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DOE OSTI2021

3D Bacterial flagella as both synthetic biotemplates and ultrathin spacers for enhanced inter-particle coupling and solar energy harvesting

Linear light-absorbing nanomaterials are ideal for film-based solar harvesting applications as they form porous structures that can maximize the absorption and minimize the reflection of the solar light. Conventional 1D nanochains of plasmonic nanoparticle assemblies can achieve significantly broadened optical absorption through surface plasmon coupling, but their optical bands are still not broad enough to absorb through the solar spectrum and thus are not efficient solar absorbers. Here we discovered first by simulation that 3D structured nanochains of plasmonic nanoparticles presented a remarkably increased optical broadening effect and much longer redshift of the optical peaks due to the enhanced inter-particle coupling effect. Then we fabricated 3D nanochains by assembling gold nanoparticles (AuNPs) around 14 nm ultrathin bionanofibers, the bacterial flagella. Additionally, the ultrathin biotemplates enabled the 3D arrangement of 50 nm AuNPs along the nanofiber with a very small inter-particle gap, allowing the strong coupling of surface plasmons in a 3D manner. Consistent with the theoretical prediction, the 3D nanochains, when assembled into films, could effectively convert nearly the full spectrum of solar energy into heat, which was further efficiently converted into electricity through a thermoelectric generation unit. Our work represents a nanobiomaterial approach to highly efficient solar thermal power generation.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Systematic Validation of Ensemble Cloud-Process Simulations using Polarimetric Radar Observations and Simulator over the NASA Wallops Flight Facility

The BiLateral Operational Storm-Scale Observation and Modeling (BLOSSOM) project was initiated to establish a long-term supersite to improve understanding of cloud physical states and processes as well as to support satellite and climate model programs over the WFF site via a bilateral approach of storm-scale observations and process modeling. This study highlights a noble systematic validation framework of the BLOSSOM ensemble cloud-process simulations through mixed-phase, light-rain, and deep-convective precipitation cases. The framework consists of creating a domain-shifted ensemble of large-scale forcing datasets, and configuring and performing cloud-process simulations with three different bulk microphysics schemes. Validation uses NASA S-band dual-POLarimetric radar (NPOL) observations in the form of statistical composites and skill scores via a polarimetric radar simulator and newly developed CfRad Data tool (CfRAD). While the simulations capture the overall structures of the reflectivity composites, polarimetric signals are still poorly simulated, mainly due to a lack of representation of ice microphysics diversity in shapes, orientation distributions, and their complex mixtures. Despite the limitation, this new ensemble-based validation framework demonstrates that 1) no particular forcing or microphysics scheme outperforms the rest and 2) the skill scores of coarse- and fine-resolution ensemble simulations with different domain-shifted forcing and microphysics schemes are highly correlated with each other with no clear improvement. On the other hand, this suggests that coarse-resolution ensemble simulations are relevant for selecting the best meteorological forcing and microphysics scheme before conducting computationally demanding large eddy simulations (LESs) in support of aircraft and satellite instrument development as well as cloud-precipitation-convection parameterizations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels

Abstract Kainate receptors (KARs) are a subtype of ionotropic glutamate receptor (iGluR) channels, a superfamily of ligand-gated ion channels which mediate the majority of excitatory neurotransmission in the central nervous system. KARs modulate neuronal circuits and plasticity during development and are implicated in neurological disorders, including epilepsy, depression, schizophrenia, anxiety, and autism. Calcium-permeable KARs undergo ion channel block, but the therapeutic potential of channel blockers remains underdeveloped, mainly due to limited structural knowledge. Here, we present closed-state structures of GluK2 KAR homotetramers in complex with ion channel blockers NpTx-8, PhTx-74, Kukoamine A, and spermine. We find that blockers reside inside the GluK2 ion channel pore, intracellular to the closed M3 helix bundle-crossing gate, with their hydrophobic heads filling the central cavity and positively charged polyamine tails spanning the selectivity filter. Molecular dynamics (MD) simulations of our structures illuminate interactions responsible for different affinity and binding poses of the blockers. Our structures elucidate the trapping mechanism of KAR channel block and provide a template for designing new blockers that can selectively target calcium-permeable KARs in neuropathologies.

Science & Technology - Other Topics↗

DOE OSTI2020

Anisotropic X-Ray Scattering of Transiently Oriented Water

We study the structural dynamics of liquid water by time-resolved anisotropic x-ray scattering under the optical Kerr effect condition. In this way, we can separate the anisotropic scattering decay of 160 fs from the delayed temperature increase of ~ 0.1 K occurring at 1 ps and quantify transient changes in the O-O pair distribution function. Polarizable molecular dynamics simulations reproduce well the experiment, indicating transient alignment of molecules along the electric field, which shortens the nearest-neighbor distances. In addition, analysis of the simulated water local structure provides evidence that two hypothesized fluctuating water configurations exhibit different polarizability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

LANL Contributions to pyiron: An integrated development environment for computational materials science

To support and accelerate the development of simulation protocols in atomistic modelling, we introduce an integrated development environment (IDE) for computational materials science called pyiron (http://pyiron.org). The pyiron IDE combines a web based source code editor, a job management system for build automation, and a hierarchical data management solution. The core components of the pyiron IDE are pyiron objects based on an abstract class, which links application structures such as atomistic structures, projects, jobs, simulation protocols and computing resources with persistent storage and an interactive user environment. The simulation protocols within the pyiron IDE are constructed using the Python programming language. To highlight key concepts of this tool as well as to demonstrate its ability to simplify the implementation and testing of simulation protocols we discuss two applications. In these examples we show how pyiron supports the whole life cycle of a typical simulation, seamlessly combines ab initio with empirical potential calculations, and how complex feedback loops can be implemented. While originally developed with focus on ab initio thermodynamics simulations, the concepts and implementation of pyiron are general thus allowing to employ it for a wide range of simulation topics.

Janssen, Jan↗

DOE OSTI2019

Divergence in land surface modeling: linking spread to structure

Divergence in land carbon cycle simulation is persistent and widespread. Regardless of model intercomparison project, results from individual models diverge significantly from each other and, in consequence, from reference datasets. Here we link model spread to structure using a 15-member ensemble of land surface models from the Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) as a test case. Our analysis uses functional benchmarks and model structure as predicted by model skill in a machine learning framework to isolate discrete aspects of model structure associated with divergence. We also quantify how initial conditions prejudice present-day model outcomes after centennial-scale transient simulations. Overall, the functional benchmark and machine learning exercises emphasize the importance of ecosystem structure in correctly simulating carbon and water cycling, highlight uncertainties in the structure of carbon pools, and advise against hard parametric limits on ecosystem function. We also find that initial conditions explain 90% of variation in global satellite-era values—initial conditions largely predetermine transient endpoints, historical environmental change notwithstanding. As MsTMIP prescribes forcing data and spin-up protocol, the range in initial conditions and high levels of predetermination are also structural. Our results suggest that methodological tools linking divergence to discrete aspects of model structure would complement current community best practices in model development.

58 GEOSCIENCES↗

DOE OSTI2018

A New Standard DNA Damage (SDD) Data Format

Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called “indirect” damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates intermodel comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to significantly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2019

Simulating seawater intrusion in a complex coastal karst aquifer using an improved variable-density flow and solute transport–conduit flow process model

VDFST-CFP (variable-density flow and solute transport–conduit flow process) is a density-dependent discrete-continuum numerical model for simulating seawater intrusion in a dual-permeability coastal karst aquifer. A previous study (Xu and Hu 2017) simulates variable-density flow only in a single conduit, and studies the parameter sensitivities only in the horizontal case (2D domain as horizontal section) by the VDFST-CFP model. This paper focuses on the density-dependent vertical case (2D domain as vertical section) with two major improvements: 1) when implementing double-conduit networks in the domain, simulated intruded plumes in the porous medium are extended in the double-conduit scenario, compared to the single-conduit system; 2) by quantifying micro-textures on the conduit wall by the Goudar-Sonnad equation and considering macro-structures as local head loss. Sensitivity analysis shows that medium hydraulic conductivity, conduit diameter and effective porosity are important parameters for simulating seawater intrusion in the discrete-continuum system. On the other hand, rougher micro-structures and additional macro-structure components on the conduit wall would reduce the distance of seawater intrusion to the conduit system, but, rarely affect salinity distribution in the matrix. Compared to the equivalent mean roughness height, the new method (with more detailed description of structure) simulates seawater intrusion slightly landward in the conduit system. Here, the macro-structure measured by local head loss is more reasonable but needs further study on conduit flow. Xu and Hu (2017) Development of a discrete-continuum VDFST-CFP numerical model for simulating seawater intrusion to a coastal karst aquifer with a conduit system.

58 GEOSCIENCES↗

DOE OSTI2026

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗

DOE OSTI2023

Multi-Task Learning of Scanning Electron Microscopy and Synthetic Thermal Tomography Images for Detection of Defects in Additively Manufactured Metals

One of the key challenges in laser powder bed fusion (LPBF) additive manufacturing of metals is the appearance of microscopic pores in 3D-printed metallic structures. Quality control in LPBF can be accomplished with non-destructive imaging of the actual 3D-printed structures. Thermal tomography (TT) is a promising non-contact, non-destructive imaging method, which allows for the visualization of subsurface defects in arbitrary-sized metallic structures. However, because imaging is based on heat diffusion, TT images suffer from blurring, which increases with depth. We have been investigating the enhancement of TT imaging capability using machine learning. In this work, we introduce a novel multi-task learning (MTL) approach, which simultaneously performs the classification of synthetic TT images, and segmentation of experimental scanning electron microscopy (SEM) images. Synthetic TT images are obtained from computer simulations of metallic structures with subsurface elliptical-shaped defects, while experimental SEM images are obtained from imaging of LPBF-printed stainless-steel coupons. MTL network is implemented as a shared U-net encoder between the classification and the segmentation tasks. Results of this study show that the MTL network performs better in both the classification of synthetic TT images and the segmentation of SEM images tasks, as compared to the conventional approach when the individual tasks are performed independently of each other.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Atomic Structure and Dynamics of Unusual and Wide-Gap Phase-Change Chalcogenides: A GeTe 2 Case

Brain-inspired computing, reconfigurable optical metamaterials, photonic tensor cores, and many other advanced applications require next-generation phase-change materials (PCMs) with better energy efficiency and a wider thermal and spectral range for reliable operations. Germanium ditelluride (GeTe 2 ), with higher thermal stability and a larger bandgap compared to current benchmark PCMs, appears promising for THz metasurfaces and the controlled crystallization of atomically thin 2D materials. Using high-energy X-Ray diffraction supported by first-principles simulation, the atomic structure in semiconducting pulsed laser deposition films and metallic high-temperature liquids is investigated. The results suggest that the structural and chemical metastability of GeTe 2 , leading to disproportionation into GeTe and Te, is related to high internal pressure during a semiconductor–metal transition, presumably occurring in the supercooled melt. Similar phenomena are expected for canonical GeS 2 and GeSe 2 under high temperatures and pressures.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

CFD-DEM study of bubble properties in a cylindrical fluidized bed of Geldart Group D particles and comparison with prior MRI data

Numerical simulations of a freely bubbling cylindrical fluidized bed are carried out using a coupled computational fluid dynamics and discrete element method (CFD-DEM) model and compared to recent experimental data. The experiments were conducted using high-resolution and high-frequency magnetic resonance imaging providing high-fidelity data of the bubbling within a central 10 mm slice of the bed. Qualitatively, we nd more regular (i.e., less chaotic) structures in the simulated beds than observed experimentally. Quantitatively, however, the bubble diameter and number of bubbles as a function of height within the bed is predicted well by the base model. Unfortunately, the regularity in the simulations manifests as a considerable discrepancy in the speed of the (dense) emulsion phase. The simulated velocity probability distribution functions show an accumulation of low-speed regions and deficiency of high-speed regions. A simple parametric study of the base model is also carried out considering many of the most common CFD-DEM modeling parameters. It is found that the fluid grid size, geometry resolution, transfer kernel and drag law did not have a significant effect on bubble or particle dynamics.

42 ENGINEERING↗

DOE OSTI2019

Broadband (0–5 Hz) Fully Deterministic 3D Ground‐Motion Simulations of a Magnitude 7.0 Hayward Fault Earthquake: Comparison with Empirical Ground‐Motion Models and 3D Path and Site Effects from Source Normalized Intensities

We report on high‐performance computing (HPC) fully deterministic simulation of ground motions for a moment magnitude (⁠Mw⁠) 7.0 scenario earthquake on the Hayward fault resolved to 5 Hz using the SW4 finite‐difference code. We computed motions obeying physics‐based 3D wave propagation at a regional scale with an Mw 7.0 kinematic rupture model generated following Graves and Pitarka (2016). Both plane‐layered (1D) and 3D Earth models were considered, with 3D subsurface material properties and topography interpolated from a model of the U.S. Geological Survey (USGS). The resulting ground‐motion intensities cover a broader frequency range than typically considered in regional‐scale simulations, including higher frequencies relevant for engineering analysis of structures. Median intensities for sites across the domain are within the reported between‐event uncertainties (⁠τ⁠) of ground‐motion models (GMMs) across spectral periods 0.2–10 s (frequencies 0.1–5 Hz). The within‐event standard deviation ϕ of ground‐motion intensity measurement residuals range 0.2–0.5 natural log units with values consistently larger for the 3D model. Source‐normalized ratios of intensities (3D/1D) reveal patterns of path and site effects that are correlated with known geologic structure. These results demonstrate that earthquake simulations with fully deterministic wave propagation in 3D Earth models on HPC platforms produce broadband ground motions with median and within‐event aleatory variability consistent with empirical models. Systematic intensity variations for the 3D model caused by path and site effects suggest that these epistemic effects can be estimated and removed to reduce variation in site‐specific hazard estimates. This study motivates future work to evaluate the validity of the USGS 3D model and investigate the development of path and site corrections by running more scenarios.

Rodgers, Arthur J.↗

DOE OSTI2023

Nonresonant coherent amplitude transfer in attosecond four-wave-mixing spectroscopy

Attosecond four-wave mixing (FWM) spectroscopy using an extreme ultraviolet (XUV) pulse and two noncollinear near-infrared (NIR) pulses is employed to measure Rydberg wave packet dynamics resulting from XUV excitation of a 3s electron in atomic argon into a series of autoionizing 3s –1 np Rydberg states ~29 eV. The emitted signals from individual Rydberg states exhibit oscillatory structure and persist well beyond the expected lifetimes of the emitting Rydberg states. These results reflect substantial contributions of longer-lived Rydberg states to the FWM emission signals of each individually detected state. A wave packet decomposition analysis reveals that coherent amplitude transfer occurs predominantly from photoexcited 3s –1 (n + 1) p states to the observed 3s –1 np Rydberg states. The experimental observations are reproduced by time-dependent Schrödinger equation simulations using electronic structure and transition moment calculations. Finally, the theory highlights that coherent amplitude transfer is driven nonresonantly to the 3s –1 np states by the NIR light through 3s –1 (n + 1)s and 3s –1 (n – 1)d dark states during the FWM process.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Reconfigurable structure and tunable transport in synchronized active spinner materials

Ensembles of actuated colloids are excellent model systems to explore emergent out-of-equilibrium structures, complex collective dynamics, and design rules for the next generation materials. Here, we demonstrate that ferromagnetic microparticles suspended at an air-water interface and energized by an external rotating magnetic field spontaneously form dynamic ensembles of synchronized spinners in a certain range of the excitation field parameters. Each spinner generates strong hydrodynamic flows, and collective interactions of the multiple spinners promote a formation of dynamic lattices. On the basis of experiments and simulations, we reveal structural transitions from liquid to nearly crystalline states in this novel active spinner material and demonstrate that dynamic spinner lattices are reconfigurable, capable of self-healing behavior and that the transport of embedded inert cargo particles can be remotely tuned by the parameters of the external excitation field. Our findings provide insights into the behavior of active spinner materials with reconfigurable structural order and tunable functionalities.

36 MATERIALS SCIENCE↗

DOE OSTI2019

High-Fidelity Simulation of Flow-Induced Vibrations in Helical Steam Generators for Small Modular Reactors

Flow-induced vibration (FIV) is a widespread problem in energy systems as they rely on fluid movement for energy conversion. Vibrating structures may be damaged as fatigue or wear occur. Given the importance of reliable components in the nuclear industry, FIV has long been a major concern in the safety and operation of nuclear reactors. In particular, nuclear fuel rods and steam generators have been known to suffer from FIV and related failures. In this paper we discuss the use of the computational fluid dynamics code Nek5000 coupled to the structural code Diablo to simulate the flow in helical coil heat exchangers and associated FIV. In particular, one-way coupled calculations are performed, where pressure and tractions data are loaded into the structural model. The main focus of this paper is on validation of this capability. Fluid-only Nek5000 large eddy simulations are first compared against dedicated high-resolution experiments. Then, one-way coupled calculations are performed with Nek5000 and Diablo for two data sets that provide FIV data for validation. These calculations were aimed at simulating available legacy FIV experiments in helical steam generators in the turbulent buffeting regime. In this regime one-way coupling is judged sufficient since the pressure loads do not cause substantial displacements. It is also the most common source of vibration in helical steam generators at the low flows expected in integral pressurized water reactors. We discuss validation of two-way coupled experiments and benchmarks toward the simulation of fluid elastic instability. We briefly discuss the application of these methods to grid-to-rod fretting.

Flow-Induced Vibration↗

DOE OSTI2019

Hydrodynamic and Structural Response Modeling of a Prototype Floating Membrane Reservoir System for Pumped Storage Hydropower

Hydrodynamic, computational fluid dynamics, and finite-element modeling were performed for a novel floating membrane reservoir system design for closed-loop pumped storage hydropower application. The conceptual design, which is now protected under an invention disclosure with a patent pending, offers a potential low-cost, low-impact solution to address the high costs, long investment return periods, and environmental disruptions encountered with traditional pumped storage development while offering modularity to enable replication at many locations. Prior to physical tests on a prototype, this paper documents the response analysis and modeling completed to simulate hydraulic and structural performance under different reservoir deployment and alignment arrangements, evaluate system stability, and refine the conceptual design. The results indicate that the excitation frequency from vortex shedding is at least an order of magnitude lower than the water sloshing frequencies in the reservoir, the structural natural frequency of the entire reservoir, and the vibrational frequencies of the side membranes, although excitation frequencies from other sources could cause mechanical resonance under certain conditions. To control destabilizing effects and prevent rocking motion and vibration, the authors conclude that the design could be improved by including a support structure around the floating reservoir, which could also provide floating-membrane containment, improve safety, and facilitate vertical reservoir movement. These conclusions, based on hydrodynamic and structural response modeling, help define specifications for upcoming full-scale prototype construction, deployment, and testing. This study demonstrates standard modeling technique application to an innovative design for which similar applications have not been previously evaluated. As a result, the refined design is capable of improving the scalability and feasibility of pumped storage hydropower in the United States and will be considered for commercialization following prototype testing.

13 HYDRO ENERGY↗

DOE OSTI2023

Social network structure and the spread of complex contagions from a population genetics perspective

Ideas, behaviors, and opinions spread through social networks. If the probability of spreading to a new individual is a non-linear function of the fraction of the individuals’ affected neighbors, such a spreading process becomes a “complex contagion”. This non-linearity does not typically appear with physically spreading infections, but instead can emerge when the concept that is spreading is subject to game theoretical considerations (e.g. for choices of strategy or behavior) or psychological effects such as social reinforcement and other forms of peer influence (e.g. for ideas, preferences, or opinions). Here we study how the stochastic dynamics of such complex contagions are affected by the underlying network structure. Motivated by simulations of complex contagions on real social networks, we present a framework for analyzing the statistics of contagions with arbitrary non-linear adoption probabilities based on the mathematical tools of population genetics. The central idea is to use an effective lower-dimensional diffusion process to approximate the statistics of the contagion. This leads to a tradeoff between the effects of ”selection” (microscopic tendencies for an idea to spread or die out), random drift, and network structure. Our framework illustrates intuitively several key properties of complex contagions: stronger community structure and network sparsity can significantly enhance the spread, while broad degree distributions dampen the effect of selection compared to random drift. Finally, we show that some structural features can exhibit critical values that demarcate regimes where global contagions become possible for networks of arbitrary size. Our results draw parallels between the competition of genes in a population and memes in a world of minds and ideas. Our tools provide insight into the spread of information, behaviors, and ideas via social influence, and highlight the role of macroscopic network structure in determining their fate.

59 BASIC BIOLOGICAL SCIENCES↗