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DOE OSTI2023

Quantum dynamics simulations of the 2D spectroscopy for exciton polaritons

We develop an accurate and numerically efficient non-adiabatic path-integral approach to simulate the non-linear spectroscopy of exciton–polariton systems. This approach is based on the partial linearized density matrix approach to model the exciton dynamics with explicit propagation of the phonon bath environment, combined with a stochastic Lindblad dynamics approach to model the cavity loss dynamics. Through simulating both linear and polariton two-dimensional electronic spectra, we systematically investigate how light–matter coupling strength and cavity loss rate influence the optical response signal. Our results confirm the polaron decoupling effect, which is the reduced exciton–phonon coupling among polariton states due to the strong light–matter interactions. We further demonstrate that the polariton coherence time can be significantly prolonged compared to the electronic coherence outside the cavity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

GPAW: An open Python package for electronic structure calculations

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe–Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn–Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

An experimental study of the existence regions and non-linear interactions of drift wave and Kelvin–Helmholtz instabilities in a linear magnetized plasma

Experimental observations of the intrinsic excitation and non-linear interactions of drift wave (DW) and Kelvin–Helmholtz (KH) instabilities in a linear magnetized plasma column are presented. The experiments are carried out in the inverse mirror plasma experimental device (IMPED)—a cylindrical, magnetized, linear plasma machine designed to study low-frequency waves and instabilities in plasma. A novel feature of IMPED is the ability to control plasma profiles, such as the density n(r)⁠, electron temperature T e (r)⁠, and plasma potential V p (r) by varying the ratio Rm of the magnetic field in the main chamber to that in the source chamber. At high values of Rm, higher-density gradient scale length promotes the drift wave (DW) instability while lower Rm value results in a higher radial electric field, inducing a sheared poloidal flow that enhances the dominance of the Kelvin–Helmholtz (KH) mode. The background and fluctuating plasma parameters are characterized using various configurations of multiple in situ electric probes at different spatial locations to quantify the local gradients that excite the low-frequency primary instabilities. Statistical, spectral, and bispectral analysis of the density and potential signals help identify these modes in terms of wave number, frequency, phase, and amplitude and also delineate the nature of their non-linear interactions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Dynamical attractors in contracting spacetimes dominated by kinetically coupled scalar fields

We present non-perturbative numerical relativity simulations of slowly contracting spacetimes in which the scalar field driving slow contraction is coupled to a second scalar field through an exponential non-linear σ model-type kinetic interaction. These models are important because they can generate a nearly scale-invariant spectrum of super-Hubble density fluctuations fully consistent with cosmic microwave background observations. We show that the non-linear evolution rapidly approaches a homogeneous, isotropic and flat Friedmann-Robertson-Walker (FRW) geometry for a wide range of inhomogeneous and anisotropic initial conditions. Ultimately, we find, the kinetic coupling causes the evolution to deflect away from flat FRW and towards a novel Kasner-like stationary point, but in general this occurs on time scales that are too long to be observationally relevant.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Machine learning of hidden variables in multiscale fluid simulation

Solving fluid dynamics equations often requires the use of closure relations that account for missing microphysics. For example, when solving equations related to fluid dynamics for systems with a large Reynolds number, sub-grid effects become important and a turbulence closure is required, and in systems with a large Knudsen number, kinetic effects become important and a kinetic closure is required. By adding an equation governing the growth and transport of the quantity requiring the closure relation, it becomes possible to capture microphysics through the introduction of ‘hidden variables’ that are non-local in space and time. The behavior of the ‘hidden variables’ in response to the fluid conditions can be learned from a higher fidelity or ab-initio model that contains all the microphysics. In our study, a partial differential equation simulator that is end-to-end differentiable is used to train judiciously placed neural networks against ground-truth simulations. We show that this method enables an Euler equation based approach to reproduce non-linear, large Knudsen number plasma physics that can otherwise only be modeled using Boltzmann-like equation simulators such as Vlasov or particle-in-cell modeling.

42 ENGINEERING↗

DOE OSTI2021

Influence of inhomogeneous stochasticity on the falsifiability of mean-field theories and examples from accretion disc modelling

ABSTRACT Despite spatial and temporal fluctuations in turbulent astrophysical systems, mean-field theories can be used to describe their secular evolution. However, observations taken over time scales much shorter than dynamical time scales capture a system in a single state of its turbulence ensemble. Comparing with mean-field theory can falsify the latter only if the theory is additionally supplied with a quantified precision. The central limit theorem provides appropriate estimates to the precision only when fluctuations contribute linearly to an observable and with constant coherent scales. Here, we introduce an error propagation formula that relaxes both limitations, allowing for non-linear functional forms of observables and inhomogeneous coherent scales and amplitudes of fluctuations. The method is exemplified in the context of accretion disc theories, where inhomogeneous fluctuations in the surface temperature are propagated to the disc emission spectrum – the latter being a non-linear and non-local function of the former. The derived precision depends non-monotonically on emission frequency. Using the same method, we investigate how binned spectral fluctuations in telescope data change with the spectral resolving power. We discuss the broader implications for falsifiability of a mean-field theory.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Magnetorotational dynamo can generate large-scale vertical magnetic fields in 3D GRMHD simulations of accreting black holes

ABSTRACT Jetted astrophysical phenomena with black hole engines, including binary mergers, jetted tidal disruption events, and X-ray binaries, require a large-scale vertical magnetic field for efficient jet formation. However, a dynamo mechanism that could generate these crucial large-scale magnetic fields has not been identified and characterized. We have employed three-dimensional global general relativistic magnetohydrodynamical simulations of accretion discs to quantify, for the first time, a dynamo mechanism that generates large-scale magnetic fields. This dynamo mechanism primarily arises from the non-linear evolution of the magnetorotational instability (MRI). In this mechanism, large non-axisymmetric MRI-amplified shearing wave modes, mediated by the axisymmetric azimuthal magnetic field, generate and sustain the large-scale vertical magnetic field through their non-linear interactions. We identify the advection of magnetic loops as a crucial feature, transporting the large-scale vertical magnetic field from the outer regions to the inner regions of the accretion disc. This leads to a larger characteristic size of the, now advected, magnetic field when compared to the local disc height. We characterize the complete dynamo mechanism with two time-scales: one for the local magnetic field generation, $t_{\rm gen}$, and one for the large-scale scale advection, $t_{\rm adv}$. Whereas the dynamo we describe is non-linear, we explore the potential of linear mean field models to replicate its core features. Our findings indicate that traditional $\alpha$-dynamo models, often computed in stratified shearing box simulations, are inadequate and that the effective large-scale dynamics is better described by the shear current effects or stochastic $\alpha$-dynamos.

Astronomy & Astrophysics↗

DOE OSTI2022

A detailed analysis of the dynamics of fast neutrino flavor conversions with scattering effects

We calculate the dynamics of fast neutrino flavor conversions with Boltzmann collisions of neutrino scatterings in a homogeneous system. We find the enhancement or suppression of the flavor conversions in various setups of the collision terms. We analyze the mechanism of fast flavor conversions based on the motion of polarization vectors in the cylindrical coordinate analogous to a pendulum motion. The phases of the all the polarization vectors synchronize in the linear evolution phase, and the phase deviation from the Hamiltonian governs the neutrino flavor conversions. In a non-linear regime of flavor conversions, the collision terms induce a spiral motion of the polarization vector and gradually make the phase space smaller. The collision terms align all of the polarization vectors, and the flavor conversions eventually settle into equilibrium when the distributions of neutrinos become isotropic. Though our current analysis does not fully clarify the non-linear phenomena of fast flavor conversions, the framework of the pendulum motion gives a new insight into this complicated phenomenon that will be helpful in further studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

The Artificial Scientist: in-Transit Machine Learning of Plasma Simulations

Large-scale simulations or scientific experiments produce petabytes of data per run. This poses massive challenges for I/O and storage when scientific analysis workflows are run manually offline. Unsupervised deep learning-based techniques to extract patterns and non-linear relations from these large amounts of data provide a way to build scientific understanding from raw data, reducing the need for manual pre-selection of analysis steps, but require exascale compute and memory to process the full dataset available. In this paper, we demonstrate a heterogeneous streaming workflow in which plasma simulation data is streamed directly to a Machine Learning (ML) application training a model on the simulation data in-transit, completely circumventing the capacity-constrained filesystem bottleneck. This workflow employs openPMD to provide a high level interface to describe scientific data and also uses ADIOS2, to transfer volumes of data that exceed the capabilities of the filesystem. We employ experience replay to avoid catastrophic forgetting in learning from this non-steady state process in a continual manner and adapt it to improve model convergence while learning in-transit. As a proof-of-concept, we approach the ill-posed inverse problem of predicting particle dynamics from radiation in a particle-incell (PIConGPU) simulation of the Kelvin-Helmholtz instability (KHI). We detail hardware-software co-design challenges as we scale PIConGPU to full Frontier, the Top-1 system as of June 2024 Top500 list.

Kelling, Jeffrey [Helmholtz-Zentrum Dresden Rossen↗

DOE OSTI2024

Impact of beam–beam effects on absolute luminosity calibrations at the CERN Large Hadron Collider

At the Large Hadron Collider (LHC), absolute luminosity calibrations obtained by the van der Meer (vdM) method are affected by the mutual electromagnetic interaction of the two beams. The colliding bunches experience relative orbit shifts, as well as optical distortions akin to the dynamic-β effect, that both depend on the transverse beam separation and must therefore be corrected for when deriving the absolute luminosity scale. In the vdM regime, the beam–beam parameter is small enough that the orbit shift can be calculated analytically. The dynamic-β corrections to the luminometer calibrations, however, had until the end of Run 2 been estimated in the linear approximation only. In this report, the influence of beam–beam effects on the vdM-based luminosity scale is quantified, together with the associated systematic uncertainties, by means of simulations that fully take into account the non-linearity of the beam–beam force, as well as the resulting non-Gaussian distortions of the transverse beam distributions. Two independent multiparticle simulations, one limited to the weak-strong approximation and one that models strong-strong effects in a self-consistent manner, are found in excellent agreement; both predict a percent-level shift of the absolute pp-luminosity values with respect to those assumed until recently in the physics publications of the LHC experiments. These results also provide guidance regarding further studies aimed at reducing the beam–beam-related systematic uncertainty on beam–beam corrections to absolute luminosity calibrations by the van der Meer method.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

A manifold learning perspective on surrogate modeling of nitrate concentration in the Kansas River

Abstract A non-linear surrogate model of nitrate concentration in the Kansas River (USA) is described. The model is an (almost) Piece-wise Linear response surface that provides a mean field approximation to the dynamics of the measured data for nitrate plus nitrite (target product) correlations to turbidity and chlorophyll-a concentrations (input variables). The method extends the United States Geological Survey’s linear procedures for surrogate data modeling allowing for better approximations for river systems exhibiting algal blooms due to nutrient-rich source waters. The model and visualization procedures illustrated in the Kansas River example should be generally applicable to many medium-size rivers in agricultural regions.

Tufillaro, Nicholas (ORCID:0009000628968832)↗

DOE OSTI2021

Data-Driven Specification of Earth's Magnetic Field

As our society is increasingly dependent on technologies in space, predicting space weather becomes ever more important. We have come to rely on technologies such as cellphones, GPS, the Internet, and other commercial and military assets. In order to protect these systems a high priority is to develop better understanding of the harmful conditions of space weather encountered in the near-Earth radiation environment which are mostly dictated by the dynamics of energetic charged particles. The main objective of our proposal was to improve the specification and forecast of the particle distribution in the Earth’s inner magnetosphere using data assimilation together with machine learning (ML) algorithms in our ring current-atmosphere interactions model with self-consistent magnetic and electric fields (RAM-SCBE). Specifically, we explored the application of machine learning algorithms to emulate and improve, through infusion of observational data, the magnetic field (SCBE) of our ring current model. Our work advanced towards the characterization of the RAM-SCBE particle flux field and its potentially different simulation scenarios. We explored how the model behaves in a number of simulation scenarios in order to better understand how the model reacts to perturbations in the solar wind. We were able to capture this behavior through the simulation of an ensemble of RAM-SCB model solutions. The ensemble showed the important correlations between the particle fluxes and the magnetic field. We were able to start the training of a neural network (Autoencoder) to identify the dominant features of the magnetic field, and the main correlations (linear and non-linear) between the particle fluxes and the magnetic field. Our next steps consists of training a neural network to capture the time evolution of the dominant features and obtain a consistent surrogate model for the RAM-SCB.

42 ENGINEERING↗

DOE OSTI2023

SIF and Vegetation Indices in the US Midwestern Agroecosystems, 2016-2021, Carbon Monitoring System (CMS)

This dataset contains half-hourly ground solar-induced chlorophyll fluorescence (SIF) and vegetation indices including NDVI, EVI, Red edge chlorophyll index, green chlorophyll index, and photochemical reflectance index at seven crop sites in Nebraska and Illinois for the period 2016-2021. Four sites were located at Eddy Covariance (EC) tower sites (sites US-Ne2, US-Ne3, US-UiB, and US-UiC), and three sites were located on private farms (sites Reifsteck, Rund, and Reinhart). The sites were either miscanthus, corn-soybean rotation or corn-corn-soybean rotation. The spectral data for SIF retrieval and hyperspectral reflectance for vegetation index calculation were collected by the FluoSpec2 system, installed near planting, and uninstalled after harvest to collect whole growing-season data. Raw nadir SIF at 760 nm from different algorithms (sFLD, 3FLD, iFLD, SFM) are included. SFM_nonlinear and SFM_linear represent the Spectral fitting method (SFM) with the assumption that fluorescence and reflectance change with wavelength non-linearly and linearly, respectively. Additional data include two SIF correction factors including calibration coefficient adjustment factor (f_cal_corr_QEPRO) and upscaling nadir SIF to eddy covariance footprint factor (ratio_EC footprint, SIF pixel), and measured FPAR from quantum sensors and Rededge NDVI calculated FPAR. The data are provided in comma-separated values (CSV) format.

Ameriflux↗

DOE OSTI2021

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Technical note: A modified formulation of dynamic energy budget theory for faster computation of biological growth

Abstract. The mass conservation equation in the presence of boundary fluxes and chemical reactions from non-equilibrium thermodynamics is used to derive a modified dynamic energy budget (mDEB) model. Compared to the standard dynamic energy budget (sDEB) model (Kooijman, 2009), this modified formulation does not place the dilution effect in the mobilization kinetics of reserve biomass, and it maintains the partition principle for reserve mobilization dynamics for both linear and non-linear kinetics. Overall, the mDEB model shares most features with the sDEB model. However, for biological growth that requires multiple nutrients, the mDEB model is computationally much more efficient by not requiring numerical iterations for obtaining the specific growth rate. In an example of modeling the growth of Thalassiosira weissflogii in a nitrogen-limiting chemostat, the mDEB model was found to have almost the same accuracy as the sDEB model while requiring almost half of the computing time of the sDEB model. Since the sDEB model has been successfully applied in numerous studies, we believe that the mDEB model can help improve the modeling of biological growth and the associated ecosystem processes in various contexts.

Tang, Jinyun↗

DOE OSTI2021

Midfidelity Model Verification for a Point-Absorbing Wave Energy Converter with Linear Power Takeoff: Preprint

In the preliminary design stage of a wave energy converter (WEC), fast and reliable simulation tools are required. High-fidelity numerical models are usually employed to study the wave-structure interaction, yet the computational cost is demanding. Instead, mid-fidelity models provide simulations in the order of real time. In this study, Uppsala University WEC operates in a relatively mild sea state and is modeled using WEC-Sim. The model is verified based on OpenFOAM simulations. To analyze the ability of mid-fidelity model to capture the WEC dynamics, the system is investigated separately in 1, 2 and 3 DoF. The contribution of viscous phenomena is examined. Moreover, linear and weakly non-linear solutions provided by WEC-Sim are studied. The results obtained indicate that the viscous effects in heave and surge motion can be neglected but not for the pitch. The weakly non-linear WEC-Sim solution successfully agrees with the CFD, whereas the linear solution could drive to misleading results.

CFD↗

DOE OSTI2021

Midfidelity Model Verification for a Point-Absorbing Wave Energy Converter with Linear Power Take-Off

CFD↗

DOE OSTI2022

Stability analysis of a one-dimensional multiphysics model of a molten salt fast reactor

Reactor designs with a fast neutron spectrum have recently moved into the research focus for possible Generation IV reactor concepts - a representative of which is the molten salt fast reactor (MSFR). In order to assess the safety and reliability of this reactor concept, it is necessary to obtain knowledge of the system behaviour. An important part of this research concerns the dynamical stability of the MSFR. Research regarding the MSFR stability so far has either been using linearized models for stability criteria or only been examining certain transients at fixed parameter values. This work delivers a comprehensive stability analysis for a non-linearized MSFR model, and a wide range of values for all relevant parameters. For this purpose, a one-dimensional MSFR model was set up, taking neutron kinetics and thermal hydraulics in the form of a system of differential equations into account. The stability of this model was investigated by means of the numerical tool MATCONT, which was used to monitor the evolution of a so-called fixed-point solution, here referring to the steady state at operating conditions of the system, while system parameters got varied. The MATCONT analyses showed no loss of stability for any of the considered parameter variations and no solutions that might co-exist in parallel with the steady-state fixed-point solution. Therefore these results indicate a stable fixed point to which all solution transients converge, making the considered MSFR model insusceptible to deviations from the equilibrium. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗