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DOE OSTI2020

WHONDRS-GUI: a web application for global survey of surface water metabolites

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811 , which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server ( https://xmlin.shinyapps.io/whondrs/ ).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Characterizing laser-heated polymer foams with simultaneous x-ray fluorescence spectroscopy and Thomson scattering at the Matter in Extreme Conditions Endstation at LCLS

Understanding the behavior of polymer foams at high energy density conditions is crucial to advance inertial fusion energy research. Here, we present a new experimental platform designed to measure the thermodynamic state of these materials at megabar pressures. At the Matter in Extreme Conditions Endstation of the Linac Coherent Light Source, we heat samples using an optical, high-intensity, femtosecond laser and dynamically probe them with ultra-short, coherent x-ray pulses of high peak brightness. We perform x-ray Thomson scattering measurements in forward and backward scattering geometries to capture both collective and non-collective electron behavior in the sample. Simultaneously, x-ray fluorescence spectroscopy is used to measure the emission from a mid-Z dopant, providing complementary information on the plasma conditions. By combining these techniques, we obtain temporally resolved temperature measurements of the transient warm dense matter states. Our initial experiments designed to benchmark the platform with carbon samples yielded data resolving the ultrafast response to laser heating with sub-picosecond resolution, measuring plasma temperatures exceeding 50 eV. These findings lay the foundation for precision studies of the dynamic evolution of laser-heated polymer foams.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016–2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Stone, Nathan E.↗

DOE OSTI2021

Unexpected structural/motional mode of water intercalated into an α-crystalline zirconium phosphate deduced by 31 P and 2 H solid-state MAS NMR spectra

Here, in developing the approach to understanding dynamics of intercalates in layered materials, crystalline-layered zirconium phosphate Zr (HPO 4 ) 2 ·0.35D2O has been prepared and characterized by the 1 H, 31 P, and 2 H solid-state MAS NMR spectra, including 31 P and 2 H T 1 measurements. At temperatures >253 K, the intercalated water shows two spectrally-distinguished deuterons unprecedentedly with different DQCC's and 2 H T 1 times, one of which is hydrogen bonded. The collected data allowed to identify an unexpected bonding/dynamic mode of water molecules, which experience fast rotation around the hydrogen bond, formed with a zirconium-coordinated oxygen. The low-temperature 2 H MAS NMR experiments have demonstrated the presence of additional hydrogen bond P—(H)O˙˙˙ DO, population of which grows on cooling to 195 K corresponding to the doubly hydrogen-bonded immobile water molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗

DOE OSTI2018

Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain

Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 – a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution – reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1–3 regions ‘sense’ nucleic acids, ‘regulate’ the HNH conformational transition, and ultimately ‘lock’ the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1–3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Guest Editorial: Advanced Data-Analytics for Power System Operation, Control, and Enhanced Situational Awareness

Along with the smart grid development, modern power systems are entering a ‘data-intensive’ era. A vast volume of data from power grids is being collected through advanced sensing and communication technologies, such as smart metering data, phasor measurement data, as well as meteorological data (e.g., wind speed and solar irradiance) related to renewable power generation. Such data contains comprehensive information about the power system covering equipment's health status, power grid's static and dynamic characteristics, renewable power generation, customers’ electricity usage pattern, etc. Therefore, advanced data-analytics techniques are needed to convert such data to knowledge for practical applications. In line with the trend of widespread data-driven applications in power systems, this Special Issue aims to present state-of-the-art research works on advanced data-analytics for power system's operation, control, and situational awareness. There are in total twenty-six papers accepted for publication in this Special Issue through careful peer reviews and revisions. Under the overarching theme of data-driven applications in power systems, the selected papers are broadly categorised into five topics. The summary of every topic is given below. You are, however, strongly encouraged to read the full paper if interested.

Xu, Yan↗

DOE OSTI2014

Magnetic interactions in γ-Fe{sub 2}O{sub 3}@SiO{sub 2} nanocomposites

Structural and magnetic properties of γ-Fe{sub 2}O{sub 3} nanoparticles of 4 nm diameter, dispersed into silica SiO{sub 2} matrix with a wide range value of volume fraction (0.05 to 1), were investigated. Produced γ-Fe{sub 2}O{sub 3}@SiO{sub 2} nanocomposites consist of an assembly of very small single domain magnetic object (<10 nm) with a random distribution of both inter-particle distance and direction of particle magnetic moment. We focused on the determination of a magnetic percolation threshold, defined as the magnetic particles concentration value above which the magnetic properties of isolated particles vanished in favor of a magnetic collective behavior induced by magnetic interactions. A percolation threshold value of 0.63 was obtained by a local probe technique such as {sup 57}Fe Mössbauer spectrometry and confirmed by global magnetic measurements through zero-field cooled, field-cooled, and ac susceptibility data. Below this threshold, dynamic ac magnetization measurements show a thermally activated Arrhenius dependence of the blocking temperature of superparamagnetic nanoparticles and above this critical value, one observes a slowing down of their dynamic properties, which lead toward the establishment of a spin-glass like state.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Intermolecular correlations of liquid and glassy CS 2 studied by synchrotron radiation x-ray diffraction

How is the orientation of molecular liquids ordered on cooling? What are the basic structures of molecular glasses, e.g., close to the crystalline structure or some special structures such as icosahedral cluster? These are long-standing questions in liquid and glass physics. Here, we have constructed a novel cryostat to prepare simple molecular glasses by vapor deposition and performed in situ synchrotron radiation x-ray diffraction experiments. The glassy state of a simple molecule CS 2 , which cannot be vitrified by normal liquid quenching, was successfully prepared with this instrument, and its diffraction data were collected in a wide Q-range of 0.16–25.7 Å -1 with a high-energy diffractometer at BL04B2, SPring-8. The diffraction data of liquid CS 2 were also recorded in a wide temperature range of 160–300 K. These diffraction data were analyzed with molecular dynamics simulations and reverse Monte Carlo modelings to investigate orientational correlation. From the obtained 3D structure models, the orientational correlation between neighboring CS 2 molecules was investigated quantitatively as a function of temperature. At room temperature, the parallel and T-shaped arrangements are preferred for the nearest neighbor correlation. On cooling, these arrangements are developed gradually, and its rate became prominent below the melting temperature (162 K). In the glassy state, the slipped-parallel arrangement is dominant as well as the T-shaped arrangement. Both arrangements appear in the CS 2 crystal, indicating that the structure of glassy CS 2 is close to that of crystalline CS 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

A TWO-COMPONENT JET MODEL FOR THE TIDAL DISRUPTION EVENT SWIFT J164449.3+573451

We analyze both the early- and late-time radio and X-ray data of the tidal disruption event (TDE) Swift J1644+57. The data at early times (≲ 5 days) necessitate separation of the radio and X-ray emission regions, either spatially or in velocity space. This leads us to suggest a two-component jet model, in which the inner jet is initially relativistic with Lorentz factor Γ ≈ 15, while the outer jet is trans-relativistic, with Γ ≲ 1.2. This model enables a self-consistent interpretation of the late-time radio data, both in terms of peak frequency and flux. We solve the dynamics, radiative cooling, and expected radiation from both jet components. We show that while during the first month synchrotron emission from the outer jet dominates the radio emission, at later times, radiation from ambient gas collected by the inner jet dominates. This provides a natural explanation to the observed re-brightening, without the need for late-time inner engine activity. After 100 days, the radio emission peak is in the optically thick regime, leading to a decay of both the flux and peak frequency at later times. Our model's predictions for the evolution of radio emission in jetted TDEs can be tested by future observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Measurement of carbon condensates using small-angle x-ray scattering during detonation of the high explosive hexanitrostilbene

The dynamics of carbon condensation in detonating high explosives remains controversial. Detonation model validation requires data for processes occurring at nanometer length scales on time scales ranging from nanoseconds to microseconds. A new detonation endstation has been commissioned to acquire and provide time-resolved small-angle x-ray scattering (SAXS) from detonating explosives. Hexanitrostilbene (HNS) was selected as the first to investigate due to its ease of initiation using exploding foils and flyers, vacuum compatibility, high thermal stability, and stoichiometric carbon abundance that produces high carbon condensate yields. The SAXS data during detonation, collected with 300 ns time resolution, provide unprecedented signal fidelity over a broad q-range. This fidelity permits the first analysis of both the Guinier and Porod/power-law regions of the scattering profile during detonation, which contains information about the size and morphology of the resultant carbon condensate nanoparticles. To bolster confidence in these data, the scattering angle and intensity were additionally cross-referenced with a separate, highly calibrated SAXS beamline. The data show that HNS produces carbon particles with a radius of gyration of 2.7 nm in less than 400 ns after the detonation front has passed, and this size and morphology are constant over the next several microseconds. These data directly contradict previous pioneering work on RDX/TNT mixtures and TATB, where observations indicate significant particle growth (50% or more) continues over several microseconds. The power-law slope is about −3, which is consistent with a complex disordered, irregular, or folded sp{sup 2} sub-arrangement within a relatively monodisperse structure possessing radius of gyration of 2.7 nm after the detonation of HNS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Numerical Modeling of Atmospheric Rime Ice Accretion on an Airfoil Using an Eulerian Approach

This paper presents an approach to numerically simulate the inherently unsteady rime ice accretion problem on a two-dimensional airfoil and elucidate the associated variations under different icing conditions. The airflow field and the water impingement on the airfoil are obtained based on an Eulerian two-phase model. A dynamic mesh strategy is employed to unsteadily account for the changes in the ice profile and its impact on the air and droplet flow by continuously reconstructing the computational grid at each time-step through smoothing and layering mechanisms. All main icing modules including the airflow field, droplet trajectory, icing thickness profile, and mesh management are fully coupled within the same computational framework without resorting to any external tools. Classical icing theory is employed to model the rime ice roughness, and it is assumed that the ice accretes in a direction normal to the airfoil surface. The governing Reynolds-averaged Navier–Stokes (RANS) conservation equations along with the energy and continuity equations are solved to produce the velocity and temperature fields. A convective film heat transfer coefficient is computed based on the surface heat flux and a recovery temperature which takes into account the dissipative heat release in the boundary layer in the vicinity of the airfoil surface. With the implemented strategy and calculating the convective heat transfer coefficient, the water film thickness is also calculated along with the ice shape. Furthermore, the model is validated by comparing the local collection efficiency distribution and ice shape with experimental data, and the results show that the implemented approach provides acceptable predictions of ice accretion profiles and rates.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NASA NTRS2018

Laboratory Evaluation of Dynamic Routing of Air Traffic in an En Route Arrival Metering Environment

Arrival air traffic operations in the presence of convective weather are subject to uncertainty in aircraft routing and subsequently in flight trajectory predictability. Current management of arrival operations in weather-impacted airspace results in significant flight delay and suspension of arrival metering operations. The Dynamic Routing for Arrivals in Weather (DRAW) concept provides flight route amendment advisories to Traffic Management Coordinators to mitigate the impacts of convective weather on arrival operations. DRAW provides both weather conflict and schedule information for proposed route amendments, allowing air traffic managers to simultaneously evaluate weather avoidance routing and potential schedule and delay impacts. Subject matter experts consisting of retired Traffic Management Coordinators and retired Sector Controllers with arrival metering experience participated in a simulation study of Fort Worth Air Route Traffic Control Center arrival operations. Data were collected for Traffic Management Coordinator and Sector Controller participants over three weeks of simulation activities in October, 2017. Traffic Management Coordinators reported acceptable workload levels, a positive impact on their ability to manage arrival traffic while using DRAW, and initiated weather mitigation reroutes earlier while using DRAW. Sector Controllers also reported acceptable workload levels while using DRAW.

Air Traffic Management↗

NASA NTRS2018

Laboratory Evaluation of Dynamic Routing of Air Traffic in an En Route Arrival Metering Environment

Air Traffic Management↗

DOE OSTI2022

Collectivity in Ultraperipheral Pb+Pb Collisions at the Large Hadron Collider

In this work, we present the first full (3+1)D dynamical simulations of ultraperipheral Pb+Pb collisions at the Large Hadron Collider. Extrapolating from p + Pb collisions, we explore whether a quasireal photon γ* interacting with the lead nucleus in an ultraperipheral collision can create a many-body system exhibiting fluid behavior. Assuming strong final-state interactions, we provide model results for charged hadron multiplicity, identified particle mean transverse momenta, and charged hadron anisotropic flow coefficients, and compare them with experimental data from the ALICE and ATLAS Collaborations. The elliptic flow hierarchy between p + Pb and γ*+Pb collisions is dominated by the difference in longitudinal flow decorrelations and reproduces the experimental data well. We have demonstrated that our theoretical framework provides a quantitative tool to study particle production and collectivity for all system sizes, ranging from central heavy-ion collisions to small asymmetric collision systems at the Relativistic Heavy-Ion Collider and the Large Hadron Collider and even at the future Electron-Ion Collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2016

An Overview of the Monte Carlo Application ToolKit (MCATK)

MCATK is a C++ component-based Monte Carlo neutron-gamma transport software library designed to build specialized applications and designed to provide new functionality in existing general-purpose Monte Carlo codes like MCNP; it was developed with Agile software engineering methodologies under the motivation to reduce costs. The characteristics of MCATK can be summarized as follows: MCATK physics – continuous energy neutron-gamma transport with multi-temperature treatment, static eigenvalue (k and α) algorithms, time-dependent algorithm, fission chain algorithms; MCATK geometry – mesh geometries, solid body geometries. MCATK provides verified, unit-tested Monte Carlo components, flexibility in Monte Carlo applications development, and numerous tools such as geometry and cross section plotters. Recent work has involved deterministic and Monte Carlo analysis of stochastic systems. Static and dynamic analysis is discussed, and the results of a dynamic test problem are given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2003

Group dynamics and catecholamines during long-duration confinement in an isolated environment

INTRODUCTION: The objectives of this study were to investigate possible relationships between catecholamine excretion and long-duration confinement in an isolated environment. METHODS: Stays of long duration were made by Group I (n = 4, all Russian, weeks 1-34), Group II (n = 4, mixed nationality, weeks 3-18), and Group III (n = 4, mixed nationality, weeks 22-38); other groups joined the residents for 1-wk intervals at weeks #13, #19, and #33. Data were collected from Groups I and III. RESULTS: In both Group I and Group III, the daily epinephrine excretion was significantly elevated during and after confinement compared with the pre-isolation baseline (p < 0.05), but remained mostly within normal limits during the experiment. During isolation, epinephrine excretion was significantly higher, compared with other weeks in isolation, during weeks #19 and #27 for Group I, and during week #30 for Group III. In both Group I and Group II, norepinephrine excretion increased significantly during and after isolation (p < 0.05) and was above the normal range. The daily norepinephrine excretion was significantly higher (p < 0.05) in Group I during weeks #12, #13, and #27, and during week #30 for Group III. DISCUSSION: Epinephrine excretion generally remained in the normal range. However, occasional elevations occurred due to psychological stress, which apparently correlate with changes in group dynamics. Norepinephrine excretion was above the normal range and was correlated with social events. These results suggest that to ensure optimum crew performance, entire crews along with their visiting crews should be selected collectively, rather than individually.

Non-programmatic↗

DOE OSTI2023

Beam Dynamics Challenges in the Muon g-2 Experiment

The muon&s;s anomalous magnetic moment $a_{\mu}$ has hinted at physics beyond the standard model for nearly 20 years. The Muon $g-2$ experiment at Fermilab aims to measure $a_{\mu}$ to 140 parts per billion (ppb) precision. The 460 ppb result from its first data run (Run-1), released in 2021, agreed with the previous 2006 Brookhaven Muon $g-2$ result. The experimental average stands in tension with the standard model theory $a_{\mu}$ prediction by $4.2 \sigma$. The result of Run-2/3 data analysis is set be released in summer 2023, and will improve on the Run-1 precision by a factor of two. With the data collected in all six runs, the experiment is on track to produce a 140 ppb measurement of $a_{\mu}$. If the experiment and theory central values are both unchanged, the tension would exceed $5 \sigma$. The measurement is accomplished by injecting muons into a magnetic storage ring and precisely measuring two observable frequencies: $\omega_a$, the muons&s; anomalous precession frequency, and $\tilde{\omega}&s;_p$, the precession frequency of protons which determines the magnetic field strength experienced by the muons. This thesis presents a selection of muon beam dynamics effects which are critical for reaching the experiment precision goal. A system of detectors assists with the challenging beam injection into the storage ring, and a measurement of the injected beam provides input for simulating the stored beam dynamics. A new method is introduced to reduce a critical systemic caused by time dependence in the stored beam momentum, enabled by a detector which directly profiles the stored beam. Finally the analysis of $\tilde{\omega}&s;_p$, the muon-weighted magnetic field, for the Run-2/3 result is presented. Systematics of $\tilde{\omega}&s;_p$ due to beam effects are evaluated in detail, and shown to be sub-dominant.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗