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DOE OSTI2020

Gas Transport in the Insensitive High Explosive PBX 9502

Small-scale laboratory experiments were performed to analyze gas transport mechanics in PBX 9502, an insensitive high explosive (IHE) composition. Two independent investigations are reported here. First, gas permeametry and dynamic pycnometry techniques were used to measure the molecular flow (Knudsen) coefficient and the internally interconnected void fraction of pristine and thermally damaged samples in two uniaxial pressing orientations. The permeability of PBX 9502 was found to be unmeasurably low (of the same order of magnitude as PTFE) with gas transport being diffusion-dominated. Secondly, a pressure vessel experiment was developed to measure quasi-static and dynamic gas generation as the explosive was heated to self-ignition (cookoff). The gas generation results and the permeability/diffusivity findings provide evidence that PBX 9502 remains impermeable until seconds prior to self-ignition. At ignition, internal void-pressure drives macro-scale cracking and the sample becomes uniformly incorporated in the following deconsolidating deflagration. These results are discussed within the context of previous observations of pressure-dependent cookoff behavior of PBX 9502 and provide a more complete description of thermal damage evolution in this explosive composition.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2023

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Hydration-Induced Disorder Lowers the Energy Barriers for Methyl Rotation in Drug Molecules

The thermally activated dynamics of methyl groups are important for biochemical activity as they allow for a more efficient sampling of the energy landscape. In this work, we compare methyl rotations in the dry and variously hydrated states of three primary drugs under consideration to treat the recent coronavirus disease (COVID-19), namely, hydroxychloroquine and its sulfate, dexamethasone and its sodium diphosphate, and remdesivir. We find that the main driving force behind the considerable reduction in the activation energy for methyl rotations in the hydrated state is the hydration-induced disorder in the methyl group local environments. Furthermore, the activation energy for methyl rotations in the hydration-induced disordered state is much lower than that in an isolated drug molecule, indicating that neither isolated molecules nor periodic crystalline structures can be used to analyze the potential landscape governing the side group dynamics in drug molecules. Instead, only the explicitly considered disordered structures can provide insight.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A Chemodynamical Census of the Milky Way's Ultra-Faint Compact Satellites. I. A First Population-Level Look at the Internal Kinematics and Metallicities of 19 Extremely-Low-Mass Halo Stellar Systems

Deep, wide-area photometric surveys have uncovered a population of compact ($r_{1/2} \approx$ 1-15 pc), extremely-low-mass ($M_* \approx$ 20-4000 $M_{\odot}$) stellar systems in the Milky Way halo that are smaller in size than known ultra-faint dwarf galaxies (UFDs) and substantially fainter than most classical globular clusters (GCs). Very little is known about the nature and origins of this population of "Ultra-Faint Compact Satellites" (UFCSs) owing to a dearth of spectroscopic measurements. Here, we present the first spectroscopic census of these compact systems based on Magellan/IMACS and Keck/DEIMOS observations of 19 individual UFCSs, representing $\sim$2/3 of the known population. We securely measure mean radial velocities for all 19 systems, velocity dispersions for 15 (predominantly upper limits), metallicities for 17, metallicity dispersions for 8, and $\textit{Gaia}$-based mean proper motions for 18. This large new spectroscopic sample provides the first insights into population-level trends for these extreme satellites. We demonstrate that: (1) the UFCSs are kinematically colder, on average, than the UFDs, disfavoring very dense dark matter halos in most cases, (2) the UFCS population is chemically diverse, spanning a factor of $\sim$300 in mean iron abundance ($\rm -3.3 \lesssim [Fe/H] \lesssim -0.8$), with multiple systems falling beneath the "metallicity floor" proposed for GCs, and (3) while some higher-metallicity and/or younger UFCSs are clearly star clusters, the dynamical and/or chemical evidence allows the possibility that up to $\sim$50% of the UFCSs in our sample (9 of 19) may represent the smallest and least-massive galaxies yet discovered.

Cerny, William [Yale U.] (ORCID:0000000316977062)↗

DOE OSTI2018

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice ( Oryza sativa ) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. As a result, we present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Viscoplastic Interpretation of Localized Compaction Creep in Porous Rock

Recent laboratory evidence shows that compaction creep in porous rocks may develop through stages of acceleration, especially if the material is susceptible to strain localization. This paper provides a mechanical interpretation of compaction creep based on viscoplasticity and nonlinear dynamics. For this purpose, a constitutive operator describing the evolution of compaction creep is defined to evaluate the spontaneous accumulation of pore collapse within an active compaction band. This strategy enables the determination of eigenvalues associated with the stability of the response which is able to differentiate decelerating from accelerating strain. This mathematical formalism was linked to a constitutive law able to simulate compaction localization. Material point simulations were then used to identify the region of the stress space where unstable compaction creep is expected, showing that accelerating strains correspond to pulses of inelastic strain rate. Such pulses were also found in full-field numerical analyses of delayed compaction, revealing that they correspond to stages of inception and propagation of new bands across the volume of the simulated sample. These results illustrate the intimate relation between the spatial patterns of compaction and their temporal dynamics, showing that while homogeneous compaction develops with decaying rates of accumulation, localized compaction occurs through stages of accelerating deformation caused by the loss of strength taking place during the formation of a band. In addition, they provide a predictive modeling framework to simulate and explain the spatio-temporal dynamics of compaction in porous sedimentary formations.

58 GEOSCIENCES↗

DOE OSTI2023

Optimal PMU design based on sampling model and sensitivity analysis

The precise measurements of the synchrophasor and frequency from phasor measurement units (PMUs) are widely used in power grid applications. With the improvement of the technique, applications always require stable dynamic performance and higher accuracy for the synchrophasor and frequency measurements, which is challenging for PMU development. To evaluate the contribution of PMU hardware to measurement accuracy, this paper proposes a general-purpose sampling model to analyze the measurement error. In the proposed sampling model, a strict mathematical derivation is derived, where its error is purely determined by the parameters of the PMU hardware. The sensitivity analysis is carried out by three methods, including mathematical analysis, computer simulation, and variance-based sensitivity analysis. Through the sensitivity analysis, this paper establishes the systematic formulation and the inclusion of synchrophasor, frequency, and ROCOF. Experimental results based on the real-world testbench involving distribution-level PMUs match the mathematical analysis conclusion, which verifies the correctness of the general-purpose sampling model. Furthermore, a strategy for the optimal PMU design is proposed, which could guide PMU design in the future.

42 ENGINEERING↗

DOE OSTI2017

Imaging the Hydrogen Absorption Dynamics of Individual Grains in Polycrystalline Palladium Thin Films in 3D

Defects such as dislocations and grain boundaries often control the properties of polycrystalline materials. In nanocrystalline materials, investigating this structure-function relationship while preserving the sample remains challenging because of the short length scales and buried interfaces involved. Here we use Bragg coherent diffractive imaging to investigate the role of structural inhomogeneity on the hydriding phase transformation dynamics of individual Pd grains in polycrystalline films in three-dimensional detail. In contrast to previous reports on single- and polycrystalline nanoparticles, we observe no evidence of a hydrogen-rich surface layer and consequently no size dependence in the hydriding phase transformation pressure over a 125-325 nm size range. We do observe interesting grain boundary dynamics, including reversible rotations of grain lattices while the material remains in the hydrogen-poor phase. The mobility of the grain boundaries, combined with the lack of a hydrogen-rich surface layer, suggests that the grain boundaries are acting as fast diffusion sites for the hydrogen atoms. Such hydrogen-enhanced plasticity in the hydrogen poor phase provides insight into the switch from the size-dependent behavior of single-crystal nanoparticles to the lower transformation pressures of polycrystalline materials and may play a role in hydrogen embrittlement.

Yau, Allison↗

DOE OSTI2018

The Ability of Soil Pore Network Metrics to Predict Redox Dynamics Is Scale Dependent

Variations in microbial community structure and metabolic efficiency are governed in part by oxygen availability, which is a function of water content, diffusion distance, and oxygen demand; for this reason, the volume, connectivity, and geometry of soil pores may exert primary controls on spatial metabolic diversity in soil. Here, we combine quantitative pore network metrics derived from X-ray computed tomography (XCT) with measurements of electromotive potentials to assess how the metabolic status of soil depends on variations of the overall pore network architecture. Contrasting pore network architectures were generated using a Mollisol—A horizon, and compared to intact control samples from the same soil. Mesocosms from each structural treatment were instrumented with Pt-electrodes to record available energy dynamics during a regimen of varying moisture conditions. We found that volume-based XCT-metrics were more frequently correlated with metrics describing changes in available energy than medial-axis XCT-metrics. An abundance of significant correlations between pore network metrics and available energy parameters was not only a function of pore architecture, but also of the dimensions of the sub-sample chosen for XCT analysis. Pore network metrics had the greatest power to statistically explain changes in available energy in the smallest volumes analyzed. Our work underscores the importance of scale in observations of natural systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

On the measurement of shape: With applications to lunar regolith

With the renewed commitment from NASA and other commercial entities for a presence on the Moon, the importance of understanding the characteristics of lunar regolith and how to utilize it have become the target of increasing scrutiny. Much of what is known about lunar regolith was collected during and immediately after the Apollo program, however, analytical techniques and instrumentation have advanced in leaps and bounds in the subsequent decades. Specifically, dynamic image analysis systems have advanced to the point that millions of particles can have morphological characteristics automatically determined in relatively short time frames. Particle morphological data was collected on several lunar samples and a pair of widely used regolith simulants to ascertain the accuracy of these simulants and to explore statistical analysis methods of these large datasets. It is found that these morphology datasets can vary widely depending on the particle size of the particles, and simple averaging of the data skews the results heavily towards the numerically abundant size ranges, the fines. Different reporting methods are suggested to ameliorate these problems. When applied to the lunar regolith, the particles are noted to be less morphologically complex than initially suspected. Compared to the lunar material, the simulants are found to contain some more morphological variability and angular grains. Such difference is likely due to the wildly different comminution processes that these different powder systems are subjected to.

2D shape↗

DOE OSTI2015

X-ray studies of dynamic aging in an aluminum alloy subjected to severe plastic deformation

In this work, X-ray scattering methods were applied for a quantitative characterization of the microstructure of an aluminum alloy of the Al–Mg–Si system during dynamic aging realized through the high pressure torsion technique. A qualitative and quantitative phase analysis of the alloy was performed, together with Al alloy lattice parameter determination. From the reflections broadening the effective size of the coherent scattering domains and the lattice microstrain were determined in the framework of the Halder–Wagner approach. Using the method of small-angle X-ray scattering, the quantitative characteristics of the size, shape and spatial distribution of the secondary phase particles formed in the Al alloy during dynamic aging were established. In order to validate the obtained results, the method of small-angle X-ray scattering was preliminarily tested on similar samples after artificial aging and compared with the results from small-angle neutron diffraction widely known in literature. - Highlights: • Spherical fcc β-Mg2Si precipitates formed in Al 6201 alloy during dynamic aging in the course of severe plastic deformation. • The size, shape and distribution of the precipitates due to artificial and dynamic aging were revealed by SAXS method. • Monoclinic needle-like β' precipitates and Al5FeSi intermetallic phase were detected in 6201 alloy after T6 treatment.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Dynamics of Coupled Magnetic Vortices in Trilayer Conducting Nanocylinder

Solving numerically the generalized Landau–Lifshitz equation, we have carried out the micromagnetic investigation of the dynamics of two dipole-coupled magnetic vortices in a trilayer nanocolumn under the action of the external magnetic field directed perpendicular to the sample plane and spin-polarized electric field. The possible existence of different regimes of vortex motion, depending on the polarized current, is demonstrated. The current dependence of the oscillation frequency for the case of stationary dynamics of coupled vortices with the same frequency has been established. The possibility of controlling the frequency of the stationary vortex motion and tuning the control current amplitude by the external magnetic field is shown. Using the analytical method for simplified description of the dynamics of coupled vortices, the current and magnetic-field dependences of the frequency have been obtained, which are qualitatively consistent with the numerical data.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2016

Dynamic Importance Measures in the ADAPT Framework

Probabilistic Risk Assessment (PRA) uses fault tree/event tree analysis to evaluate the environmental impacts of nuclear power plants due to internal or external initiating events. In a fault tree, basic failure events are assembled using primarily And/Or logic to determine the combinations of failures that lead to failure of the system as a whole. An event tree is forward-facing, and begins with a single initiating event. From there the analysis considers what event may occur next, and branches out among the possible configurations of occurrence and non-occurrence of that event. This branching continues until user-defined end states are reached. End states may include a safe and stable configuration of the plant, or any number of differing failure states. Both fault and event trees require basic event probabilities as inputs to provide insight on the likelihood of different outcomes. PRA has been applied to nuclear power plants as an analysis tool since the 1975 Reactor Safety Study. In a traditional PRA, the order of events is prescribed by the analyst and each event is typically a binary aleatory uncertainty: occurrence or non-occurrence. Discrete dynamic event tree (DDET) analysis eliminates this subjectivity in ordering of events by using the output of a dynamic system model (simulator) to inform the branching. Branching conditions are triggered by the existence of a relevant plant state in the code, and therefore only occur as physically appropriate. The DDET approach also allows consideration of both epistemic and aleatory uncertainties on a phenomenologically and stochastically consistent platform. One current limitation of DDETs is the assessment of results, which is not as well developed as in traditional PRA. A concept that is used in PRA to assess the significance of a basic event is the concept of importance measures (IMs). In traditional PRA, IMs only consider the likelihood of occurrence of non-occurrence of a basic event. The application of importance measures to DDETs must take into consideration not only the occurrence and non-occurrence of an event, but also uncertain timing or severity. This work describes three general dynamic importance measures (DIMs) as implemented in the Analysis of Dynamic Accident Progression Trees (ADAPT) DDET driver code. The measures account for the change in progression of the DDET resulting from the different values of each uncertain variable under investigation. The DIMs are applied to a sample DDET to demonstrate the type of insights that may be gained from each one. These measures will facilitate comparison of the impact of dynamic branching events on a consequence of interest, which also allow DDETs to be used in prioritizing plant investments. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

GROWdb US River Systems - Samples

GROW Overview We developed the Genome Resolved Open Watersheds database (GROWdb), which aims to increase genomic sampling and understanding of global river microbiomes. An emphasis of GROWdb is to create a publicly available and ever-expanding microbial genome database that is focused on rivers while being interoperable with databases from other ecosystems. GROWdb is based on a network-of-networks approach to move beyond a small collection of well-studied rivers, towards a spatially distributed, global network of systematic observations. GROWdb represents the first microbial, river-focused resource parsed at various scales from genes to MAGs to community level including expression and potential based measurements that will be of interest to microbiologists, ecologists, geochemists, hydrologists, and modelers. Dataset Acknowledgement GROWdb contains data from various research campaigns, please acknowledge the following data generators, as appropriate: WHONDRS derived genomes or samples - include this statement in your acknowledgements: “This study used data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) under the River Corridor Science Focus Area (SFA) at the Pacific Northwest National Laboratory (PNNL) that was generated at the U.S. Department of Energy (DOE) Joint Genome Institute User Facility. PNNL is operated by Battelle Memorial Institute for the U.S. DOE under Contract No. DE-AC05-76RL01830. The SFA is supported by the U.S. DOE, Office of Biological and Environmental Research (BER), Environmental System Science (ESS) Program.” Total Samples loaded onto this Narrative: 178 Note: Not all GROW samples may be loaded into KBase Data Availability The data underlying GROWdb are accessible across various platforms to ensure all levels of data structure are widely available. First, all reads and MAGs are publicly hosted on National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. Second, all data related data presented here including MAG annotations, extended data tables, phylogenetic tree files, antibiotic resistance gene database files, and MAG abundance tables are available in Zenodo (link). Beyond the flat database files listed above, our aim for GROWdb was to maximize data use by making the data available in searchable and interactive platforms including the National Microbiome Data Collaborative (NMDC) data portal, the Department of Energy’s Systems Biology Knowledgebase (KBase), and a GROW specific user interface released here, GROWdb Explorer. Each platform provides different ways to interact with GROWdb: NMDC GROWdb formed a pilot project for the NMDC. Specifically, individual GROWdb datasets (metagenomes, metatranscriptomes, etc) are easily accessible and searchable through the NMDC data portal, where they are systematically connected to each other and to a rich suite of sample information and standard analysis results, following Findable, Accessible, Interoperable, and Reusable (FAIR) data practices. KBase GROWdb is publicly available within KBase, including samples (this Narrative), MAGs, and corresponding genome scale metabolic models. Access within KBase allows for immediate access and reuse of data, including comparison to private data using KBase’s 500+ analysis tools. Other linked narratives in KBase: GROW Metagenome Assembled Genomes (MAGs) GROW Metabolic Models GROWdb Explorer GROWdb data is also explorable through a graphical user interface built through the Colorado State University Geospatial Centroid (https://geocentroid.shinyapps.io/GROWdatabase/), allowing users to search and graph microbial and spatial data simultaneously. In summary, this microbial genome resource represents the first publicly available genome collection from rivers and offers data that can be leveraged across microbiome studies. GROWdb is an expanding repository to incorporate and unify global river multi-omic data for the future.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Nonequilibrium phases and segregation for skyrmions on periodic pinning arrays

Using particle-based simulations, we examine the collective dynamics of skyrmions interacting with periodic pinning arrays, focusing on the impact of the Magnus force on the sliding phases. As a function of increasing pinning strength, we find a series of distinct dynamical phases, including an interstitial flow phase, a moving disordered state, a moving crystal, and a segregated cluster state. The transitions between these states produce signatures in the skyrmion lattice structure, the skyrmion Hall angle, the velocity fluctuation distributions, and the velocity-force curves. The moving clustered state is similar to the segregated state recently observed in continuum-based simulations with strong quenched disorder. The segregation arises from the drive dependence of the skyrmion Hall angle, and appears in the strong pinning limit when the skyrmions have nonuniform velocities, causing different portions of the sample to have different effective skyrmion Hall angles. As a result, we map the evolution of the dynamic phases as a function of the system density, the ratio of the Magnus force to the dissipative term, and the ratio of the number of skyrmions to the number of pinning sites.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Few-cycle Regime Atomic Force Microscopy

Abstract Traditionally, dynamic atomic force microscopy (AFM) techniques are based on the analysis of the quasi-steady state response of the cantilever deflection in terms of Fourier analysis. Here we describe a technique that instead exploits the often disregarded transient response of the cantilever through a relatively modern mathematical tool, which has caused important developments in several scientific fields but that is still quite unknown in the AFM context: the wavelet analysis. This tool allows us to localize the time-varying spectral composition of the initial oscillations of the cantilever deflection when an impulsive excitation is given (as in the band excitation method), a mode that we call the few-cycle regime . We show that this regime encodes very meaningful information about the tip-sample interaction in a unique and extremely sensitive manner. We exploit this high sensitivity to gain detailed insight into multiple physical parameters that perturb the dynamics of the AFM probe, such as the tip radius, Hamaker constant, sample’s elastic modulus and height of an adsorbed water layer. We validate these findings with experimental evidence and computational simulations and show a feasible path towards the simultaneous retrieval of multiple physical parameters.

42 ENGINEERING↗