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DOE OSTI2024

Explicit simulation of the Brownian rotation of arbitrary shaped aerosol particles using quaternions

The shape of an aerosol particle strongly influences its mass and momentum transfer cross-sections, charging properties, and other physical properties. Here, we present an explicit time-stepping procedure to simulate the rotational Brownian motion of arbitrary shaped aerosol particles by solving Euler’s equation of rotation. A Langevin formulation of the rotation equations is used, wherein Brownian motion due to thermal collisions between a particle and background gas molecules is represented using a stochastic fluctuating torque and fluid resistance is included as a drag torque. To avoid singularities associated with describing the orientation of a shape with Euler angles, we employ a quaternion formulation that leads to first-order stochastic differential equations to describe the evolution of the angular position and angular velocity of a rigid body. We perform all the rotational dynamics calculations in the body-fixed frame of reference attached to the rotating shape whose basis vectors are the normalized eigenvectors of the inertia tensor of the particle. Numerical solutions to rotation under torque-free conditions, damped rotation without Brownian motion, and stochastic rotation for arbitrary shapes are presented and discussed. The presented method enables time-resolved simulation of Brownian rotation for direct comparison with experimentally measured trajectories or statistical measures. The second order accuracy of the used time-stepping procedure places a severe restriction on the timestep that can be used for obtaining accurate results. Animations of presented simulations are included for visualizing rotational motion at various gas pressures. To aid implementation, MATLAB ® codes are also provided. Extension to include translation Brownian motion is straightforward.

Roy, Mrittika↗

DOE OSTI2022

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium

The “genomic shock” hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession “Bhyb26.” We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species’ similarity in transposable element load may account for the subtlety of the observed genome dominance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Visualization of fast ion phase-space flow in plasmas well-below, near and well-above Alfvén eigenmode stability threshold in tokamak

Abstract Transport of fast ions along certain local phase space paths, referred to as fast ion phase-space flow, has been systematically measured by an imaging neutral particle analyzer (INPA) in three plasma regimes, which are well-below, near, and well-above the Alfvén eigenmode stability threshold (Du et al 2021 Phys. Rev. Lett. 127 235002). (1) In plasmas well-below the Alfvén eignenmodes (AE) stability threshold, fast ions are well-confined on passing particle orbits without noticeable transport over the phase space. The observed INPA images agree well with the synthetic INPA images, using the fast ion distribution predicted by neoclassical theory. (2) In plasmas near the AE stability threshold, INPA images in the presence of AE activity moderately deviate from those without AE activity. The image difference can be well interpreted by AE-driven, phase-space fast ion flow. Paths of this flow over the velocity space (or streamlines) are reconstructed by the intersection lines of curved E ʹ and µ surfaces, referred to as E ʹ and µ line (where E ′ ≡ E − ( ω / n ) P ζ ; E , P ζ and µ are the energy, canonical toroidal momentum and magnetic moment of ions; ω and n are the angular frequency and toroidal mode number of AEs, respectively). Resonant fast ions move radially inward by gaining energy and move radially outward by losing energy and the trajectory well aligns with the E ʹ and µ lines that pass through the mode resonances near the injection energy of neutral beams. (3) In plasmas well-above the AE stability threshold, fast ion phase-space dynamics shows additional features. Fast ions are transported out of the birth positions so promptly along the streamlines that the slowing-down process from the injection energy is not observable, exhibiting strong critical gradient behavior at local phase space. As a result, the increase of electron temperature is very small, in spite of an increase of beam power by ∼ 45 % . It should be emphasized that the directions of phase-space transport, induced by AEs with different frequencies, structures and mode numbers, do not largely differ.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Advanced Closures for Nonlinear Fluid Simulations of Plasmas (Final Report)

Advanced Closures for Nonlinear Fluid Simulations of Plasmas E. Held, Utah State University (Principal Investigator) J.-Y. Ji, Utah State University (Co-Investigator) Utah State University (USU) continued to develop and apply closures for hybrid fluid/kinetic simulations of magnetized fusion plasmas. The closures developed by USU's fusion theory and computation group use the drift ordering and are referred to as "continuum" and "general moment" approaches. They differ in their representation for the distribution functions which probabilistically describe the density of particles in 5 dimensional phase space. The two chosen velocity variables, needed in studies of kinetic physics for magnetized plasmas, are the speed and the component of a particle's velocity along the magnetic field. In magnetized plasmas, the charged particle trajectories are tied closely to the magnetic field lines. Both approaches account for binary interactions between particles using the Coulomb collision operator. Theoretical and computational development along both lines provided avenues for verification between the two approaches. This funding allowed USU to further develop physically accurate and numerically efficient models that advance our understanding of kinetic physics in experiments like the International Thermonuclear Experimental Reactor (ITER). The ITER device will likely prove the physical practicality of thermonuclear fusion by producing 500 megawatts of clean, abundant fusion power. This work helped to realize this goal by advancing our simulation capability using hybrid fluid/kinetic models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Continental United States climate projections based on thermodynamic modification of historical weather

Abstract Regional climate models can be used to examine how past weather events might unfold under different climate conditions by simulating analogue versions of those events with modified thermodynamic conditions (i.e., warming signals). Here, we apply this approach by dynamically downscaling a 40-year sequence of past weather from 1980–2019 driven by atmospheric re-analysis, and then repeating this 40-year sequence a total of 8 times using a range of time-evolving thermodynamic warming signals that follow 4 80-year future warming trajectories from 2020–2099. Warming signals follow two emission scenarios (SSP585 and SSP245) and are derived from two groups of global climate models based on whether they exhibit relatively high or low climate sensitivity. The resulting dataset, which contains 25 hourly and over 200 3-hourly variables at 12 km spatial resolution, can be used to examine a plausible range of future climate conditions in direct reference to previously observed weather and enables a systematic exploration of the ways in which thermodynamic change influences the characteristics of historical extreme events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Conceptual design of a heavy ion beam probe diagnostic for the Wendelstein 7-X Stellarator

This article describes the current state of the design of the heavy ion beam probe (HIBP) for Wendelstein 7-X (W7-X). It will be the first HIBP diagnostic on an optimized stellarator and is designed to study electric fields and ion scale turbulence in all W7-X reference magnetic configurations. The use of an existing 2 MV accelerator, located outside of the torus hall, results in the need for a circuitous primary beamline. This increases the complexity of the ion optics design to deliver a focused beam to the plasma. To access most of the magnetic configuration space of W7-X, the secondary beamline and an energy analyzer are designed to pivot, thereby redirecting a wider range of secondary beam trajectories. Signal level estimates indicate that the equilibrium potential can be measured at all radii and that the radial coverage for potential and density fluctuations measurements depends on the plasma density.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Genome‐enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

Summary As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross‐disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene‐ and genome‐enabled surveys, and application of genome‐guided, cultivation‐independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Minimizing Ground Risk in Cellular-Connected Drone Corridors With mmWave Links

Unmanned Aircraft Systems (UASs) have been receiving significant interest and support from academia, industry, and regulatory bodies over the past decade due to their various use cases. To safely integrate UAS operations into the national airspace, particularly overpopulated regions, the risk posed to ground users, buildings, and vehicles due to unmanned aerial vehicle (UAV) flight should be minimized. This risk can be represented by a numerical metric, which we refer to in this article as the “ground risk.” Many UAS applications also depend on the presence of a reliable wireless communication link between the UAV and a control station for the transmission of UAV position, surveillance video, UAV payload commands, and other mission-related data. Such wireless communication requirements also need to be considered in the design of UAS operations. In this article, we consider both these aspects and study the design of nonintersecting trajectories for UAS operations to minimize ground risk, subject to constraints on the wireless signal strength and geometry of the trajectory, specified in terms of: 1) an enclosing cylinder within which the trajectory must lie and 2) an integrated angular change along the UAV's trajectory. The performance of a computationally expensive optimal algorithm is compared with that of a computationally faster heuristic approach within the dense urban environment of Manhattan, NY, USA. Performance evaluation using ray-tracing simulations shows that the heuristic approach performs close to the optimal algorithm at a reduced computation cost. In conclusion, this research can be utilized to make UAS operations safe and reliable and accelerate their adoption.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2025

Dynamics of McMillan mappings I. McMillan multipoles

In this article, we consider two dynamical systems: the McMillan sextupole and octupole integrable mappings, originally proposed by Edwin McMillan. Both represent the simplest symmetric McMillan maps, characterized by a single intrinsic parameter. While these systems find numerous applications across various domains of mathematics and physics, some of their dynamical properties remain unexplored. We aim to bridge this gap by providing a comprehensive description of all stable trajectories, including the parametrization of invariant curves, Poincaré rotation numbers, and canonical action–angle variables. In the second part, we establish connections between these maps and general chaotic maps in standard form. Our investigation reveals that the McMillan sextupole and octupole serve as first-order approximations of the dynamics around the fixed point, akin to the linear map and quadratic invariant (known as the Courant–Snyder invariant in accelerator physics), which represents zeroth-order approximations (referred to as linearization). Furthermore, we propose a novel formalism for nonlinear Twiss parameters, which accounts for the dependence of rotation number on amplitude. This stands in contrast to conventional betatron phase advance used in accelerator physics, which remains independent of amplitude. Notably, in the context of accelerator physics, this new formalism demonstrates its capability in predicting dynamical aperture around low-order resonances for flat beams, a critical aspect in beam injection/extraction scenarios.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects

We numerically investigate an adaptive version of the parareal algorithm in the context of molecular dynamics. This adaptive variant has been originally introduced in [1]. We focus here on test cases of physical interest where the dynamics of the system is modelled by the Langevin equation and is simulated using the molecular dynamics software LAMMPS. In this work, the parareal algorithm uses a family of machine-learning spectral neighbor analysis potentials (SNAP) as fine, reference, potentials and embedded-atom method potentials (EAM) as coarse potentials. We consider a self-interstitial atom in a tungsten lattice and compute the average residence time of the system in metastable states. Our numerical results demonstrate significant computational gains using the adaptive parareal algorithm in comparison to a sequential integration of the Langevin dynamics. We also identify a large regime of numerical parameters for which statistical accuracy is reached without being a consequence of trajectorial accuracy.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Enabling cooperative adaptive cruise control on strings of vehicles with heterogeneous dynamics and powertrains

Recent studies have shown that positive impact of Cooperative Adaptive Cruise Control (CACC) can only be guaranteed as market penetration rate increases. Removing the string homogeneity constraint is essential to encourage widespread adoption. In this work, a hierarchical architecture is proposed to enable CACC on vehicles with not only mixed dynamics but also different powertrain types. A low-level layer deals with the vehicle and powertrain dynamics to provide accurate and consistent reference speed tracking response. The high-level layer uses: (1) a Linear Parameter Varying feedback system to provide loop stability, robustness and enforce a variable time gap policy and (2) a feedforward system that processes Vehicle-to-Vehicle information to enhance string stability and response bandwidth, by dealing with the string heterogeneity. A gap management strategy is built on top of the CACC architecture to handle gap setting changes or cut-in/out situations, via a dynamics constrained time gap trajectory planning algorithm. We report the proposed work has been designed, developed and validated on three different real passenger vehicles on public highways and test tracks, showing the potential of the proposed algorithm to enable robust string stable CACC, despite the different dynamics and powertrains considered.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2023

Measurement of helicon waves with phase contrast imaging on DIII-D – A theoretical feasibility study

A DIII-D high-beta H-mode discharge, with I p = 850 kA, B t = 2.1 T n e = 4 10 19 m –3 , has been designed to validate full wave modeling of helicon waves by optimizing the expected response of the Phase Contrast Imaging diagnostic. Helicon waves have been predicted to have high current drive efficiency off-axis without facing the accessibility issues of lower-hybrid waves. To test these predictions experimentally, DIII-D has recently commissioned a high-power helicon antenna. To confidently predict the behavior of helicon waves in future devices, measurements of their fundamental properties and validation against models will be essential. Phase contrast imaging (PCI) is an absolutely calibrated internal reference interferometer able to measure density fluctuations with radial wavenumbers k R between 1.5 cm –1 and 20 cm –1 . For helicon waves 2 cm –1 < k R < 10 cm –1 is expected, allowing PCI to measure their envelope and wavenumber spectrum. This makes PCI a powerful tool for the validation of state-of-the-art models, like the AORSA full wave code. AORSA is used to compute the density perturbations measured by the PCI with 2D calculations corresponding to 11 different toroidal mode numbers combined to resolve the trajectory of the helicon wave in 3D. This is necessary because the waves travel 120 degrees toroidally from the antenna to the PCI. Here, a cold plasma finite element model (CPFEM) [4] is used to predict propagation through the scrape-off layer. The result of the CPFEM model is connected to AORSA by creating an artificial Gaussian antenna on the last closed flux surface. PCI shows best results for waves with small vertical wavenumbers k z . Modeling the helicon waves for several past DIII-D experiments shows that k z is minimized if the intersection of the helicon and the PCI laser beams occurs in the midplane. For such an optimized scenario the predicted signal level is two orders of magnitude larger than the background density fluctuations arising from broadband turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Unmanned Aerial Vehicle Path Generation for Image Collection to Assist Heliostat Field Optical Characterization

This paper focuses on applications of unmanned aerial vehicles (UAVs) for measuring optical error of heliostats in concentrating solar power (CSP) plants. In CSP, there is a need to measure solar-field optical errors, which is critical for future production improvement as well as for operations and maintenance of a heliostat field. This latter need is particularly challenging because of the large number of heliostats (over 10,000 for a utility-scale power plant) that individually track the sun in the field. To address this issue, a camera-equipped UAV, with an optimized drone flight path developed and uploaded to it, collects images of a precise reflection of the tower on each heliostat to evaluate optical error sources without interrupting plant operation. Generation of the drone path for capturing the reflected images is affected by a number technical and realistic constraints, which include the camera angle used to capture the image, the blocking of the camera view due to surrounding heliostats, the location of the camera in reference to the target heliostat, and the target heliostat position with reference to the tower. The effect of these constraints on calculating the camera position will be discussed in detail in this article. An effective drone-path algorithm is generated to fulfil the need of image collection under various constraints.

concentrated solar power↗

DOE OSTI2022

Effects of stratification and charge cooling on combustion in a gasoline direct-injection compression ignition (GDCI) engine

With the development of low temperature engine combustion strategies, performance of gasoline-type fuels under compression ignition conditions has attracted extensive research interest. Meanwhile, for the sake of co-optimization of engines and fuels for future ground transportation, identification and evaluation of general fuel properties should be a core research priority instead of endless testing of specific fuels. In this study, the roles of fuel octane sensitivity in characterizing the ignition performance of gasoline surrogates have been systematically investigated under typical gasoline direct ignition compression ignition (GDCI) engine conditions using 3D combustion CFD simulation, especially considering the subsequent in-cylinder charge stratification and charge cooling. Two different operating conditions, high boost pressure low boost temperature (beyond-RON) case and low boost pressure high boost temperature (beyond-MON) case, were considered. By comparing with our previous zero-dimensional chemical kinetic study of gasoline surrogates in advanced compression ignition (ACI) engines, the effects of stratification and charge cooling on the combustion processes are investigated. It is found that different fuel octane sensitivities lead to slight difference in equivalence ratio stratification and charge cooling due to differences in volatility. However, fuel reactivity is still the more dominant factor than the stratification and charge cooling effects in determining combustion phasing. The present results help to justify the P-T domain framework for engine autoignition analysis of overlapping pressure-temperature trajectory with ignition delay iso-contour. Here, the results also provide useful guidance to the understanding of GCI combustion process, and to the evaluation of controlling fuel properties and the selection of alternative fuels in GCI engines.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2026

Actinium–DOTA coordination in water from hybrid ML/MM: Structure, free energies, and water-exchange pathways

Quantitative simulation of trivalent ƒ-block chelates in water remains challenging because bonded and non-bonded force-field models make different approximations for coordination structure, exchange dynamics, and ion–ligand interactions in highly charged systems. Here, we develop a hybrid machine-learning/molecular-mechanics (ML/MM) framework for Ac 3+ –DOTA in explicit solvent by training an E(3)-equivariant neural network potential (MACELES) on mechanically embedded QM/MM data for Ac aquo and Ac–DOTA species and coupling it to NAMD 2.14 with particle-mesh Ewald electrostatics. Nanosecond ML/MM trajectories remain numerically stable and preserve chelate integrity, yielding a compact DOTA inner shell with an inner-sphere water coordination number of CN Ac,O w ≈ 1.7 arising from a dynamic equilibrium between one- and two-water states (37.5% and 59.9% of frames; three waters 2.5%). A 5 ns potential of mean force shows two low-lying basins at CN Ac,O w ≈ 1 and CN Ac,O w ≈ 2. DFT end-state free energies are consistent with the ML/MM profile, and DFT minimum-energy paths provide a qualitative electronic-structure reference for the observed basin connectivity. State-resolved kinetics reveal picosecond water-exchange pathways that couple hydration changes to transient DOTA arm fluctuations, and training-set comparisons show that temperature-matched Ac–DOTA data optimize energy/force accuracy while more diverse solvated data improve charge prediction. Overall, the present hybrid ML/MM model provides a practical description of Ac 3+ –DOTA hydration thermodynamics and short-time exchange behavior in explicit water at MD-like cost.

Actinium↗

DOE OSTI2023

Yaw-Augmented Control for Wind Farm Power Tracking: Preprint

This paper presents an inner-outer control loop structure which uses wake steering (yaw control) to augment pitch control for wind farms to track a power reference signal. The outer-loop yaw controller employs a recently proposed dynamic yaw model with a time-varying graph structure that accounts for dynamic changes in the farm wake interactions due to the yaw action of upstream turbines. The wake interactions within the model include the physics of the streamwise and lateral wake evolution, which collectively determine its impact on downstream turbines. The inner-loop employs a compensation scheme to account for the slow timescale effects of the yaw control actions within the faster timescale pitch control. The controller is applied to track two power trajectories (typical of secondary frequency regulation signals) using a large eddy simulation wind farm plant. The results demonstrate that the additional control authority from yaw provides some added benefit in reducing the required turbine derates needed for wind farms to track transient power increases in the proposed setting. However, the benefit decreases and pitch control alone is sufficient when the turbines are derated beyond a certain level. These findings suggest that augmenting pitch control with yaw may provide financial incentives in terms of allowing wind farms to maximize power supply to the bulk power market while still providing regulation services. Further work is needed analyze the costs versus benefits of the additional control complexity versus bandwidth in augmenting pitch control with wake steering offers in these applications.

active power control↗

DOE OSTI2022

Aircraft Icing Severity Evaluation

Aircraft icing refers to the ice buildup on the surface of an aircraft flying in icing conditions. The ice accretion on the aircraft alters the original aerodynamic configuration and degrades the aerodynamic performances and may lead to unsafe flight conditions. Evaluating the flow structure, icing mechanism and consequences is of great importance to the development of an anti/deicing technique. Studies have shown computational fluid dynamics (CFD) and machine learning (ML) to be effective in predicting the ice shape and icing severity under different flight conditions. CFD solves a set of partial differential equations to obtain the air flow fields, water droplets trajectories and ice shape. ML is a branch of artificial intelligence and, based on the data, the self-improved computer algorithms can be effective in finding the nonlinear mapping relationship between the input flight conditions and the output aircraft icing severity features.

Li, Sibo (ORCID:000000021705844X)↗

DOE OSTI2022

Modification of the Loss Cone for Energetic Particles in the Earth's Inner Magnetosphere

The behavior of energetic particles in the Earth's dipole and stretched magnetic-field models is explored with a focus on the shift of the atmospheric loss cone away from the magnetic-field direction and on non-adiabatic behavior occurring when the particle gyroradius becomes comparable with the gradient scale length of the local magnetic field. It is shown that the equatorial loss cone is aberrated away from the magnetic-field direction (pitch angle of 0°) by the perpendicular drift of a charged particle (which is referred to as the “Mozer transform” described in Mozer (1966, https://doi.org/10.1029/JZ071i011p02701). It is found that the Mozer coordinate transformation in pitch-angle/gyrophase-angle space better organizes the behavior of bounce times, mirror altitudes, drift speeds, and first adiabatic invariant. It also describes the loss-cone shift accurately for a certain range of values of the adiabaticity parameter ϵ, defined by the ratio of the particle gyroradius to the local radius of curvature of the magnetic field. For particles with larger ϵ, the Mozer transform (evaluated with the standard gradient-curvature drift) breaks down and the “central trajectory” theory can be used to calculate the angular shift of the loss cone, which now includes an Earthward shift. When ϵ becomes relatively large, stochastic field line curvature (FLC) scattering occurs: we show the intimate connection between the strength of FLC scattering and the loss-cone shift. Finally, by comparing ion orbits in the dipole and Tsyganenko (Ts89 and Ts04) magnetic fields, we conclude that the loss cone of ring-current ions is significantly modified during geomagnetically active times.

79 ASTRONOMY AND ASTROPHYSICS↗