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DOE OSTI2023

Operation Optimization using Reinforcement Learning with Integrated Artificial Reasoning Framework

In large and complex systems, operational decision-making requires a systematic analysis with a vast amount of data from both process parameters and component status monitoring. In this paper, we present an integrated artificial reasoning approach for system state transition models that can help operational decision-making with explainable and traceable reasoning. The integrated artificial reasoning framework is a physics-based approach of defining the system structure in a Bayesian network, so we leveraged it in a Markov decision process (MDP) for finding optimal operational solutions. In our proposed framework, the MDP is implemented on a dynamic Bayesian network (DBN), which represents causalities in a system. The multilevel flow modeling was utilized in order to extract these causalities in a more efficient and objective manner. Since multilevel flow modeling is based on the fundamental energy and mass conservation laws, the target system is decomposed into several mass, energy, and information structures, which serve as the basis for a DBN. The MDP consists of the processes of finding a solution for the Bellman equation, which can be derived from the conditional probability equations of the constructed DBN. System operators can capture stochastic system dynamics as multiple subsystem state transitions based on their physical relations and uncertainties coming from the component degradation process or random failures. We analyzed a simplified example system to illustrate finding an optimal operational policy with this approach.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2026

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗

DOE OSTI2020

Oscillation-like diffusion of two-dimensional liquid dusty plasmas on one-dimensional periodic substrates with varied widths

The long-time diffusion of two-dimensional dusty plasmas on a one-dimensional periodic substrate with varying widths is investigated using Langevin dynamical simulations. When the substrate is narrow and the dust particles form a single row, the diffusion is the smallest in both directions. In this study, we find that as the substrate width gradually increases to twice its initial value, the long-time diffusion of the two-dimensional dusty plasmas first increases, then decreases, and finally increases again, giving an oscillation-like diffusion with varying substrate widths. When the width increases to a specific value, the dust particles within each potential well arrange themselves in a stable zigzag pattern, greatly reducing the diffusion and leading to the observed oscillation in the diffusion with the increase in the width. In addition, the long-time oscillation-like diffusion is consistent with the number of dust particles that are hopping across the potential wells of the substrate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model

The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Impacts of Multidimensional Progenitor Perturbations on Core-collapse Supernova Explosions

Numerical studies of core-collapse supernovae have demonstrated the importance of nonradial motions in precollapse progenitors on the explosion outcome. We use the Chimera neutrino radiation hydrodynamics code running seven two-dimensional simulations of 15 M⊙ progenitors with different progenitor structures introduced by different one- and two-dimensional precollapse stellar evolution environments to examine the impacts of stellar structure and nonspherical motion in the precollapse progenitor on the development of explosions. We compare the explosion evolution of these models in terms of shock dynamics, diagnostic energy, neutrino heating, accretion, explosion geometry, nuclear abundances, and turbulent convection. We also analyze how stochastic variation impacts our simulations. Contrary to results reported in prior studies examining the impacts of multidimensional progenitors, we observe similar shock revival times and explosion development in our simulations despite differences in initial compositions and structures. We find no discernible impact from the accretion of nonradial perturbations from a multi-D progenitor onto the stalled shock in the revival and strength of explosion, as fully developed neutrino-driven convection behind the stalled shock is similar for all our models. For models with physically sourced noise in the iron core, a strong oscillation of the shock occurs after bounce and deflects infall laterally, and accelerates the saturation of the lateral turbulent kinetic energy. An examination of model stochasticity shows that any prior expected impacts on explosive outcome due to convection-related perturbations lie below the detectable threshold of numerical variation.

Chen, Chien-Hui [North Carolina State University]↗

DOE OSTI2022

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Many-Exciton Quantum Dynamics in a Ruddlesden–Popper Tin Iodide

We present a study on the many-body exciton interactions in a Ruddlesden–Popper tin halide, namely, (PEA) 2 SnI 4 (PEA = phenylethylammonium), using coherent two-dimensional electronic spectroscopy. The optical dephasing times of the third-order polarization observed in these systems are determined by exciton many-body interactions and lattice fluctuations. We investigate the excitation-induced dephasing (EID) and observe a significant reduction of the dephasing time with increasing excitation density as compared to its lead counterpart (PEA) 2 PbI 4 , which we have previously reported in a separate publication [J. Chem. Phys. 2020, 153, 164706]. Surprisingly, we find that the EID interaction parameter is four orders of magnitude higher in (PEA) 2 SnI 4 than that in (PEA) 2 PbI 4 . This increase in the EID rate may be due to exciton localization arising from a more statically disordered lattice in the tin derivative. This is supported by the observation of multiple closely spaced exciton states and the broadening of the linewidth with increasing population time (spectral diffusion), which suggests a static disordered structure relative to the highly dynamic lead-halide. Additionally, we find that the exciton nonlinear coherent lineshape shows evidence of a biexcitonic state with low binding energy (<10 meV) not observed in the lead system. We model the lineshapes based on a stochastic scattering theory that accounts for the interaction with a nonstationary population of dark background excitations. Our study provides evidence of differences in the exciton quantum dynamics between tin- and lead-based Ruddlesden–Popper metal halides (RPMHs) and links them to the exciton–exciton interaction strength and the static disorder aspect of the crystalline structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Time-resolved turbulent dynamo in a laser plasma

Understanding magnetic-field generation and amplification in turbulent plasma is essential to account for observations of magnetic fields in the universe. A theoretical framework attributing the origin and sustainment of these fields to the so-called fluctuation dynamo was recently validated by experiments on laser facilities in low-magnetic-Prandtl-number plasmas (Pm < 1). However, the same framework proposes that the fluctuation dynamo should operate differently when Pm ≳ 1, the regime relevant to many astrophysical environments such as the intracluster medium of galaxy clusters. This paper reports an experiment that creates a laboratory Pm ≳ 1 plasma dynamo. We provide a time-resolved characterization of the plasma’s evolution, measuring temperatures, densities, flow velocities, and magnetic fields, which allows us to explore various stages of the fluctuation dynamo’s operation on seed magnetic fields generated by the action of the Biermann-battery mechanism during the initial drive-laser target interaction. The magnetic energy in structures with characteristic scales close to the driving scale of the stochastic motions is found to increase by almost three orders of magnitude and saturate dynamically. It is shown that the initial growth of these fields occurs at a much greater rate than the turnover rate of the driving-scale stochastic motions. Here, our results point to the possibility that plasma turbulence produced by strong shear can generate fields more efficiently at the driving scale than anticipated by idealized magnetohydrodynamics (MHD) simulations of the nonhelical fluctuation dynamo; this finding could help explain the large-scale fields inferred from observations of astrophysical systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Framework for idealized climate simulations with spatiotemporal stochastic clouds and planetary-scale circulations

In climate predictions, clouds are the leading source of uncertainty. This is partly because, to simulate the fluid dynamics of climate over the entire globe, a large grid spacing must be used, so clouds are a subgrid-scale parametrization rather than a resolved feature. Here, a framework is investigated with finer grid spacing of O(1) or O(10)km so that some clouds are not subgrid-scale; instead, clouds evolve on the numerical grid. This cloud evolution is achieved using stochastic modeling. Hence, the framework is idealized in the sense that the full fluid dynamics of cloud circulations is still not resolved, and simplified vertical structures are used. Nevertheless, the fluid dynamics model includes evolving clouds that interactively adjust in size, shape, lifetime, and regional coverage. In addition, different cloud types are included with different roles in the climate system, including deep convective clouds and also boundary-layer clouds such as shallow cumulus and stratocumulus clouds. Other basic aspects of the idealized climate system are planetary-scale circulations (e.g., Walker circulation) and radiation. With these ingredients (evolving clouds, planetary-scale circulations, and radiation), the framework has the potential for idealized investigations of climate change with interactive cloud–radiative feedback of individual clouds. Here, the formulation of the model equations is presented, and numerical simulations are shown to illustrate the model dynamics and climate change.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Time-resolved turbulent dynamo in a laser plasma

Understanding magnetic-field generation and amplification in turbulent plasma is essential to account for observations of magnetic fields in the universe. A theoretical framework attributing the origin and sustainment of these fields to the so-called fluctuation dynamo was recently validated by experiments on laser facilities in low-magnetic-Prandtl-number plasmas (Pm<1). However, the same framework proposes that the fluctuation dynamo should operate differently when Pm≳1, the regime relevant to many astrophysical environments such as the intracluster medium of galaxy clusters. This paper reports an experiment that creates a laboratory Pm≳1 plasma dynamo. We provide a time-resolved characterization of the plasma’s evolution, measuring temperatures, densities, flow velocities, and magnetic fields, which allows us to explore various stages of the fluctuation dynamo’s operation on seed magnetic fields generated by the action of the Biermann-battery mechanism during the initial drive-laser target interaction. The magnetic energy in structures with characteristic scales close to the driving scale of the stochastic motions is found to increase by almost three orders of magnitude and saturate dynamically. It is shown that the initial growth of these fields occurs at a much greater rate than the turnover rate of the driving-scale stochastic motions. Our results point to the possibility that plasma turbulence produced by strong shear can generate fields more efficiently at the driving scale than anticipated by idealized magnetohydrodynamics (MHD) simulations of the nonhelical fluctuation dynamo; this finding could help explain the large-scale fields inferred from observations of astrophysical systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Holographic open quantum systems: toy models and analytic properties of thermal correlators

We present a unified picture of open quantum systems, the theory of a system probing a noisy thermal environment, distilling lessons learnt from previous holographic analyses. Our treatment is applicable both when the system is coupled to short-lived (Markovian), and long-lived (non-Markovian) environmental degrees of freedom. The thermal environment is modeled using an asymptotically AdS black hole, and the systems of interest are simple probe field theories. The effective stochastic dynamics of the system is governed by real-time thermal correlators, which we compute using the gravitational Schwinger-Keldysh (grSK) geometry. We describe the structure of arbitrary tree-level contact and exchange Witten diagrams in the grSK geometry. In particular, we argue, that all such diagrams reduce to integrals supported on a single copy of the exterior of the black hole. The integrand is obtained as a multiple discontinuity of a function comprising ingoing boundary-bulk propagators, monodromy functions which appear as radial Boltzmann weights, and vertex factors. These results allow us to deduce the analytic structure of real-time thermal n-point functions in holographic CFTs. We illustrate the general statements by a two-dimensional toy model, dual to fields in the BTZ background, which we argue captures many of the essential features of generic open holographic QFTs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Physics-based modeling and data analytics [Slides]

This presentation contains a summary of ongoing work within the physics-based modeling and data analytics work package within the Nuclear Materials Discovery and Qualification initiative (NMDQi). Topics include work on MOOSE-based crystal plasticity, molecular dynamics modeling of recombination in metals and alloys, the MOOSE Stochastic Tools Module, and machine learning and atomistic modeling to predict thermo-kinetic properties of nuclear structural materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

16S amplicon sequencing↗

DOE OSTI2025

Thermally induced mimicry of quantum cluster excitations and implications for the magnetic transition in FePSe 3

In two dimensional magnets, the interplay of thermal fluctuations and spin anisotropy control the existence of long-range magnetic order. In the van der Waals antiferromagnets FePX 3 , orbital degeneracy in the 𝑡 2⁢𝑔 levels of the Fe 2+ ions in octahedral coordination yields strong uniaxial anisotropy, which stabilizes magnetic order up to 𝑇 ≈ 100 K. Recent inelastic neutron scattering measurements around the magnetic ordering transition have shown the existence of a broad spectrum of magnetic fluctuations with nontrivial momentum dependence, which has been interpreted as evidence for localized entangled cluster excitations. In this paper, we offer an alternative interpretation using classical nonlinear spin dynamics simulations. We present stochastic Landau Lifshitz dynamics simulations that reproduce the neutron scattering measurements of Chen et al. [npj Quantum Mater. 9, 40 (2024)] on FePSe 3 . These calculations faithfully explain the dynamical structure factor's momentum and energy dependence and point to a classical origin for the excitations observed in neutron spectroscopy and that the order-disorder transition can be understood in terms of thermal fluctuations overcoming the anisotropy energy.

Landau-Lifschitz-Gilbert equation↗

DOE OSTI2023

Operation Optimization Using Reinforcement Learning with Integrated Artificial Reasoning Framework

Kim, Junyung↗

DOE OSTI2022

Protein drift-diffusion dynamics and phase separation in curved cell membranes and dendritic spines: Hybrid discrete-continuum methods

We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine discrete particle descriptions with continuum-level models for tracking the individual protein drift-diffusion dynamics when coupled to continuum fields. We show how our approaches can be used to investigate phenomena motivated by protein kinetics within dendritic spines. The spine geometry is hypothesized to play an important biological role regulating synaptic strength, protein kinetics, and self-assembly of clusters. We perform simulation studies for model spine geometries varying the neck size to investigate how phase-separation and protein organization is influenced by different shapes. We also show how our methods can be used to study the roles of geometry in reaction-diffusion systems including Turing instabilities. Furthermore, our methods provide general approaches for investigating protein kinetics and drift-diffusion dynamics within curved membrane structures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Large-scale atomistic model construction of subbituminous and bituminous coals for solvent extraction simulations with reactive molecular dynamics

Large-scale atomistic models for complex polycyclic aromatic hydrocarbon systems help understand the chemical properties and behaviors of complex feedstocks such as coal or petroleum. However, the development and utilization of large-scale models remain limited due to the difficulty in achieving the varied structural characteristics necessary to capture stochastic nature of these feedstocks. Here we demonstrate a systematic workflow to construct stochastic molecular systems from a broad analytical suite: high-resolution transmission electron microscopy (HRTEM), carbon-13 nuclear magnetic resonance spectroscopy ( 13 C NMR), laser desorption ionization mass spectroscopy (LDI-MS), and elemental analysis. We present a model construction and analysis utility of a new Python-based module. We selected one subbituminous and three high-volatile bituminous coals to construct large-scale models (~40,000 atoms). The constructed models were utilized to examine the affinity for solvent extraction (naphthalene or tetralin) and the effect of structural properties (e.g., aromatic cluster size, functional groups, and cross-linking) in reactive molecular dynamics simulations. Complex chemical reactions were monitored with bond order transitions, intermediates formation, and mass distributions. Reactive molecular dynamics simulations suggest a plausible chemical extraction process and products for the complex fossil feedstocks. The results indicated that radical formations with bond breaking of bridging oxygens and carbons were required at high temperatures to facilitate hydrogeneration and extraction of gas molecules from radical-free molecules. We observed that aliphatic chains of tetralin were easily decomposed and combined with radicals to form small size of molecules with aryl bonding, mainly increasing molecules in the 500–1000 Da, while naphthalene had little impact on chemical extraction process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

TurboRVB: A many-body toolkit for ab initio electronic simulations by quantum Monte Carlo

TurboRVB is a computational package for ab initio Quantum Monte Carlo (QMC) simulations of both molecular and bulk electronic systems. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC) and diffusion Monte Carlo in its robust and efficient lattice regularized variant. A key feature of the code is the possibility of using strongly correlated many-body wave functions (WFs), capable of describing several materials with very high accuracy, even when standard mean-field approaches [e.g., density functional theory (DFT)] fail. The electronic WF is obtained by applying a Jastrow factor, which takes into account dynamical correlations, to the most general mean-field ground state, written either as an antisymmetrized geminal power with spin-singlet pairing or as a Pfaffian, including both singlet and triplet correlations. This WF can be viewed as an efficient implementation of the so-called resonating valence bond (RVB) Ansatz, first proposed by Pauling and Anderson in quantum chemistry [L. Pauling, The Nature of the Chemical Bond (Cornell University Press, 1960)] and condensed matter physics [P.W. Anderson, Mat. Res. Bull 8, 153 (1973)], respectively. The RVB Ansatz implemented in TurboRVB has a large variational freedom, including the Jastrow correlated Slater determinant as its simplest, but nontrivial case. Moreover, it has the remarkable advantage of remaining with an affordable computational cost, proportional to the one spent for the evaluation of a single Slater determinant. Therefore, its application to large systems is computationally feasible. The WF is expanded in a localized basis set. Several basis set functions are implemented, such as Gaussian, Slater, and mixed types, with no restriction on the choice of their contraction. The code implements the adjoint algorithmic differentiation that enables a very efficient evaluation of energy derivatives, comprising the ionic forces. Thus, one can perform structural optimizations and molecular dynamics in the canonical NVT ensemble at the VMC level. For the electronic part, a full WF optimization (Jastrow and antisymmetric parts together) is made possible, thanks to state-of-the-art stochastic algorithms for energy minimization. In the optimization procedure, the first guess can be obtained at the mean-field level by a built-in DFT driver. The code was efficiently parallelized by using a hybrid MPI-OpenMP protocol, which is also an ideal environment for exploiting the computational power of modern Graphics Processing Unit accelerators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗