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At least 217 records · Page 12

All sources NASA NTRS DOE OSTI

DOE OSTI2020

A Dynamic Amplitude-Correcting Gradient Estimation Technique to Align X-ray Focusing Optics

High-brightness X-rays, as produced at synchrotrons and X-ray free electron laser (XFEL) facilities, are used to characterize materials in a variety of scientific experiments. In most cases, effective use of the high-energy light requires precisely-aligned focusing optics; one example being a compound refractive lens (CRL). To align a CRL, the position and rotation must be optimized along four axes. In practice, this is a labor-intensive, time-consuming manual process that can monopolize scarce experimental time at the necessary X-ray facilities. Models of the expected Xray transmission function suggest that this task can be automated; however, the temporally-varying intensity at X-ray free electron laser facilities preclude the direct use of standard implementations of optimization solvers such as steepest descent algorithms. In this paper, we propose a novel technique to estimate the gradient of noisy functions with temporally-varying amplitudes. We construct this dynamicamplitude correction by systematically sampling a fixed central location within the standard finite difference stencil, accounting for the observed changes in time, and normalizing the difference quotients against those fluctuations. In addition to a rigorous error analysis of the sampling technique, we demonstrate its efficacy in stochastic descent optimization methods. Further, we demonstrate how this approach may be implemented to optimize X-ray focusing optics at synchrotrons or XFEL facilities

97 MATHEMATICS AND COMPUTING↗

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↗

DOE OSTI2024

Force-Free Identification of Minimum-Energy Pathways and Transition States for Stochastic Electronic Structure Theories

Here, the accurate mapping of potential energy surfaces (PESs) is crucial to our understanding of the numerous physical and chemical processes mediated by atomic rearrangements, such as conformational changes and chemical reactions, and the thermodynamic and kinetic feasibility of these processes. Stochastic electronic structure theories, e.g., Quantum Monte Carlo (QMC) methods, enable highly accurate total energy calculations that in principle can be used to construct the PES. However, their stochastic nature poses a challenge to the computation and use of forces and Hessians, which are typically required in algorithms for minimum-energy pathway (MEP) and transition state (TS) identification, such as the nudged elastic band (NEB) algorithm and its climbing image formulation. Here, we present strategies that utilize the surrogate Hessian line-search method, previously developed for QMC structural optimization, to efficiently identify MEP and TS structures without requiring force calculations at the level of the stochastic electronic structure theory. By modifying the surrogate Hessian algorithm to operate in path-orthogonal subspaces and at saddle points, we show that it is possible to identify MEPs and TSs by using a force-free QMC approach. We demonstrate these strategies via two examples, the inversion of the ammonia (NH 3 ) molecule and the nucleophilic substitution (S N 2) reaction F – + CH 3 F → FCH 3 + F – . We validate our results using Density Functional Theory (DFT)- and Coupled Cluster (CCSD, CCSD(T))-based NEB calculations. We then introduce a hybrid DFT-QMC approach to compute thermodynamic and kinetic quantities, free energy differences, rate constants, and equilibrium constants that incorporates stochastically optimized structures and their energies, and show that this scheme improves upon DFT accuracy. Our methods generalize straightforwardly to other systems and other high-accuracy theories that similarly face challenges computing energy gradients, paving the way for highly accurate PES mapping, transition state determination, and thermodynamic and kinetic calculations at significantly reduced computational expense.

Iyer, Gopal R.↗

DOE OSTI2023

Efficient Bayesian inference with latent Hamiltonian neural networks in No-U-Turn Sampling

When sampling for Bayesian inference, one popular approach in the computational field is to use Hamiltonian Monte Carlo (HMC) and specifically the No-U-Turn Sampler (NUTS), which automatically decides the end time of the Hamiltonian trajectory. However, HMC and NUTS can require numerous numerical gradients of the target density and can prove slow in practice when relying on computationally expensive forward models. We propose Latent Hamiltonian neural networks (L-HNNs) with HMC and NUTS for solving Bayesian inference problems. Once trained, L-HNNs do not require numerical gradients of the target density during sampling, and hence numerous evaluations of the forward computational model. Moreover, L-HNNs satisfy important properties such as perfect time reversibility and Hamiltonian conservation, making them well-suited for use within HMC and NUTS because stationarity can be shown. We also propose the integration of L-HNNs in an online error monitoring scheme, in which numerical gradients of the target density are used for a few samples whenever the L-HNNs prediction errors are large. This online error monitor scheme prevents sample degeneracy in regions of low probability density and ensures robust uncertainty quantification. We demonstrate L-HNNs in NUTS with online error monitoring on several analytical examples involving complex, heavy-tailed, and high-local-curvature probability densities. We then demonstrate the applicability of L-HNNs in NUTS to two computational case studies, namely the Allen-Cahn stochastic partial differential equation and an elliptic partial differential equation with 25 and 50 inference parameters, respectively. Overall, the L-HNNs in NUTS with online error monitoring satisfactorily inferred these probability densities. In conclusion, compared to traditional NUTS, L-HNNs in NUTS with online error monitoring required 1–2 orders of magnitude fewer numerical gradients of the target density and improved the effective sample size (ESS) per gradient (which is a measure of both the sampling quality and the computational expense) by an order of magnitude.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1974

Cosmic ray scintillations. II - General theory of interplanetary scintillations

The motion of charged particles in a stochastic magnetic field with nonzero mean is considered via a generalized quasi-linear expansion of Liouville's equation. The general result is an equation relating cosmic ray scintillations to magnetic fluctuations and to cosmic ray gradients. The resonant interaction between particles and the random magnetic field is considered in detail, and the effect of nonlinear terms in the equations is considered. The nonlinear terms are important in damping out initial conditions and in determining conditions near cyclotron resonances. The application of the theory to the propagation of cosmic rays during quiet times in interplanetary space is considered. It is concluded that cosmic ray scintillations in interplanetary space may provide useful information about interplanetary particles and fields and also about nonlinear plasma interactions.

Owens, A. J.↗

DOE OSTI2022

Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean

Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on “who is doing what, where, and how?”, this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory—determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1976

A kinetic-theory approach to turbulent chemically reacting flows

The paper examines the mathematical and physical foundations for the kinetic theory of reactive turbulent flows, discussing the differences and relation between the kinetic and averaged equations, and comparing some solutions of the kinetic equations obtained by the Green's function method with those obtained by the approximate bimodal method. The kinetic method described consists essentially in constructing the probability density functions of the chemical species on the basis of solutions of the Langevin stochastic equation for the influence of eddies on the behavior of fluid elements. When the kinetic equations are solved for the structure of the diffusion flame established in a shear layer by the bimodal method, discontinuities in gradients of the mean concentrations at the two flame edges appear. This is a consequence of the bimodal approximation of all distribution functions by two dissimilar half-Maxwellian functions, which is a very crude approximation. These discontinuities do not appear when the solutions are constructed by the Green's function method described here.

Chung, P. M.↗

DOE OSTI2025

Specificity and tunability of efflux pumps: A new role for the proton gradient?

Efflux pumps that transport antibacterial drugs out of bacterial cells have broad specificity, commonly leading to broad spectrum resistance and limiting treatment strategies for infections. It remains unclear how efflux pumps can maintain this broad spectrum specificity to diverse drug molecules while limiting the efflux of other cytoplasmic content. We have investigated the origins of this broad specificity using theoretical models informed by the experimentally determined structural and kinetic properties of efflux pumps. We developed a set of mathematical models describing operation of efflux pumps as a discrete cyclic stochastic process across a network of states characterizing pump conformations and the presence/absence of bound ligands and protons. These include a minimal three-state model that lends itself to clear analytic calculations as well as a five-state model that relaxes some of the simpler model’s most strict assumptions. We found that the pump specificity is determined not solely by the drug affinity to the pump–as is commonly assumed–but it is also directly affected by the periplasmic pH and the transmembrane potential. Therefore, changes to the proton concentration gradient and voltage drop across the membrane can influence how effective the pump is at extruding a particular drug molecule. Furthermore, we found that while both the proton concentration gradient across the membrane and the transmembrane potential contribute to the thermodynamic force driving the pump, their effects on the efflux enter not strictly in a combined proton motive force. Rather, they have two distinguishable effects on the overall throughput. These results highlight the unexpected effects of thermodynamic driving forces out of equilibrium and illustrate how efflux pump structure and function are conducive to the emergence of multidrug resistance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Temperature drives local contributions to beta diversity in mountain streams: stochastic and deterministic processes

Community variation (i.e. beta diversity) in geographical coenoclines is of substantial interest in ecology, yet the elevational patterns in beta diversity are still understudied, and no general conclusions have been reached. Here, we explored local contributions to beta diversity (LCBD) of stream bacteria, diatoms and macroinvertebrates on mountainsides. Across all taxa, we revealed a general U-shaped LCBD-elevation relationships (LCBDer), suggesting higher uniqueness of community composition at the two ends of the elevational gradients. This pattern was confirmed by coenocline simulations based on observed communities, and supported by the dominance of species replacement in total beta diversity. Across mountains and taxonomic groups, temperature was the main environmental factor underlying elevational patterns in LCBD and its metric relatives, which were also mediated by local environmental variables. The observed magnitudes of U-shaped LCBDer across mountains and taxonomic groups were specifically related to the heterogeneity of stream morphology, and the mean annual temperature on each mountain. U-shaped LCBDer were strengthened by the occurrence of generalist species with large elevational ranges, while rare species had a lesser effect on the patterns. Raup-Crick beta diversity indicated that both stochastic and deterministic processes drove the community assembly, and the latter one was positively related to the magnitudes of LCBDer. Our synthesis across mountains and taxonomic groups clearly shows that there are consistent elevational patterns in LCBD among taxonomic groups, and that these patterns are explained by similar ecological mechanisms, producing a more complete picture in understanding and bridging the spatial variation in biodiversity under changing climate.

Wang, Jianjun↗

DOE OSTI2026

A Stochastic Quasi-Newton Method in the Absence of Common Random Numbers

We present Q-SASS, a quasi-Newton method for unconstrained stochastic optimization that does not rely on common random numbers. Most existing quasi-Newton approaches leverage common random numbers to construct second-order updates. However, motivated by challenges in variational quantum algorithms—where such coordination is not possible—we consider the setting in which function values and gradients are accessible only through noisy probabilistic zeroth- and first-order oracles, and no common random numbers can be exploited. We derive high-probability tail bounds on the iteration complexity of our algorithm for nonconvex, convex, and strongly convex (more generally, those satisfying the PL condition) objective functions. Finally, we demonstrate the empirical benefits of our quasi-Newton updating scheme on both synthetic and quantum chemistry problems.

Complexity bound↗

DOE OSTI2024

Correlation Between Microscopic Current Fluctuations Observed at Ultra-Microelectrodes and Macroscopic Bulk Electrolysis Performance in Redox-Active Microemulsions

Microemulsions (μEs) have been proposed as redox flow battery (RFB) electrolytes that maximize ionic conductivity and charge capacity by synergizing two immiscible phases. However, charge transfer during electrolysis in μEs is poorly understood. Here, we show that ultramicroelectrode electrolysis of ferrocene-loaded μEs –20%, 60%, and 90% water - reveals stochastic current fluctuations. These are differentiated in the scanning electrochemical microscopy (SECM) geometry, where power spectral density analysis showed distinct changes in the frequency contributions. SECM in the substrate generation-tip collection mode showed that fluctuations arise under mass-transfer control. Significant differences in the diffusion coefficient of ferrocene species were deducted from SECM approach curves, suggesting phase transfer behavior. Using bulk electrolysis, we calculated the charge accessibility and cycling behavior in the μEs. A decrease in the stochastic behavior of the μEs seems to correlate to a higher accessibility and cycling performance, with the 90% water μE displaying the best reversibility and the 60% the lowest. Altogether, these results suggest that Marangoni-type convection driven by concentration gradients and/or μE restructuring during charge transfer play a role in the electrochemical performance of μEs. This presents opportunities for screening and diagnosing the performance of these emerging RFB electrolytes.

25 ENERGY STORAGE↗

NASA NTRS2012

Upper-Ocean Heat Balance Processes and the Walker Circulation in CMIP5 Model Projections

Considerable uncertainty remains as to the importance of mechanisms governing decadal and longer variability of the Walker Circulation, its connection to the tropical climate system, and prospects for tropical climate change in the face of anthropogenic forcing. Most contemporary climate models suggest that in response to elevated CO2 and a warmer but more stratified atmosphere, the required upward mass flux in tropical convection will diminish along with the Walker component of the tropical mean circulation as well. Alternatively, there is also evidence to suggest that the shoaling and increased vertical stratification of the thermocline in the eastern Pacific will enable a muted SST increase there-- preserving or even enhancing some of the dynamical forcing for the Walker cell flow. Over the past decade there have been observational indications of an acceleration in near-surface easterlies, a strengthened Pacific zonal SST gradient, and globally-teleconnected dislocations in precipitation. But is this evidence in support of an ocean dynamical thermostat process posited to accompany anthropogenic forcing, or just residual decadal fluctuations associated with variations in warm and cold ENSO events and other stochastic forcing? From a modeling perspective we try to make headway on this question by examining zonal variations in surface energy fluxes and dynamics governing tropical upper ocean heat content evolution in the WCRP CMIP5 model projections. There is some diversity among model simulations; for example, the CCSM4 indicates net ocean warming over the IndoPacific region while the CSIRO model concentrates separate warming responses over the central Pacific and Indian Ocean regions. The models, as with observations, demonstrate strong local coupling between variations in column water vapor, downward surface longwave radiation and SST; but the spatial patterns of changes in the sign of this relationship differ among models and, for models as a whole, with observations. Our analysis focuses initially on probing the inter-model differences in energy fluxes / transports and Walker Circulation response to forcing. We then attempt to identify statistically the El Nino- / La Nina-related ocean heat content variability unique to each model and regress out the associated energy flux, ocean heat transport and Walker response on these shorter time scales for comparison to that of the anthropogenic signals.

Robertson, F. R.↗

DOE OSTI2024

Differentiable stochastic halo occupation distribution

ABSTRACT In this work, we demonstrate how differentiable stochastic sampling techniques developed in the context of deep reinforcement learning can be used to perform efficient parameter inference over stochastic, simulation-based, forward models. As a particular example, we focus on the problem of estimating parameters of halo occupation distribution (HOD) models that are used to connect galaxies with their dark matter haloes. Using a combination of continuous relaxation and gradient re-parametrization techniques, we can obtain well-defined gradients with respect to HOD parameters through discrete galaxy catalogue realizations. Having access to these gradients allows us to leverage efficient sampling schemes, such as Hamiltonian Monte Carlo, and greatly speed up parameter inference. We demonstrate our technique on a mock galaxy catalogue generated from the Bolshoi simulation using a standard HOD model and find near-identical posteriors as standard Markov chain Monte Carlo techniques with an increase of ∼8× in convergence efficiency. Our differentiable HOD model also has broad applications in full forward model approaches to cosmic structure and cosmological analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Stochastic Approximation for Multi-period Simulation Optimization with Streaming Input Data

We consider a continuous-valued simulation optimization (SO) problem, where a simulator is built to optimize an expected performance measure of a real-world system while parameters of the simulator are estimated from streaming data collected periodically from the system. At each period, a new batch of data is combined with the cumulative data and the parameters are re-estimated with higher precision. The system requires the decision variable to be selected in all periods. Therefore, it is sensible for the decision-maker to update the decision variable at each period by solving a more precise SO problem with the updated parameter estimate to reduce the performance loss with respect to the target system. We define this decision-making process as the multi-period SO problem and introduce a multi-period stochastic approximation (SA) framework that generates a sequence of solutions. Two algorithms are proposed: Re-start SA (ReSA) reinitializes the stepsize sequence in each period, whereas Warm-start SA (WaSA) carefully tunes the stepsizes, taking both fewer and shorter gradient-descent steps in later periods as parameter estimates become increasingly more precise. We show that under suitable strong convexity and regularity conditions, ReSA and WaSA achieve the best possible convergence rate in expected sub-optimality either when an unbiased or a simultaneous perturbation gradient estimator is employed, while WaSA accrues significantly lower computational cost as the number of periods increases. In addition, we present the regularized ReSA, which obviates the need to know the strong convexity constant and achieves the same convergence rate at the expense of additional computation.

Computer Science↗

DOE OSTI2025

On the Sampling-Based Computation of Nash Equilibria Under Uncertainty via the Nikaido–Isoda Function

We consider the computation of an equilibrium of a stochastic Nash equilibrium problem, where the player objectives are assumed to be L 0 -Lipschitz continuous and convex, given rival decisions with convex and closed player-specific feasibility sets. To address this problem, we consider minimizing a suitably defined value function defined using the Nikaido–Isoda function. Such an avenue does not necessitate either monotonicity properties of the concatenated gradient map or potentiality requirements on the game but does require a suitable regularity requirement under which a stationary point is a Nash equilibrium. We design and analyze a sampling-enabled projected-gradient-response method, reliant on inexact resolution of a player-level best-response subproblem. Here, by deriving suitable Lipschitzian guarantees on the value function, we derive both asymptotic guarantees for the sequence of generated iterates as well as rate and complexity guarantees for computing a stationary point by appropriate choices of the sampling rate and inexactness sequence.

Nikaido-Isoda function↗

DOE OSTI2024

Coupled Thermo-Hydro-Mechanical Processes in Fractured Rocks: Some Past Scientific Highlights and Future Research Directions

Abstract Coupled thermo-hydro-mechanical (THM) processes in fractured rocks have been a topic of intense scientific research for more than 30 years. The present paper takes a look into the past and highlights some scientific advances which are of an unusual “out-of-the-box” nature, and then looks forward and discusses possible directions of future research in this interesting field of study. Concerning future research directions, we see a trend from a focus on coupled THM processes in single fractures or a few interacting fractures, to the study of coupled THM behavior in complex fracture network systems where the fractures act collectively giving rise to local stress concentration points and points of large pressure gradients. Three examples of future research directions are presented. First is an effort towards identifying characterizing parameters of a fracture network that play a direct controlling role in major coupled THM phenomena (such as induced seismicity and flow channeling), rather than parameters of stochastic distributions of fractures in the network. The second example of research direction is accounting for the heterogeneity and hierarchy of fractures in a fault or fracture zone which has been associated with major THM events in a number of geo-energy projects. The third example is at the opposite end of the first; here it is recognized that in some cases, the coupled THM processes in fractured rocks may be controlled dominantly by only a few key bridges. Identification, characterization, and evaluation of these key bridges should be one of the important research directions in the coming days.

58 GEOSCIENCES↗

NASA NTRS1975

Computation of output feedback gains for linear stochastic systems using the Zangnill-Powell Method

Because conventional optimal linear regulator theory results in a controller which requires the capability of measuring and/or estimating the entire state vector, it is of interest to consider procedures for computing controls which are restricted to be linear feedback functions of a lower dimensional output vector and which take into account the presence of measurement noise and process uncertainty. To this effect a stochastic linear model has been developed that accounts for process parameter and initial uncertainty, measurement noise, and a restricted number of measurable outputs. Optimization with respect to the corresponding output feedback gains was then performed for both finite and infinite time performance indices without gradient computation by using Zangwill's modification of a procedure originally proposed by Powell. Results using a seventh order process show the proposed procedures to be very effective.

Kaufman, H.↗

NASA NTRS1977

Computation of output feedback gains for linear stochastic systems using the Zangwill-Powell method

Kaufman, H.↗