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At least 217 records · Page 12

Data From: Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N-2, Journal of Geophysical Research-Biogeosciences

This data package contains pumping data (.txt), parameter matrices, and R code (.R, .RData) to perform bootstrapping for parameter selection for the bioclogging model development. The pumping data were collected from the Russian River Riverbank Filtration site located in Sonoma County, California from 2010-2017 from three riverbank collection wells located alongside the study site. The pumping data is directly correlated with water table oscillations, so the code performs these correlations and simulates stochastic versions of water table oscillations. See Metadata Description.pdf for full details on dataset production. This dataset must be used with the R programming language. This dataset and R code is associated with the publication "Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N-2"This research was supported by the Jane Lewis Fellowship from the University of California, Berkeley, the Sonoma County Water Agency (SCWA), the Roy G. Post Foundation Scholarship, the U.S. Department of Energy, Office of Science Graduate Student Research (SCGSR) Program, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award DE-AC02-05CH11231, and the UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany.

54 ENVIRONMENTAL SCIENCES↗

Nyx: A Massively Parallel AMR Code for Computational Cosmology

Nyx is a highly parallel, adaptive mesh, finite-volume N-body compressible hydrodynamics solver for cosmological simulations. It has been used to simulate different cosmological scenarios with a recent focus on the intergalactic medium and Lyman alpha forest. Together, Nyx, the compressible astrophysical simulation code, Castro, and the low Mach number code MAESTROeX, make up the AMReX-Astrophysics Suite of open-source, adaptive mesh, performance-portable astrophysical simulation codes. Other examples of cosmological simulation research codes include Enzo, Enzo-P/Cello, RAMSES, ART, FLASH, Cholla, as well as Gadget, Gasoline, Arepo, Gizmo, and SWIFT.

79 ASTRONOMY AND ASTROPHYSICS↗

Dark Radiation Constraints on Heavy QCD Axions

The naturalness problem of PQ symmetry motivates study of the heavy QCD axion, with masses m a > 1 MeV generated at scales above the QCD scale, and low values of the PQ symmetry breaking scale, ƒ a . We compute the abundance of such axions in a model-independent way, assuming only that they freeze-out after reheating from inflation, and are not subsequently diluted by new physics. If these axions decay between neutrino decoupling and the last scatter era of the Cosmic Microwave Background (CMB), they dilute the neutrinos and their abundance is constrained by CMB measurements of the energy density in dark radiation, N eff . We accurately compute this bound using a numerical code to evolve the axion momentum distribution, including many key processes and effects previously ignored. We assume that the only relevant axion decays are to final states involving Standard Model particles. We determine regions of (m a , ƒ a ) that will give a signal in N eff at CMB Stage 4 experiments. We similarly compute the N eff bound and CMB Stage 4 signal for heavy axions that can decay to light mirror photons. Finally, we compute the bounds on heavy axions with mass below 1 MeV that decay after the era of CMB last scatter, from their contribution to cold or hot dark matter or N eff at this era.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Microstability of β ~ 1 tokamak equilibria

High-power-density tokamaks offer a potential solution to design cost-effective fusion devices. One way to achieve high power density is to operate at a high β value (the ratio of thermal to magnetic pressure), i.e. β~1 . However, a β~1 state may be unstable to various pressure- and current-driven instabilities or have unfavourable microstability properties. To explore these possibilities, we generate β~1 equilibria and investigate their stability. First, we demonstrate the generation of high-β equilibria with the computer code VMEC. We then analyse these equilibria to determine their stability against the infinite-n ideal-ballooning mode. We follow that by engaging in a detailed microstability study using the GS2 code, beginning with assessments of electrostatic ion-temperature-gradient and trapped election mode instabilities. We observe interesting behaviour for the high-β equilibria – stabilization of these modes through two distinct mechanisms – large negative local shear and reversal of electron precession drift. Finally, we perform electromagnetic gyrokinetic simulations and observe enhanced stability in the outer core of high-β equilibria and absence of kinetic ballooning modes in the negative-triangularity, high-β equilibria. The enhanced outer-core stability of high-β equilibria is different from their lower-β counterparts and offers an alternative, potentially favourable regime of tokamak operation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Improving Performance of M-to-N Processing and Data Redistribution in In Transit Analysis and Visualization

In an in transit setting, a parallel data producer, such as a numerical simulation, runs on one set of ranks M, while a data consumer, such as a parallel visualization application, runs on a different set of ranks N. One of the central challenges in this in transit setting is to determine the mapping of data from the set of M producer ranks to the set of N consumer ranks. This is a challenging problem for several reasons, such as the producer and consumer codes potentially having different scaling characteristics and different data models. The resulting mapping from M to N ranks can have a significant impact on aggregate application performance. In this work, we present an approach for performing this M-to-N mapping in a way that has broad applicability across a diversity of data producer and consumer applications. We evaluate its design and performance with a study that runs at high concurrency on a modern HPC platform. By leveraging design characteristics, which facilitate an “intelligent” mapping from M-to-N, we observe significant performance gains are possible in terms of several different metrics, including time-to-solution and amount of data moved.

Loring, Burlen↗

Improving Performance of M-to-N Processing and Data Redistribution in In Transit Analysis and Visualization

In an in transit setting, a parallel data producer, such as a numerical simulation, runs on one set of ranks M, while a data consumer, such as a parallel visualization application, runs on a different set of ranks N: One of the central challenges in this in transit setting is to determine the mapping of data from the set of M producer ranks to the set of N consumer ranks. This is a challenging problem for several reasons, such as the producer and consumer codes potentially having different scaling characteristics and different data models. The resulting mapping from M to N ranks can have a significant impact on aggregate application performance. In this work, we present an approach for performing this M-to-N mapping in a way that has broad applicability across a diversity of data producer and consumer applications. We evaluate its design and performance with a study that runs at high concurrency on a modern HPC platform. By leveraging design characteristics, which facilitate an ''intelligent'' mapping from M-to-N, we observe significant performance gains are possible in terms of several different metrics, including time-to-solution and amount of data moved.

Loring, Burlen↗

Preparing for the next pandemic via transfer learning from existing diseases with hierarchical multi-modal BERT: a study on COVID-19 outcome prediction

Abstract Developing prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ( $${\textsc {TransMED}}$$ T R A N S MED ) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of $${\textsc {TransMED}}$$ T R A N S MED ’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis. $${\textsc {TransMED}}$$ T R A N S MED ’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

SOURCES4D

SOURCES is a code for computing neutron source rates and spectra from spontaneous fission (including delayed neutrons) and (alpha,n) reactions in homogeneous materials and (alpha,n) reactions in single-interface and two-interface geometries. SOURCES is a Los Alamos National Laboratory (LANL) code that is written in FORTRAN and distributed through the Radiation Safety Information Computation Center (RSICC). LANL’s last release of SOURCES to RSICC was SOURCES4C in 2002. This disclosure covers the latest version of SOURCES, SOURCES4D. This version adds sensitivity capabilities for (alpha,n) sources in homogeneous materials. Specifically, SOURCES4D writes new output that can be used to calculate, in post-processing, first and second derivatives of the (alpha,n) source rate density and spectrum with respect to nuclide densities in a homogeneous material and first derivatives of the (alpha,n) source rate density and spectrum with respect to nuclide stopping powers and (alpha,n) cross sections (nuclear data). These derivatives are useful for uncertainty quantification, predictive modeling, and other applications in neutron transport problems.

Favorite, Jeffrey A.↗

Recent progress on the APOLLO3 calculation scheme for the FLUOLE2 experiment

Studies of the neutron fluence on reactor pressure vessel and the correlated reactor lifetime issues require very good knowledge of the neutron source distribution in the reactor core and especially in the peripheral region. The FLUOLE2 experiment offers an appropriate starting configuration to investigate the possibility of using the APOLLO3 deterministic code with a two-step calculation scheme. It enables us to calculate a pin-by-pin neutron source distribution in the core, then to carry out the neutron propagation from the core to neutron detectors. In this paper, we focus on a calculation scheme dedicated to the determination of core neutron source distribution using APOLLO3 with the SHEM281 energy mesh, a Method of Characteristics (MOC) to solve the transport equation for the lattice computation step and a 20-groups 3D computation using the MINARET SN solver of APOLLO3. Reactivity and pin-by-pin reaction rate results have been analyzed. Results obtained with both lattice and core computations show a good agreement with those produced through a reference calculation using the TRIPOLI-4 Monte Carlo transport code. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

A reduced model for the ITER divertor based on SOLPS solutions for ITER Q = 10 baseline conditions: A. identifying options for the control parameters*

Edge codes such as SOLPS coupled to neutral codes such as EIRENE have become so comprehensive and sophisticated that they now constitute, in effect, 'code-experiments' that, as for actual experiments, can benefit from interpretation using simple models and conceptual frameworks, i.e. reduced models. The first task is the identification of options for the reduced model control parameters that are best suited for control of the action of the divertor, i.e. for control of target power loading and sputter-erosion, primarily. A strong correlation between the electron temperature at the divertor target, T e,t , and the neutral deuterium D 2 density at the target, n D2,t , flux-tube resolved, has recently been reported for a number of code studies including SOLPS-4.3 modeling of a set of ~50 ITER baseline cases: Q DT = 10, q 95 = 3, P SOL = 100 MW, metallic walls, and Ne seeding. This part A of the present study reports new results for largely the same ITER cases, confirming the strong correlations reported earlier between local values of T e,t , and (i) n D2,t , and (ii) normalized volumetric losses of power and pressure in the divertor. Strong correlations have now also been found, and are reported here for the first time, between T e,t and all of the divertor target quantities of practical interest. A physical explanation for this surprising result has not been fully identified; nevertheless it has encouraging implications for reduced modeling of the ITER divertor. For such ITER conditions, (i) the global Ne injection rate, Inj Ne [Ne/s], and (ii) the electron temperature at the location on the target where the peak power deposition occurs, T e,t @q ⊥,pk (eV), are found to be promising reduced model control parameters. In the companion report, part B, a reduced model for the ITER divertor is developed and described in detail, based on reversed-direction 2 point modelling, Rev2PM. The input to the reduced model is a value of the variable pair (T et @q ⟂,pk ,Inj Ne ) and the output are values of the various target as well as divertor-entrance quantities of practical interest, e.g. q ⊥,pk , n e,Xpt (the electron density at the poloidal location of the X-point), etc. In part B the reduced model is quantitatively characterized using one half of the code cases; it is then used to successfully predict (replicate) the code values of e.g. n e,Xpt for the other half of the cases.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Numerical Codes for the DESC-LSST Analysis Pipeline: Core Cosmology Library Standard Modules and Beyond wCDM Modules (Final Technical Report)

The overall objective of the project is to investigate and develop specific software modules and analysis components for the software pipeline of LSST Dark Energy Science Collaboration (DESC). Following the key projects of DESC Science Roadmap (SRM), we will write and test computer codes for the Core Cosmology Library (CCL) in order to complete its modules, functionalities, and interface to work with the analysis pipelines from the five science probes of DESC (parts of SRM deliverables CX4.2TJP, CX6.2CS). We will also code modules for CCL to test models beyond w-Cold-Dark-Matter (wCDM) and modification to gravity (MG). Interfaces for MG models will also be developed for the TJPCOSMO software which is the main pipeline of the Theory and Joint Probe (TJP) working group (deliverable TJP2.3). In order to use the full power of LSST data to constrain MG models, we will also work on constraints from nonlinear regime by running and analyzing MG N-Body simulations using a Parameterized-Post-Friedmann framework into the Gadget-2 simulation package (deliverable TJP2.2). Preliminary results for the simulations were obtained in the past. In collaboration with other DESC groups, we plan to make these simulations feedable to cosmic emulators that are practical for likelihood analyzes (deliverable TJP2.2, parts of CX6.2CS). We will also modify and integrate our current codes for consistency tests between data sets and probes into the pipeline (parts of deliverables CX8.2TJP, TJP2.3). We understand that other groups will contribute to some of these objectives but our team will focus and collaborate with others on the particular part of testing MG and models beyond wCDM and refine the DESC pipeline for this purpose. PI has been coordinating his work with the TJP and CS working groups and the DESC management team. PI is a full member of DESC since June 2013. He and his students have been contributing to LSST-DESC activities and work including TJP telecons, collaboration meetings, hack-weeks, and workshops. PI chaired or co-chaired sessions at collaboration meetings and hack-weeks about testing gravity and models beyond wCDM using LSST. He is coordinating the TJP2 projects for testing models beyond wCDM including the writing of DESC-research-note, development of code for pipeline, and N-Body simulations for MG and beyond wCDM models testable with LSST analyses. As stressed in the DESC white paper, SRM, and P5 report, one of the important questions in understanding cosmic acceleration and dark energy is to be able to distinguish whether the acceleration is due to a dark energy component in the universe or a modification to gravity. Answering these questions will have a significant impact on the question of cosmic acceleration and dark energy. The methods that we will use include analytical work, numerical code, and N-Body simulations. A first approach that that we will use consists of using growth rate parameters that enter the perturbed dynamics equations. These parameters take distinctive values for distinct gravity theories and have potential to distinguish between Dark Energy and Modified Gravity. The second method is to look for inconsistencies in Dark Energy parameter spaces using specific combinations of cosmological data sets. Our investigation addresses the Dark Energy problem that is relevant to the mission of the HEP program to understand how our universe works at its most fundamental level. It will allow us to make progress on the HEP mission to explore the nature of Dark Energy and the basic nature of space and time using future surveys such as LSST. The investigation supports the DOE HEP program Cosmic Frontier as it will contribute to the study and understanding of dark energy and fundamental properties of the universe. The investigation contributes directly to LSST-DESC key projects and their deliverables as described in the Science Road-map document to build analysis pipeline and to test dark energy and beyond wCDM models using LSST.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

How do Hydrological Variability and Human Activities Control the Spatiotemporal Changes of Riverine Nitrogen Export in the Upper Mississippi River Basin?

Excessive nitrogen export from agricultural watersheds remains a critical water quality challenge, with the Upper Mississippi River Basin (UMRB) significantly contributing to downstream eutrophication and hypoxia in the Gulf. This study investigates the spatiotemporal dynamics of riverine nitrate plus nitrite (NO 3 − + NO 2 − -N) export across the UMRB at high spatial resolution (12-digit Hydrologic Unit Codes or HUC12 subwatershed scale) during 2001−2020 and quantifies the effects of anthropogenic activities and hydrological variability on riverine NO 3 − + NO 2 − -N export changes in the region between 2001−2005 and 2016−2020. Our results revealed hotspots of substantial increases in NO 3 − + NO 2 − -N yields across the UMRB, with distinct regional patterns in driving factors. Over the entire UMRB, NO 3 − + NO 2 − -N yields increased by 9.7 kg/ha/yr on average from 2001−2005 to 2016−2020, with anthropogenic activities contributing 4.8 kg/ha/yr and hydrological variability contributing 4.9 kg/ha/yr. The northern and western UMRB had combined influences from both anthropogenic activities and hydrological variability, while the east-central regions had predominantly hydrologically driven changes. Agricultural sources, including fertilizer, manure, and biological nitrogen fixation, collectively contributed over 80% of NO 3 − + NO 2 − -N loading throughout the basin. Furthermore, this framework for disentangling human and hydrological impacts provides critical insights for developing effective and targeted watershed management strategies to reduce nutrient losses and improve water quality.

54 ENVIRONMENTAL SCIENCES↗

EDA R-Matrix Evaluations Report on n+ 9 Be, n+ 16 O [Slides]

This presentation discusses new developments in light-element R-matrix evaluation and recent light-element work. The presentation also reviewed R-matrix theory, EDAf90 code implementation, including interface EDAf90 with NJOY, ENDFtk, EXFOR/CSISRS, and a new evaluation for n+ 9 Be. The presentation concludes by stating that further development is needed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

HPB_strengthmodel

Python-implementation of the Hunter-Preston strength model, but with generalized drag coefficient B. For details, see D. N. Blaschke, A. Hunter, and D. L. Preston, Int. J. Plast. 131 (2020) 102750. This code was used to generate most of the figures in this paper.

Blaschke, Daniel N.↗

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task

A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.

Science & Technology - Other Topics↗

Encoder–decoder neural network for solving the nonlinear Fokker–Planck–Landau collision operator in XGC

An encoder–decoder neural network has been used to examine the possibility for acceleration of a partial integro-differential equation, the Fokker–Planck–Landau collision operator. This is part of the governing equation in the massively parallel particle-in-cell code XGC, which is used to study turbulence in fusion energy devices. The neural network emphasizes physics-inspired learning, where it is taught to respect physical conservation constraints of the collision operator by including them in the training loss, along with the ℓ 2 loss. In particular, network architectures used for the computer vision task of semantic segmentation have been used for training. A penalization method is used to enforce the ‘soft’ constraints of the system and integrate error in the conservation properties into the loss function. During training, quantities representing the particle density, momentum and energy for all species of the system are calculated at each configuration vertex, mirroring the procedure in XGC. This simple training has produced a median relative loss, across configuration space, of the order of 10 –4 , which is low enough if the error is of random nature, but not if it is of drift nature in time steps. The run time for the current Picard iterative solver of the operator is O(n 2 ), where n is the number of plasma species. As the XGC1 code begins to attack problems including a larger number of species, the collision operator will become expensive computationally, making the neural network solver even more important, especially since its training only scales as O(n). Here, a wide enough range of collisionality has been considered in the training data to ensure the full domain of collision physics is captured. An advanced technique to decrease the losses further will be subject of a subsequent report. Eventual work will include expansion of the network to include multiple plasma species.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Plasma rotation and diamagnetic drift effects on the resistive wall modes in the negative triangularity tokamaks

Abstract It was found previously that the negative triangularity (NT) configuration is more MHD-unstable for low n modes than the positive triangularity (PT) case, although the situation is reversed for intermediate n modes and the NT configuration becomes more stable for intermediate n modes ( n = 3 − 10 ) (Zheng et al 2021 Nucl. Fusion 61 116014). Here, n is the toroidal mode number. In this work, we extend the studies to include the rotation effects, as well as the diamagnetic drift effects, to see how the resistive wall modes (RWMs) in the NT configuration are affected as compared with the PT configuration. This is particularly motivated by noting that the wall interface with the plasma is quite different between the NT and PT configurations. It affects the plasma rotation and diamagnetic drift effects on the low n RWM. We consider the DIII-D-NT-experiment equilibrium reconstructed by the EFIT code. Based on the equilibrium g-file, the extended equilibria are constructed with the VMEC code by varying the beta values while keeping the pressure and poloidal current flux profiles basically unchanged. The bootstrap current contribution to the equilibria is taken into account with the Sauter formula. The MHD stability is then computed using the AEGIS code with the rotation and diamagnetic drift effects taken into account. We found that, although the NT configuration is less stable for n = 1 MHD modes, the rotation and diamagnetic drift stabilization effects on RWMs are more effective in the NT configuration than in the PT one. Note that even in the PT case, the stabilization of RWMs by the rotation and kinetic effects is critical. Because the low-n RWMs in the regular NT case are more unstable, the rotation and diamagnetic drift stabilization effects found in this research are important for the NT tokamak concept.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Recent progress in the design of the K-DEMO divertor

The preliminary conceptual design of the Korean fusion demonstration reactor (K-DEMO) with a major radius of 6.8 m and the fusion power of 2200 MW has been studied since 2012. The overall configuration of the K-DEMO divetor system based on the ITER-like water-cooled tungsten technology is a double-null type symmetric divertor subdivided into 32 toroidal modules for the vertical maintenance. A detached divertor scenario with impurity seeding was considered as the primary approach for the power exhaust to reduce the peak heat flux lower than the engineering limit of 10 MW/m 2 . The power exhaust performance at the scrap off layer was estimated by using UEDGE-2D code, a two-dimensional fluid transport code for collisional edge plasma and neutral species like N, Ne, and Ar. Particle and heat flux on inboard and outboard divertor targets were calculated for the detached cased depending on parameters such as the impurity seeding rate, pumping rate, and the pedestal density. On the other hand, a magnetic solution like X-divertor, snowflake divertor, and super X-divertor to expand the plasma wet area was considered for K-DEMO since the detached divertor increasing a radiation fraction by impurity seeding might be able to be unstable. However, the extremely high current of poloidal coils was required more than the engineering limit, 20 MA, to form magnetic field lines for the alternative divertors. Based on the physical calculation of the edge plasma, engineering analyses were carried out to find out the thermal and structural reliability. The thermo-hydraulic analysis confirmed thermal stability, whether all comprising materials are operating within their allowable temperature windows when the case of the peak heat flux is set to 10 MW/m 2 on the outboard divertor target. The response surface optimization method derived two optimal design candidates employing two kinds of heat sink materials, respectively: the reduced activation ferritic martensitic (RAFM) steel and CuCrZr alloy. Additionally, the drawbacks and merits of the two materials were definite. The optimal design with applying RAFM steel was vulnerable to withstand thermal and mechanical loads since low thermal conductivity caused too thin thickness of the heat sink. On the other hand, the CuCrZr alloy has critical drawbacks in terms of activation and radioactive waste despite its high thermal conductivity. Meanwhile, preliminary electromagnetic (EM) analysis was carried out to estimate the EM loads caused by the abnormal behaviors of plasma since EM loads are one of the most critical external loads for designing a DEMO divertor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗