streamflow, Biomass, and Economic Recovery Synergies and Trade-Offs

Active forest management is applied in many parts of the western United States to reduce wildfire severity, mitigate vulnerability to drought and bark beetle mortality, and more recently, to increase snow retention and late-season streamflow. A rapidly warming climate accelerates the need for these restorative treatments, but the treatment priority among forest patches varies considerably. We simulated four treatment scenarios across the 3,450 km 2 Wenatchee River basin in eastern Washington, United States. We used a decision support tool (DST) to assess trade-offs and synergies within and among treatments on wildfire risk and smoke emissions, water yield and snow retention, biomass production, and economic return. Treatment scenarios emphasized prescribed burning ( BurnOnly ), biomass production ( MaxBiomass ), gap-based thinning to optimize water yield ( IdealWater ), and a principle-based restoration scenario ( RA1 ). Fire hazard, smoke emissions, and biomass production metrics were evaluated across scenarios using the Forest Vegetation Simulator, and water yields were modeled using the Distributed Hydrology Soil Vegetation Model. Simulations were summarized to both patch- (10 1 –10 2 ha) and subwatershed- (10 3 –10 4 ha) scales, and treatment effects were evaluated against an untreated baseline landscape. We used logic models to rank effect sizes by scenario across metrics along a continuum between −1 (no or weak effect) to +1 (large effect). All treatments produced benefits across one or more ecosystem services and led to synergistic benefits to water yield and wildfire hazard reduction. Tradeoffs among resource benefits were clear in wilderness where reliance on prescribed burning without mechanical treatment increased costs and eliminated the potential for biomass recovery. The BurnOnly scenario improved fire risk metrics and streamflow, but effect sizes were lower compared to other treatments. IdealWater showed the strongest benefits overall, demonstrating the ability to capture multiple resource benefits through spatially explicit thinning. Our study provides a framework for integrating strategic and tactical models that evaluate tradeoffs and synergies gained through varied management approaches. We demonstrate the utility of decision support modeling to enhance management synergies across large landscapes.

54 ENVIRONMENTAL SCIENCES↗