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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

High-Fidelity Modeling of Curbside Driving Behavior in SUMO: Preprint

Recent advances in mobility technologies have considerably increased the need for curbside use and congestion at curb-lanes. At airports and in dense urban centers, the growing adoption of Transportation Network Companies (TNCs), such as Uber and Lyft, has led to an increase in curbside traffic due to the reduction in the use public transit and other shared modes. In dense city areas, the curbside demand and congestion were further augmented by the growing use of e-commerce, which requires home-delivery of goods. To model vehicles' curbside interactions realistically, there is a need for high-fidelity simulation models that can represent the complex interplay of vehicles as they complete pick-up or drop-off trips. Vehicles' curbside behaviors are usually not modeled with high-fidelity in microscopic simulators such Simulation of Urban of Mobility (SUMO). This paper presents such a high-resolution model for vehicle curbside behavior in SUMO, using SUMO's Traci interface. Simulations results demonstrate that the improved curbside behavior captures vehicles' curbside maneuvering more accurately than the default SUMO curbside model, and increases the curbside utilization and capacity.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2022

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

OpenStudio® HPXML workflow [SWR-25-13]

OpenStudio-HPXML allows running residential EnergyPlus™ simulations using an HPXML file for the building description. It is intended to be used by user interfaces or other automated software workflows that automatically produce the HPXML file. OpenStudio-HPXML can accommodate a wide range of different building technologies and geometries. End-to-end simulations typically run in 3-10 seconds, depending on complexity, computer platform and speed, etc. For more information on running simulations, generating HPXML files with the appropriate inputs to run EnergyPlus, etc., please visit the documentation linked below. https://openstudio-hpxml.readthedocs.io/en/latest

Horowitz, Scott↗
NASA NTRS1980

Methods of sound simulation and applications in flight simulators

An overview of methods for electronically synthesizing sounds is presented. A given amount of hardware and computer capacity places an upper limit on the degree and fidelity of realism of sound simulation which is attainable. Good sound realism for aircraft simulators can be especially expensive because of the complexity of flight sounds and their changing patterns through time. Nevertheless, the flight simulator developed at the Research Institute for Human Engineering, West Germany, shows that it is possible to design an inexpensive sound simulator with the required acoustic properties using analog computer elements. The characteristics of the sub-sound elements produced by this sound simulator for take-off, cruise and approach are discussed.

Gaertner, K. P.↗
NASA NTRS1992

Annual sea level variations in the southern tropical Indian Ocean from Geosat and shallow-water simulations

Sea level variations in the Indian Ocean north of 20 deg S are analyzed from Geosat satellite altimeter data in 1987-1988. These observed variations are compared with numerical simulations from a reduced-gravity model forced by observed winds over the same period. The first complex empirical orthogonal function of observed and simulated variations is an annual signal. For this signal, observations and simulations are highly correlated in both time and space. Off-equatorial sea level variations propagate westward and poleward as Rossby waves. The strongest annual variations occur in the southeastern tropical Indian Ocean. The maximum amplitude (about 12 cm) is located at about 90 deg E, 12 deg S, although the wind stress curl is weak there and east of it. The signal propagates from the eastern boundary to the southwest across almost all the basin.

Perigaud, Claire↗
DOE OSTI2020

Simulator for Hydrologic Unstructured Domains (SHUD v1.0): numerical modeling of watershed hydrology with the finite volume method

Abstract. Hydrologic modeling is an essential strategy for understanding and predicting natural flows, particularly where observations are lacking in either space or time or where complex terrain leads to a disconnect in the characteristic time and space scales of overland and groundwater flow. However, significant difficulties remain for the development of efficient and extensible modeling systems that operate robustly across complex regions. This paper introduces the Simulator for Hydrologic Unstructured Domains (SHUD), an integrated, multiprocess, multiscale, flexible-time-step model, in which hydrologic processes are fully coupled using the finite volume method. SHUD integrates overland flow, snow accumulation/melt, evapotranspiration, subsurface flow, groundwater flow, and river routing, thus allowing physical processes in general watersheds to be realistically captured. SHUD incorporates one-dimensional unsaturated flow, two-dimensional groundwater flow, and a fully connected river channel network with hillslopes supporting overland flow and baseflow. The paper introduces the design of SHUD, from the conceptual and mathematical description of hydrologic processes in a watershed to the model's computational structures. To demonstrate and validate the model performance, we employ three hydrologic experiments: the V-catchment experiment, Vauclin's experiment, and a model study of the Cache Creek Watershed in northern California. Ongoing applications of the SHUD model include hydrologic analyses of hillslope to regional scales (1 m2 to 106 km2), water resource and stormwater management, and interdisciplinary research for questions in limnology, agriculture, geochemistry, geomorphology, water quality, ecology, climate and land-use change. The strength of SHUD is its flexibility as a scientific and resource evaluation tool where modeling and simulation are required.

58 GEOSCIENCES↗
DOE OSTI2025

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗
NASA NTRS2000

An Automated Approach to Very High Order Aeroacoustic Computations in Complex Geometries

Computational aeroacoustics requires efficient, high-resolution simulation tools. And for smooth problems, this is best accomplished with very high order in space and time methods on small stencils. But the complexity of highly accurate numerical methods can inhibit their practical application, especially in irregular geometries. This complexity is reduced by using a special form of Hermite divided-difference spatial interpolation on Cartesian grids, and a Cauchy-Kowalewslci recursion procedure for time advancement. In addition, a stencil constraint tree reduces the complexity of interpolating grid points that are located near wall boundaries. These procedures are used to automatically develop and implement very high order methods (>15) for solving the linearized Euler equations that can achieve less than one grid point per wavelength resolution away from boundaries by including spatial derivatives of the primitive variables at each grid point. The accuracy of stable surface treatments is currently limited to 11th order for grid aligned boundaries and to 2nd order for irregular boundaries.

Dyson, Rodger W.↗
NASA NTRS2022

National Campaign (NC)-1 Strategic Conflict Management Simulation (X4) Final Report

Urban Air Mobility (UAM) enables highly automated, cooperative, passenger or cargo-carrying air transportation services in and around urban areas. UAM is a subset of the Advanced Air Mobility (AAM) concept under development by the National Aeronautics and Space Administration (NASA), the Federal Aviation Administration (FAA), and industry. The Strategic Conflict Management (SCM) Simulation, dubbed “X4”, was conducted between July 2021 and June 2022 by NASA with the FAA and industry to evolve the Provider of Services for UAM (PSU) that will be needed to ensure initial UAM operations can scale in the National Airspace System (NAS). The FAA UAM Concept of Operations (ConOps) v1 [1] served as an initial guiding document for the X4 airspace management system design to ensure the architecture supports testing of services provided by third-party service providers. To that end, the X4 architecture leveraged concepts and technologies developed for Unmanned Aircraft System (UAS) Traffic Management (UTM) while also developing and testing new capabilities and services needed for UAM. The architecture included an initial prototype of the FAA-Industry Exchange Protocol (FIDXP), third-party services such as the PSUs, and Discovery and Synchronization Service (DSS), and other new services such as Demand-Capacity Balancing (DCB) to facilitate UAM strategic conflict management. During X4, NASA led discussions and collaborated with seven industry airspace partners to develop initial airspace management concepts for UAM that drove what would be tested and evaluated during the simulations. The initial capabilities defined for PSU leveraged UTM UAS Service Supplier (USS) as a starting point and evolved to meet UAM requirements. These discussions were also an opportunity for NASA to collaborate with industry to develop a set of initial Community-Based Rules (CBRs). These CBRs enabled how UAM traffic would be cooperatively managed among UAM operators. The collaborative, iterative process of developing CBRs with industry during X4 provided insight into the challenges involved and identified the need for a suitable and effective forum for future CBR development. In parallel with these discussions, NASA conducted a series of seven software sprints and two collaborative simulations with the airspace partners that built up in complexity. Over the course of the year, all seven partners successfully completed all the sprints by demonstrating the required capabilities. They also participated in the two collaborative simulations to demonstrate how multiple PSUs could work together in a collaborative, more complex environment with higher traffic density. The X4 simulation accomplished NASA's objectives and helped advance the development of the seven participating PSUs. The lessons learned provided insight into key elements of the UAM Notional Architecture from the FAA ConOps v1 [1] and UTM technologies when applied to UAM: - Having a Concept of Use (ConUse) defined prior to the activity would accelerate the time and effort from concept development to testing. - While the UAM Notional Architecture provided a starting point for a federated architecture that support services provided by third-party providers, the USS and PSU differed in their capability definitions for operational intent submission and sharing, conformance monitoring, airspace authorization, strategic conflict management, airspace constraints and dynamic replanning. - While existing DSS developed for UTM provided a way for PSU and other UAM services (such as DCB) to discover relevant operations from each other, additional complexity and challenges were found during X4 testing and illuminated the need for a more suitable solution for UAM. Industry can leverage the results of this demonstration to accelerate UAM requirements, CBRs, and standards development. The FAA and other government municipalities and agencies will be able to leverage results to inform future policies and identify additional gaps that require further analysis, moving toward operationalization of UAM.

Urban Air Mobility↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A coupled fluid-mechanical workflow to simulate the directed energy deposition additive manufacturing process

Simulation of additive manufacturing processes can provide essential insight into material behavior, residual stress, and ultimately, the performance of additively manufactured parts. In this work, we describe a new simulation based workflow utilizing both solid mechanics and fluid mechanics based formulations within the finite element software package SIERRA (Sierra Solid Mechanics Team in Sierra/Solid Mechanics 4.52 User’s Guide SAND2019-2715. Technical report, Sandia National Laboratories, 2011) to enable integrated simulations of directed energy deposition (DED) additive manufacturing processes. In this methodology, a high-fidelity fluid mechanics based model of additive manufacturing is employed as the first step in a simulation workflow. This fluid model uses a level set field to track the location of the boundary between the solid material and background gas and precisely predicts temperatures and material deposition shapes from additive manufacturing process parameters. Next, the resulting deposition shape and temperature field from the fluid model are then mapped into a solid mechanics formulation to provide a more accurate surface topology for radiation and convection boundary conditions and a prescribed temperature field. Solid mechanics simulations are then conducted to predict the evolution of material stresses and microstructure within a part. By combining thermal history and deposition shape from fluid mechanics with residual stress and material property evolutions from solid mechanics, additional fidelity and precision are incorporated into additive manufacturing process simulations providing new insight into complex DED builds.

36 MATERIALS SCIENCE↗
DOE OSTI2023

QuDPy: A Python-based tool for computing ultrafast non-linear optical responses

Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have benefited multiple disciplines, including chemistry, biology, and physics. However, for the accurate interpretation of the corresponding multi-dimensional spectra, there is a need for precise quantum dynamical simulations based on model Hamiltonians. In this article, we present the initial release of our code, QuDPy (Quantum Dynamics in Python), which provides a robust numerical platform for performing quantum dynamics simulations based on model systems, including open quantum systems. Furthermore, a distinguishing feature of our approach is the ability to specify various high-order optical response pathways in the form of double-sided Feynman diagrams through a straightforward input syntax. This syntax outlines the time-ordering of ket-sided or bra-sided optical interactions acting on the time-evolving density matrix of the system. We utilize the quantum dynamics capabilities of QuTip to simulate the spectral response of complex systems, allowing us to compute virtually any $n$-th order optical response of the model system. To illustrate the utility of our approach, we provide a series of example calculations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Dual frequency comb spectroscopy of solid fuel pyrolysis and combustion: Quantifying the influence of moisture content in Douglas fir

As the fire research community develops multi-scale models to predict the spread of wildland fires, there is a need for well-controlled, small-scale experiments which provide benchmark data and fundamental understanding of the effects of key parameters on the combustion of wildland fuels. Here, we implement a unique suite of non-intrusive, quantitative diagnostics that simultaneously measure mass loss, surface temperature, in situ gas temperature and water vapor concentration, including the first implementation of dual frequency comb spectroscopy for the study of solid fuels. As a demonstration, we examine the effect of fuel moisture content on the burning of Douglas fir wood samples that are ignited under constant radiative heat flux from a cone calorimeter to provide benchmark data for multi-scale models. Peak flame temperatures 3 mm above the sample surface measured with the dual frequency comb laser spectrometer are in excess of 1200 K. The flame temperature decreases by over 150 K as fuel moisture content increases from 0.7% to 40%. This work demonstrates a platform for simultaneous, quantitative measurements of well-controlled small-scale experiments which provide benchmark data for the development of advanced modeling and simulations capable of capturing the complex physics present in wildland fire systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

The solubility of ErPO 4 and Er speciation in hydrothermal fluids at varying pH and salinity between 350 and 450 °C

The rare earth elements (REE) are important for the green-energy transition and can be incorporated into the REE phosphates, such as xenotime-(Y), which also hosts heavy REE (Tb– Lu). Xenotime-(Y) is a common accessory mineral in metamorphic rocks and a range of mineral deposits where it controls the mobility of heavy REE, however, the impact of high temperature aqueous fluids on the behavior of heavy REE is largely unknown. Thermodynamic modeling can be utilized as a tool to predict the mobility of REE in hydrothermal aqueous fluids, but must be supported by accurate experimental data. Here, we measured the solubility of endmember synthetic xenotime-structured ErPO4 in NaCl-HCl-NaOH-bearing aqueous solutions at 350 °C and water vapor saturation pressure, at 400 and at 450 °C and 500 bar using batch-type Inconel reactors. Erbium speciation was investigated as a function of pH from 2.8 to 8, where Er chloride species are predominant at acidic conditions (pH <3) and Er hydroxyl complexes are predominant at near- neutral to alkaline conditions (pH >3). At pH 7–9, the measured ErPO 4 solubility (-9.8 to -7.5 log m Er ) is up to 2.5 orders of magnitude lower than thermodynamic predictions (-9.4 to -6.7 log m Er ) using existing thermodynamic databases. At pH 2–3, the predicted ErPO 4 solubility is ~0.5 orders of magnitude higher at 350 °C and ~1 order of magnitude lower at 450 °C compared to experimentally measured Er concentrations. The thermodynamic properties of aqueous Er species were therefore revised in this study. The partial molal Gibbs energy of formation (Δ f G 0 T,P ) for aqueous Er hydroxyl and chloride species are optimized using GEMSFITS and the logarithmic formation constants (logβ n ( Cl,OH) ) were derived at each experimental temperature and pressure. The updated thermodynamic properties for Er hydroxyl species (Er(OH) +2 , Er(OH) 2 + , and Er(OH) 3 0 ) show that their stability shifts to more acidic conditions at and below 400 °C. The Er chloride species (ErCl +2 and ErCl 2 + ) show increased stability compared to Er hydroxyl species at temperatures of 450 °C and 0.01 mol/kg NaCl. The updated thermodynamic properties are implemented into the GEM-Selektor modeling package to investigate the mobility of Er in saline hydrothermal fluids in equilibrium with alkaline rocks. Importantly, the updated properties for Er hydroxyl species result in low Er solubility at rock equilibrated pH conditions due to an expanded hydroxyl predominance zone, but lower aqueous complex stability overall, whereas previous models suggest greater stability for aqueous Er species. Furthermore, ErPO 4 solubility increases with decreasing temperature due to the deprotonation of HCl, which increases the acidity of hydrothermal fluids and the availability of Cl - to complex with the REE. These simulations highlight how fluid-rock reaction and temperature affect the mobility of REE in hydrothermal ore-forming systems.

58 GEOSCIENCES↗
DOE OSTI2023

Accelerating discrete dislocation dynamics simulations with graph neural networks

Discrete dislocation dynamics (DDD) is a widely employed computational method to study plasticity at the mesoscale that connects the motion of dislocation lines to the macroscopic response of crystalline materials. However, the computational cost of DDD simulations remains a bottleneck that limits its range of applicability. Here, we introduce a new DDD-GNN framework in which the expensive time-integration of dislocation motion is entirely substituted by a graph neural network (GNN) model trained on DDD trajectories. As a first application, we demonstrate the feasibility and potential of our method on a simple yet relevant model of a dislocation line gliding through an array of obstacles. We show that the DDD-GNN model is stable and reproduces very well unseen ground-truth DDD simulation responses for a range of straining rates and obstacle densities, without the need to explicitly compute nodal forces or dislocation mobilities during time-integration. Our approach opens new promising avenues to accelerate DDD simulations and to incorporate more complex dislocation motion behaviors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Unraveling the 2021 Central Tennessee flood event using a hierarchical multi-model inundation modeling framework

Flood prediction systems need hierarchical atmospheric, hydrologic, and hydraulic models to predict rainfall, runoff, streamflow, and floodplain inundation. The accuracy of such systems depends on the error propagation through the modeling chain, sensitivity to input data, and choice of models. In this study, we used multiple precipitation forcings (hindcast and forecast) to drive hydrologic and hydrodynamic models to analyze the impacts of various drivers on the estimates of flood inundation depth and extent. We implement this framework to unravel the August 2021 extreme flooding event that occurred in Central Tennessee, USA. We used two radar-based quantitative precipitation estimates (STAGE4 and MRMS) as well as quantitative precipitation forecasts (QPF) from the National Weather Service Weather Prediction Center (WPC) to drive a series of models in the hierarchical framework, including the Variable Infiltration Capacity (VIC) land surface model, the Routing Application for Parallel Computation of Discharge (RAPID) river routing model, and the AutoRoute and TRITON inundation models. An evaluation with observed high-water marks demonstrates that the framework can reasonably simulate flood inundation. Despite the complex error propagation mechanism of the modeling chain, we show that inundation estimates are most sensitive to rainfall estimates. Most notably, QPF significantly underestimates flood magnitudes and inundations leading to unanticipated severe flooding for all stakeholders involved in the event. Finally, we discuss the implications of the hydrodynamic modeling framework for real-time flood forecasting.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Toward an event-level analysis of hadron structure using differential programming

Reconstructing the internal properties of hadrons in terms of fundamental quark and gluon de- grees of freedom is a central goal in nuclear and particle physics. This effort lies at the core of major experimental programs, such as the Jefferson Lab 12 GeV program and the upcoming Electron-Ion Collider. A primary challenge is the inherent inverse problem: converting large-scale observational data from collision events into the fundamental QCD-defined densities that characterize the micro- scopic structure of hadronic systems. Recent advances in AI and machine learning have opened new avenues for addressing this challenge using deep learning techniques. A particularly promising direction is the integration of complex theoretical calculations and experimental simulations into a unified framework capable of reconstructing these densities directly from event-level information. In this document, we introduce a key algorithm called LOITS, which enables differentiable program- ming within such a framework, facilitating the use of AI/ML techniques to solve the inverse problem of QCF reconstruction at the event level.

Braga, Kevin [College of William and Mary, William↗
DOE OSTI2021

Evaluating bloom potential of the green-tide forming alga Ulva ohnoi under ocean acidification and warming

Herein we discuss the occurrence of green-tides, whose bloom potential may be increased by various human activities and biogeochemical process, results in enormous economic losses and ecosystem collapse. In this study, we investigated the ecophysiology of the subtropical green-tide forming alga, Ulva ohnoi complex (hereafter: U. ohnoi), under simulated future ocean conditions in order to predict its bloom potential using photosynthesis and growth measurements, and stable isotope analyses. Our mesocosm system included four experimental conditions that simulated the individual and combined effects of elevated CO 2 and temperature, namely control (450 μatm CO 2 & 20 °C), acidification (900 μatm CO 2 & 20 °C), warming (450 μatm CO 2 & 25 °C), and greenhouse (900 μatm CO 2 & 25 °C). Photosynthetic electron transport rates (rETR) increased significantly under acidification conditions, but net photosynthesis and growth were not affected. In contrast, rETR, net photosynthesis, and growth all decreased significantly under elevated temperature conditions (i.e. both warming and greenhouse). These results represent the imbalance of energy metabolism between electron transport and O 2 production that may be expected under ocean acidification conditions. This imbalance appears to be related to carbon and nitrogen assimilation by U. ohnoi. In particular, 13 C and 15 N discrimination data suggest U. ohnoi prefers CO 2 and NH 4 + over HCO 3 - and NO 3 - as sources of carbon and nitrogen, respectively, and this results in increased N content in the thallus under ocean acidification conditions. Together, our results suggest a trade-off in which the bloom potential of U. ohnoi could increase under ocean acidification due to greater N accumulation and through the saving of energy during carbon and nitrogen metabolism, but that elevated temperatures could decrease U. ohnoi's bloom potential through a decrease in photosynthesis and growth.

54 ENVIRONMENTAL SCIENCES↗