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At least 829 records · Page 46

Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model: Modeling Archive

This archive contains the data and Python scripts required to reproduce the analyses and figures in the study: Gomez-Velez, J. D., Rathore, S. S., Cohen, M. J., & Painter, S. L. (2025). Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model. Submitted to Water Resources Research. The analysis utilizes the subgrid model Advection Dispersion Equation with Lagrangian Subgrids (ADELS) implemented in the Advanced Terrestrial Simulator (ATS; https://amanzi.github.io/ats/stable/). In this case, the ATS and Amanzi versions are (1) ATS version 1.5.1_f5ba18f8 and (2) Amanzi version 1.6-dev_53444cca4. The repository includes a Jupyter Notebook and the necessary data (Pandas DataFrames stored as pickle files) to generate the figures for the manuscript. Additionally, it contains Python scripts to create ATS input files, run the ATS simulations, and post-process the results. Finally, it provides routines for parameter estimation using the Single-Station Metabolism (SSM) model with the Differential Evolution Adaptive Metropolis (DREAM) Markov Chain Monte Carlo (MCMC) algorithm with ZS enhancements (DREAM-ZS).

54 ENVIRONMENTAL SCIENCES↗

Yttrium solid phase equation of state with uncertainty quantification

We discuss the development of an equation of state (EOS) for solid yttrium up to roughly 80 GPa. The EOS makes use of different experimental datasets, including measurements of the isobaric density, isobaric specific heat, room temperature isotherm, and principal shock Hugoniot. The fitting procedure is carried out using Markov Chain Monte Carlo (MCMC), where we fit model parameters for both the cold curve and ion thermal models simultaneously. The results show close agreement with experimental data and provide meaningful uncertainty estimates on the model parameters. This work serves as a first step towards a multiphase EOS for yttrium, which will include higher pressure solid phases (> 80 GPa), as well as modeling of the liquid phase.

36 MATERIALS SCIENCE↗

Earth-Centered, Earth-Fixed Inertial Navigation System & Error-State Kalman Filter Reference Manual

This is a self-contained reference document that derives the equations necessary to build a combined inertial navigation system and error-state Kalman filter. Coordinate transform, linear time invariant system, inertial sensing, and error-state Kalman filtering theory is built up from first principles. This theory is then leveraged to derive the system equations for two combined inertial navigation system and error-state Kalman filters: (1) a 15-state system modeling white-noise-integrating accelerometer and gyroscope biases, and (2) a 39-state system modeling static and first-order Gauss-Markov accelerometer and gyroscope biases, scale factor errors, and cross-axis sensitivity errors.

42 ENGINEERING↗

Perseveration effects in detection tasks with correlated decision intervals

An investigation of the behavior of the human decisionmaker is described for a task related to the problem of a pilot using a traffic situation display to avoid collisions. This sequential signal detection task is characterized by highly correlated signals with time varying strength. Experimental results are presented and the behavior of the observers is analyzed using the theory of Markov processes and classical signal detection theory. Mathematical models are developed which describe the main result of the experiment: that correlation in sequential signals induced perseveration in the observer response and a strong tendency to repeat their previous decision, even when they were wrong.

Gai, E. G.↗

Local structure graph models with higher-order dependence

Local structure graph models (LSGMs) describe random graphs and networks as a Markov random field (MRF)—each graph edge has a specified conditional distribution dependent on explicit neighbourhoods of other graph edges. Centered parameterizations of LSGMs allow for direct control and interpretation of parameters for large- and small-scale structures (e.g., marginal means vs. dependence). Here, we extend this parameterization to account for triples of dependent edges and illustrate the importance of centered parameterizations for incorporating covariates and interpreting parameters. Using a MRF framework, common exponential random graph models are also shown to induce conditional distributions without centered parameterizations and thereby have undesirable features. This work attempts to advance graph models through conditional model specifications with modern parameterizations, covariates and higher-order dependencies.

97 MATHEMATICS AND COMPUTING↗

Cellular Statistical Models of Broken Cloud Fields. Part IV: Effects of Pixel Size on Idealized Satellite Observations

In the fourth part of our “Cellular Statistical Models of Broken Cloud Fields” series we use the binary Markov processes framework for quantitative investigation of the effects of low resolution of idealized satellite observations on the statistics of the retrieved cloud masks. We assume that the cloud fields are Markovian and are characterized by the “actual” cloud fraction (CF) and scale length. We use two different models of observations: a simple discrete-point sampling and a more realistic “pixel” protocol. The latter is characterized by a state attribution function (SAF) which has the meaning of the probability that the pixel with a certain CF is declared cloudy in the observed cloud mask. The stochasticity of the SAF means that the cloud/clear attribution is not ideal and can be affected by external or unknown factors. We show that the observed cloud masks can be accurately described as Markov chains of pixels and use the master-matrix formalism (introduced in Part III of the series) for analytical computation of their parameters: the “observed” CF and scale length. This procedure allows us to establish a quantitative relationship (which is pixel-size dependent) between the actual and the observed cloud-field statistics. The feasibility of restoring the former from the latter is considered. The adequacy of our analytical approach to idealized observations is evaluated using numerical simulations. Comparison of the observed parameters of the simulated datasets with their theoretical expectations showed an agreement within 0.005 for the CF, while for the scale length it is within 1% in the sampling case and within 4% in the pixel case.

Mikhail D. Alexandrov↗

Predicting rare events using neural networks and short-trajectory data

Estimating the likelihood, timing, and nature of events is a major goal of modeling stochastic dynamical systems. When the event is rare in comparison with the timescales of simulation and/or measurement needed to resolve the elemental dynamics, accurate prediction from direct observations becomes challenging. In such cases a more effective approach is to cast statistics of interest as solutions to Feynman-Kac equations (partial differential equations). Here, we develop an approach to solve Feynman-Kac equations by training neural networks on short-trajectory data. Our approach is based on a Markov approximation but otherwise avoids assumptions about the underlying model and dynamics. This makes it applicable to treating complex computational models and observational data. Additionally, we illustrate the advantages of our method using a low-dimensional model that facilitates visualization, and this analysis motivates an adaptive sampling strategy that allows on-the-fly identification of and addition of data to regions important for predicting the statistics of interest. Finally, we demonstrate that we can compute accurate statistics for a 75-dimensional model of sudden stratospheric warming. This system provides a stringent test bed for our method.

97 MATHEMATICS AND COMPUTING↗

Scalable posterior approximations for large-scale Bayesian inverse problems via likelihood-informed parameter and state reduction

Two prime bottlenecks to the solution of large-scale Bayesian inverse problems are the scaling of posterior sampling algorithms to high-dimensional parameter spaces and the computational cost of forward model evaluations. However, incomplete or noisy data, the state variation and parameter dependence of the forward model, and correlations in the prior collectively provide useful structure that can be exploited for dimension reduction in this setting—both in the parameter space of the inverse problem and in the state space of the forward model. To this end, we show how to jointly construct low-dimensional subspaces of the parameter space and the state space in order to accelerate the Bayesian solution of the inverse problem. As a byproduct of state dimension reduction, we also show how to identify low-dimensional subspaces of the data in problems with high-dimensional observations. These subspaces enable approximation of the posterior as a product of two factors: (i) a projection of the posterior onto a low-dimensional parameter subspace, wherein the original likelihood is replaced by an approximation involving a reduced model; and (ii) the marginal prior distribution on the high-dimensional complement of the parameter subspace. We introduce and compare several strategies for constructing these subspaces using only a limited number of forward and adjoint model simulations. The resulting posterior approximations can rapidly be characterized using standard sampling techniques, e.g., Markov chain Monte Carlo. Two numerical examples demonstrate the accuracy and efficiency of our approach: inversion of an integral equation in atmospheric remote sensing, where the data dimension is very high; and the inference of a heterogeneous transmissivity field in a groundwater system, which involves a partial differential equation forward model with high dimensional state and parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Flood hazard model calibration using multiresolution model output

Riverine floods pose a considerable risk to many communities. Improving flood hazard projections has the potential to inform the design and implementation of flood risk management strategies. Current flood hazard projections are uncertain, especially due to uncertain model parameters. Calibration methods use observations to quantify model parameter uncertainty. With limited computational resources, researchers typically calibrate models using either relatively few expensive model runs at high spatial resolutions or many cheaper runs at lower spatial resolutions. This leads to an open question: is it possible to effectively combine information from the high and low resolution model runs? We propose a Bayesian emulation–calibration approach that assimilates model outputs and observations at multiple resolutions. As a case study for a riverine community in Pennsylvania, we demonstrate our approach using the LISFLOOD-FP flood hazard model. Here, the multiresolution approach results in improved parameter inference over the single resolution approach in multiple scenarios. Results vary based on the parameter values and the number of available models runs. Our method is general and can be used to calibrate other high dimensional computer models to improve projections.

multiresolution↗

Tau-REx I: A next generation retrieval code for exoplanetary atmospheres

Spectroscopy of exoplanetary atmospheres has become a well established method for the characterization of extrasolar planets. We here present a novel inverse retrieval code for exoplanetary atmospheres. T-REx(Tau Retrieval for Exoplanets) is a line-by-line radiative transfer fully Bayesian retrieval framework. T-REx includes the following features:(1) the optimized use of molecular line lists from the ExoMol project; (2) an unbiased atmospheric composition prior selection, through custom built pattern recognition software; (3) the use of two independent algorithms to fully sample the Bayesian likelihood space: nested sampling as well as a more classical Markov Chain Monte Carlo approach; (4) iterative Bayesian parameter and model selection using the full Bayesian Evidence as well as the Savage–Dickey Ratio for nested models; and (5) the ability to fully map very large parameter spaces through optimal code parallelization and scalability to cluster computing. In this publication we outline the T-REx framework and demonstrate, using a theoretical hot-Jupiter transmission spectrum, the parameter retrieval and model selection. We investigate the impact of signal-to-noise ratio and spectral resolution on the retrievability of individual model parameters, both in terms of error bars on the temperature and molecular mixing ratios as well as its effect on the model’s global Bayesian evidence.

79 ASTRONOMY AND ASTROPHYSICS↗

A Global Analysis of Light and Charge Yields in Liquid Xenon

Here, we present an updated model of light and charge yields from nuclear recoils in liquid xenon with a simultaneously constrained parameter set. A global analysis is performed using measurements of electron and photon yields compiled from all available historical data, as well as measurements of the ratio of the two. These data sweep over energies from keV and external applied electric fields from V/cm. The model is constrained by constructing global cost functions and using a simulated annealing algorithm and a Markov Chain Monte Carlo approach to optimize and find confidence intervals on all free parameters in the model. This analysis contrasts with previous work in that we do not unnecessarily exclude datasets nor impose artificially conservative assumptions, do not use spline functions, and reduce the number of parameters used in NEST v 0.98. Here, we report our results and the calculated best-fit charge and light yields. These quantities are crucial to understanding the response of liquid xenon detectors in the energy regime important for rare event searches such as the direct detection of dark matter particles.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Lens covariance effects on likelihood analyses of CMB power spectra

Non-Gaussian correlations induced in CMB power spectra by gravitational lensing needs to be included in likelihood analyses for future CMB experiments. We present a simple but accurate likelihood model which includes these correlations and use it for Markov Chain Monte Carlo parameter estimation from simulated lensed CMB maps in the context of ΛCDM and extensions which include the sum of neutrino masses or the dark energy equation of state w. If lensing-induced covariance is not taken into account for a CMB-S4 type experiment, the errors for one combination of parameters in each case would be underestimated by more then a factor of two and lower limits on w could be misestimated substantially. The frequency of falsely ruling out the true model or finding tension with other data sets would also substantially increase. Our analysis also enables a separation of lens and unlensed information from CMB power spectra, which provides for consistency tests of the model and, if combined with other such measurements, a nearly lens-sample-variance free test for systematics and new physics in the unlensed spectrum. This parameterization also leads to a simple effective likelihood that can be used to assist model building in case consistency tests of ΛCDM fail.

79 ASTRONOMY AND ASTROPHYSICS↗

Integrating Chlorophyll fapar and Nadir Photochemical Reflectance Index from EO-1/Hyperion to Predict Cornfield Daily Gross Primary Production

The concept of light use efficiency (Epsilon) and the concept of fraction of photosynthetically active ration (PAR) absorbed for vegetation photosynthesis (PSN), i.e., fAPAR (sub PSN), have been widely utilized to estimate vegetation gross primary productivity (GPP). It has been demonstrated that the photochemical reflectance index (PRI) is empirically related to ε. An experimental US Department of Agriculture (USDA) cornfield in Maryland was selected as our study field. We explored the potential of integrating fAPAR(sub chl) (defined as the fraction of PAR absorbed by chlorophyll) and nadir PRI (PRI(sub nadir)) to predict cornfield daily GPP. We acquired nadir or near-nadir EO-1/Hyperion satellite images that covered the cornfield and took nadir in-situ field spectral measurements. Those data were used to derive the PRI(sub nadir) and fAPAR (sub chl). The fAPAR (sub chl) is retrieved with the advanced radiative transfer model PROSAIL2 and the Metropolis approach, a type of Markov Chain Monte Carlo (MCMC) estimation procedure. We define chlorophyll light use efficiency Epsilon (sub chl) as the ratio of vegetation GPP as measured by eddy covariance techniques to PAR absorbed by chlorophyll (Epsilon(sub chl) = GPP/APAR (sub chl). Daily Epsilon (sub chl) retrieved with the EO-1 Hyperion images was regressed with a linear equation of PRI (sub nadir) Epsilon (sub chl) = Alpha × PRI (sub nadir) + Beta). The satellite Epsilon(sub chl- PRI (sub nadir) linear relationship for the cornfield was implemented to develop an integrated daily GPP model [GPP = (Alpha × PRI(sub nadir) + Beta) × fAPAR (sub chl) × PAR], which was evaluated with fAPAR (sub chl) and PRI (sub nadir) retrieved from field measurements. Daily GPP estimated with this fAPAR (sub chl-) PRI (nadir) integration model was strongly correlated with the observed tower in-situ daily GPP (R(sup 2) = 0.93); with a root mean square error (RMSE) of 1.71 g C mol−(sup -1) PPFD and coefficient of variation (CV) of 16.57%. Both seasonal Epsilon (sub chl) and PRI (sub nadir) were strongly correlated with fAPAR (sub chl ) retrieved from field measurements, which indicates that chlorophyll content strongly affects seasonal epsilon (sub chl) and PRI (sub nadir). We demonstrate the potential capacity to monitor GPP with space-based visible through shortwave infrared (VSWIR) imaging spectrometers such as NASA's soon to be decommissioned EO- 1/Hyperion and the future Hyperspectral Infrared Imager (HyspIRI).

HyspIRI↗

Improvement of observer/Kalman filter identification (OKID) by residual whitening

This paper presents a time-domain method to identify a state space model of a linear system and its corresponding observer/Kalman filter from a given set of general input-output data. The identified filter has the properties that its residual is minimized in the least squares sense, orthogonal to the time-shifted versions of itself, and to the given input-output data sequence. The connection between the state space model and a particular auto-regressive moving average description of a linear system is made in terms of the Kalman filter and a deadbeat gain matrix. The procedure first identifies the Markov parameters of an observer system, from which a state space model of the system and the filter gain are computed. The developed procedure is shown to improve results obtained by an existing observer/Kalman filter identification method, which is based on an auto-regressive model without the moving average terms. Numerical and experimental results are presented to illustrate the proposed method.

Phan, Minh↗

Optimal carbon storage reservoir management through deep reinforcement learning

Model-based optimization plays a central role in energy system design and management. The complexity and high-dimensionality of many process-level models, especially those used for geosystem energy exploration and utilization, often lead to formidable computational costs when the dimension of decision space is also large. This work adopts elements of recently advanced deep learning techniques to solve a sequential decision-making problem in applied geosystem management. Specifically, a deep reinforcement learning framework was formed for optimal multiperiod planning, in which a deep Q-learning network (DQN) agent was trained to maximize rewards by learning from high-dimensional inputs and from exploitation of its past experiences. To expedite computation, deep multitask learning was used to approximate high-dimensional, multistate transition functions. Both DQN and deep multitask learning are pattern based. As a demonstration, the framework was applied to optimal carbon sequestration reservoir planning using two different types of management strategies: monitoring only and brine extraction. Both strategies are designed to mitigate potential risks due to pressure buildup. Results show that the DQN agent can identify the optimal policies to maximize the reward for given risk and cost constraints. Finally, experiments also show that knowledge the agent gained from interacting with one environment is largely preserved when deploying the same agent in other similar environments.

15 GEOTHERMAL ENERGY↗

Slope-Aspect Induced Climate Differences Influence How Water Is Exchanged Between the Land and Atmosphere

Cross-slope climate differences in the midlatitudes are ecologically important, and impact vegetation-mediated water balance between the earth surface and the atmosphere. We made high-resolution in situ observations of air temperature, relative humidity, soil moisture, insolation, and sap velocity observations on 14 Pacific madrone trees (Arbutus menziesii) spanning adjacent north and south slopes at the University of California's Angelo Coast Range Reserve. To understand the cross-slope response of sap velocity, a proxy for transpiration, to microclimate, we modeled the sap velocity on each slope using a transpiration model driven by ambient environment and parameterized with a Markov Chain Monte Carlo parameter estimation process. The results show that trees on opposing slopes do not follow a shared pattern of physiological response to transpiration drivers. This means that the observed sap velocity differences are not due entirely to observed microclimate differences, but also due to population-level physiological differences, which indicates acclimation to inhabited microclimate. While our present data set and analytical tools do not identify mechanisms of acclimation, we speculate that differing proportions of sun-adapted and shade-adapted leaves, differences in stomatal regulation, and cross-slope root zone moisture differences could explain some of the observed and modeled differences.

54 ENVIRONMENTAL SCIENCES↗

Unifying Model-Based and Reactive Programming within a Model-Based Executive

Real-time, model-based, deduction has recently emerged as a vital component in AI's tool box for developing highly autonomous reactive systems. Yet one of the current hurdles towards developing model-based reactive systems is the number of methods simultaneously employed, and their corresponding melange of programming and modeling languages. This paper offers an important step towards unification. We introduce RMPL, a rich modeling language that combines probabilistic, constraint-based modeling with reactive programming constructs, while offering a simple semantics in terms of hidden state Markov processes. We introduce probabilistic, hierarchical constraint automata (PHCA), which allow Markov processes to be expressed in a compact representation that preserves the modularity of RMPL programs. Finally, a model-based executive, called Reactive Burton is described that exploits this compact encoding to perform efficIent simulation, belief state update and control sequence generation.

Williams, Brian C.↗