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All sources NASA NTRS DOE OSTI

DOE OSTI2020

MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX

Cryogenic electron microscopy (cryo-EM) offers the unique potential to capture conformational heterogeneity, by solving multiple three-dimensional classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport-based metric to interpolate barycenters between EM maps and produce morphing trajectories.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Ion temperature clamping in Wendelstein 7-X electron cyclotron heated plasmas

The neoclassical transport optimization of the Wendelstein 7-X stellarator has not resulted in the predicted high energy confinement of gas fueled electron-cyclotron-resonance-heated (ECRH) plasmas as modelled in (Turkin et al 2011 Phys. Plasmas 18 022505) due to high levels of turbulent heat transport observed in the experiments. The electron-turbulent-heat transport appears non-stiff and is of the electron temperature gradient (ETG)/ion temperature gradient (ITG) type (Weir et al 2021 Nucl. Fusion 61 056001). As a result, the electron temperature T e can be varied freely from 1 keV–10 keV within the range of P ECRH = 1–7 MW, with electron density n e values from 0.1–1.5 × 10 20 m –3 . By contrast, in combination with the broad electron-to-ion energy-exchange heating profile in ECRH plasmas, ion-turbulent-heat transport leads to clamping of the central ion temperature at T i ~ 1.5 keV ± 0.2 keV. In a dedicated ECRH power scan at a constant density of $\langle n_{e} \rangle$ = 7 × 10 19 m –3 , an apparent 'negative ion temperature profile stiffness' was found in the central plasma for (r/a < 0.5), in which the normalized gradient ∇T i /T i decreases with increasing ion heat flux. The experiment was conducted in helium, which has a higher radiative density limit compared to hydrogen, allowing a broader power scan. This 'negative stiffness' is due to a strong exacerbation of turbulent transport with an increasing ratio of T e /T i in this electron-heated plasma. This finding is consistent with electrostatic microinstabilities, such as ITG-driven turbulence. Theoretical calculations made by both linear and nonlinear gyro-kinetic simulations performed by the GENE code in the W7-X three-dimensional geometry show a strong enhancement of turbulence with an increasing ratio of T e /T i . The exacerbation of turbulence with increasing T e /T i is also found in tokamaks and inherently enhances ion heat transport in electron-heated plasmas. This finding strongly affects the prospects of future high-performance gas-fueled ECRH scenarios in W7-X and imposes a requirement for turbulence-suppression techniques.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Optimizing lane reversals in transportation networks to reduce traffic congestion: A global optimization approach

This paper studies how to reduce the overall travel time of commuters in a transportation network by reversing the direction of some lanes in the network using a macroscopic network-wide perspective. Similar to the Network Design Problem, the lane reversal problem has been shown to be NP-hard given the dependence of the users’ route selection on the lane direction decision. Herein, we propose and compare three efficient methods to solve the routing and lane reversal problem jointly. First, we introduce an alternating method that decouples the routing and lane assignment problems. Second, we propose a Frank–Wolfe method that jointly takes gradient steps to adjust both the lane assignment and routing decisions. Third, we propose a convex approximation method that uses a threshold-based approach to convexify the joint routing and lane reversal objective. The convex approximation method is advantageous since it finds a global optimum solution for the approximated problem and it enables the possibility to include linear constraints. Using this method, we extend the main formulation to be able to limit a maximum number of reversed lanes, as well as to incorporate multiple origin–destination (OD) patterns. We test the proposed methods in a case study using the transportation network of Eastern Massachusetts where our results indicate an overall reduction in travel times of 4.7% by selecting the best 15 reversals. Moreover, using a small test network, we investigate the performance of the lane reversal strategies as a function of the OD demand symmetry. As expected, we observe that when the OD demand is very asymmetric (e.g., for a single OD pair, evacuations, large events), the reduction in travel times is larger than the symmetric case, reaching travel time reductions of 60%.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Quantum Ratcheted Photophysics in Energy Transport

In this paper, we explore the scope of vibrations as quantum ratchets that serve as nonthermal routes to achieving population transport in systems where excitation transport between molecules is otherwise energetically unfavorable. In addition to their role as channels of transport, we investigate the effect of resonance of the vibrations, which are described by Huang-Rhys mixing, with excitonic energy gaps, which leads to strongly mixed vibronic excitons. Finally, we explore the interplay of resonance and Huang-Rhys mixing with electronic coupling between the molecules, in the presence of a dissipative bath, in optimizing transport in such systems. Furthermore, we find that while resonance is desirable, a moderate electronic coupling has a stronger positive effect in contrast to a large electronic coupling, which results in delocalized excitations across molecules and hampers unidirectional transport. We also report a special resonance regime that is able to circumvent the transport problems arising from large electronic couplings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1998

Neural Network and Regression Approximations in High Speed Civil Transport Aircraft Design Optimization

Nonlinear mathematical-programming-based design optimization can be an elegant method. However, the calculations required to generate the merit function, constraints, and their gradients, which are frequently required, can make the process computational intensive. The computational burden can be greatly reduced by using approximating analyzers derived from an original analyzer utilizing neural networks and linear regression methods. The experience gained from using both of these approximation methods in the design optimization of a high speed civil transport aircraft is the subject of this paper. The Langley Research Center's Flight Optimization System was selected for the aircraft analysis. This software was exercised to generate a set of training data with which a neural network and a regression method were trained, thereby producing the two approximating analyzers. The derived analyzers were coupled to the Lewis Research Center's CometBoards test bed to provide the optimization capability. With the combined software, both approximation methods were examined for use in aircraft design optimization, and both performed satisfactorily. The CPU time for solution of the problem, which had been measured in hours, was reduced to minutes with the neural network approximation and to seconds with the regression method. Instability encountered in the aircraft analysis software at certain design points was also eliminated. On the other hand, there were costs and difficulties associated with training the approximating analyzers. The CPU time required to generate the input-output pairs and to train the approximating analyzers was seven times that required for solution of the problem.

Patniak, Surya N.↗

DOE OSTI2025

Future marine biofuels in the port of Seattle region

Marine transportation, a vital global sector, emits 3% of global annual greenhouse gas emissions, which are predicted to increase in the future. Marine biofuels derived from biomass or waste sources like wood residue, waste oil and municipal solid waste can be used for decarbonization. However, limited studies have explored if sufficient marine biofuels could be produced and supplied to major regional ports given feedstock, supply chain and technological constraints. We fill this gap by evaluating the feasibility of supplying marine biofuels to the Port of Seattle. The Regional Bio-Economy Model (RBEM) and the Freight and Fuel Transportation Optimization Tool (FTOT) are used to build scenarios for simulating marine biofuel production in the Port region. We harmonized technoeconomic assumptions for RBEM and FTOT, input FTOT feedstock utilization and routing outputs into RBEM, and modelled conversion, feedstock, and policy scenario variations in RBEM. In RBEM, overall biofuel production was constrained primarily by the biofuel cost, and then by feedstock availability. Providing policy incentives and reducing permitting time frames alleviated these constraints and spurred the buildout of a robust industry through industrial learning dynamics in the initial years. With these measures in place, the RBEM results show that 100% of fuel demand at the Port can be supplied by biofuels with policy incentives and suitable technoeconomic conditions, but the addition of transportation cost considerations using FTOT led to 27.8% of demand being able to be met by biofuels at reasonable fuel delivery cost.

09 BIOMASS FUELS↗

DOE OSTI2024

Towards Next-Generation Urban Decision Support Systems through AI-Powered Construction of Scientific Ontology Using Large Language Models—A Case in Optimizing Intermodal Freight Transportation

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. However, addressing complex urban and environmental management challenges often demands deep expertise in domain science and informatics. This expertise is essential for deriving data and simulation-driven insights that support informed decision-making. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs) to create knowledge representations for supporting operations research. By adopting ChatGPT-4 API as the reasoning core, we outline an applied workflow that encompasses natural language processing, Methontology-based prompt tuning, and Generative Pre-trained Transformer (GPT), to automate the construction of scenario-based ontologies using existing research articles and technical manuals of urban datasets and simulations. From these ontologies, knowledge graphs can be derived using widely adopted formats and protocols, guiding various tasks towards data-informed decision support. The performance of our methodology is evaluated through a comparative analysis that contrasts our AI-generated ontology with the widely recognized pizza ontology, commonly used in tutorials for popular ontology software. We conclude with a real-world case study on optimizing the complex system of multi-modal freight transportation. Our approach advances urban decision support systems by enhancing data and metadata modeling, improving data integration and simulation coupling, and guiding the development of decision support strategies and essential software components.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

Earth mover’s distance as a measure of CP violation

We introduce a new unbinned two sample test statistic sensitive to CP violation utilizing the optimal transport plan associated with the Wasserstein (earth mover’s) distance. The efficacy of the test statistic is shown via two examples of CP asymmetric distributions with varying sample sizes: the Dalitz distributions of B 0 → K + π – π 0 and of D 0 → π + π – π 0 decays. The windowed version of the Wasserstein distance test statistic is shown to have comparable sensitivity to CP violation as the commonly used energy test statistic, but also retains information about the localized distributions of CP asymmetry over the Dalitz plot. For large statistic datasets we introduce two modified Wasserstein distance based test statistics — the binned and the sliced Wasserstein distance statistics, which show comparable sensitivity to CP violation, but improved computing time and memory scalings. Finally, general extensions and applications of the introduced statistics are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

SHAPER: can you hear the shape of a jet?

The identification of interesting substructures within jets is an important tool for searching for new physics and probing the Standard Model at colliders. Many of these substructure tools have previously been shown to take the form of optimal transport problems, in particular the Energy Mover’s Distance (EMD). In this work, we show that the EMD is in fact the natural structure for comparing collider events, which accounts for its recent success in understanding event and jet substructure. We then present a Shape Hunting Algorithm using Parameterized Energy Reconstruction (SHAPER), which is a general framework for defining and computing shape-based observables. SHAPER generalizes N-jettiness from point clusters to any extended, parametrizable shape. This is accomplished by efficiently minimizing the EMD between events and parameterized manifolds of energy flows representing idealized shapes, implemented using the dual-potential Sinkhorn approximation of the Wasserstein metric. We show how the geometric language of observables as manifolds can be used to define novel observables with built-in infrared-and-collinear safety. We demonstrate the efficacy of the SHAPER framework by performing empirical jet substructure studies using several examples of new shape-based observables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Pileup and Infrared Radiation Annihilation (PIRANHA): a paradigm for continuous jet grooming

Jet grooming is an important strategy for analyzing relativistic particle collisions in the presence of contaminating radiation. Most jet grooming techniques introduce hard cutoffs to remove soft radiation, leading to discontinuous behavior and associated experimental and theoretical challenges. In this paper, we introduce Pileup and Infrared Radiation Annihilation (Piranha), a paradigm for continuous jet grooming that overcomes the discontinuity and infrared sensitivity of hard-cutoff grooming procedures. We motivate Piranha from the perspective of optimal transport and the Energy Mover’s Distance and review Apollonius Subtraction and Iterated Voronoi Subtraction as examples of Piranha-style grooming. We then introduce a new tree-based implementation of Piranha, Recursive Subtraction, with reduced computational costs. Finally, we demonstrate the performance of Recursive Subtraction in mitigating sensitivity to soft distortions from hadronization and detector effects, and additive contamination from pileup and the underlying event.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model to investigate the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

High protonic resistance of hydrocarbon-based cathodes in PEM fuel cells under low humidity conditions: Origin, implication, and mitigation

Hydrocarbon-based electrodes for proton-exchange membrane fuel cells face challenges in closing the performance gap with electrodes based on perfluorosulfonic acid ionomers, particularly under low humidity conditions. Alongside increased oxygen transport resistance and higher kinetic-induced overpotentials, the protonic resistance of these fluorine-free electrodes is the primary hurdle to improved performance. This study systematically investigates the origin and impact of the cathode protonic resistance on fuel cell performance, utilizing sulfonated phenylated polyphenylenes as hydrocarbon ionomers. Electrochemical characterization at low relative humidity (≤50 %) reveal a high protonic resistance arising from both lower conductivity of the hydrocarbon thin film compared to the bulk membrane and increased cathode tortuosity at a gas transport-optimized ionomer to carbon (I/C) ratio of 0.2. The poor protonic resistance at low relative humidities leads to a non-homogeneous current distribution across the thickness of the cathode electrode, resulting in lower catalyst utilization. To address this issue, reducing the thickness of the cathode CL while maintaining a constant Pt loading (i.e., increasing the Pt on carbon ratio) significantly reduces protonic resistance. This improvement compensates for the kinetic disadvantages of highly loaded carbon particles and results in a considerable performance increase by 40 % at 0.75 V under low relative humidities.

25 ENERGY STORAGE↗

DOE OSTI2026

Not all fugitives are bad: The case for using them to form low tortuosity - high porosity electrodes

This work focuses on the inclusion of an insoluble fugitive phase during slurry processing to form composite battery electrodes. The fugitive phases consist of natural derived products like alginic acid, sucrose, rice and potato starch, and carrageenans such as Irish Moss and synthetic pore-formers based on polymethyl methacrylate. The fugitive phases can be anaerobically thermally removed (350 °C) during binder crosslinking and electrode drying steps, resulting in electrodes with low tortuosities (approaching theoretical Bruggemann limits for spherical particles) and high porosities approaching 80%. The resulting ∼3 mg/cm 2 loaded electrodes suffer from poor electrical connectivity, lowering the effective material utilization, but represent an approach that could be utilized for the formation of solid-state batteries with infilling of materials into well-defined pores and optimized transport pathways.

25 ENERGY STORAGE↗

DOE OSTI2020

Leveraging Sequential Doping of Semiconducting Polymers to Enable Functionally Graded Materials for Organic Thermoelectrics

With the ability to modulate electronic properties through molecular doping coupled with ease in processability, semiconducting polymers are at the forefront in enabling organic thermoelectric devices for thermal energy management. In contrast to uniform thermoelectric material properties, an alternative route focuses on functionally graded materials (FGMs) where one spatially controls and optimizes transport properties across the length of a thermoelectric material. While primarily studied in the context of inorganic materials, the concept of FGMs for organic thermoelectrics has not been explored. Herein, we introduce how molecular doping of semiconducting polymers enables spatial compositional control of thin-film FGMs. Specifically, we utilize sequential vapor doping of poly[2,5-bis(3-tetradecylthiophen-2-yl) thieno [3,2-b]thiophene] (PBTTT) with the small molecule acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) to fabricate the simplest form of FGMs – double- segmented thin films. The two thin-film segments are of equal length (7.5 mm), but each set to different doping levels. Our study focuses on understanding the thermoelectric properties (Seebeck coefficient, α, and electronic conductivity, σ) and structural properties (through X-ray scattering, UV-vis-NIR spectroscopy, and Raman spectroscopy) within and across the two segments. We observe the presence of a small diffuse interfacial region of 0.5 – 1 mm between the two segments where the doping level and transport properties vary continuously. Despite the diffuse interface, the measured effective Seebeck coefficient (αeff) across the two segments is simply the average of α within each segment. Importantly, this experimental result is consistent with reported mathematical models describing αeff in graded thermoelectric materials. Finally, our results demonstrate the facile fabrication and characterization of functionally graded organic thermoelectric materials, providing guidelines for further development on more complex FGMs.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Learning to simulate high energy particle collisions from unlabeled data

In many scientific fields which rely on statistical inference, simulations are often used to map from theoretical models to experimental data, allowing scientists to test model predictions against experimental results. Experimental data is often reconstructed from indirect measurements causing the aggregate transformation from theoretical models to experimental data to be poorly-described analytically. Instead, numerical simulations are used at great computational cost. We introduce Optimal-Transport-based Unfolding and Simulation (OTUS), a fast simulator based on unsupervised machine-learning that is capable of predicting experimental data from theoretical models. Without the aid of current simulation information, OTUS trains a probabilistic autoencoder to transform directly between theoretical models and experimental data. Identifying the probabilistic autoencoder’s latent space with the space of theoretical models causes the decoder network to become a fast, predictive simulator with the potential to replace current, computationally-costly simulators. Here, we provide proof-of-principle results on two particle physics examples, Z-boson and top-quark decays, but stress that OTUS can be widely applied to other fields.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Path-Based Dictionary Augmentation: A Framework for Improving $k$ -Sparse Image Processing

In this study, we have previously shown that augmenting orthogonal matching pursuit (OMP) with an additional step in the identification stage of each pursuit iteration yields improved $k$ -sparse reconstruction and denoising performance relative to baseline OMP. At each iteration a “path” or geodesic, is generated between the two dictionary atoms that are most correlated with the residual and from this path a new atom that has a greater correlation to the residual than either of the two bracketing atoms is selected. Here, we provide new computational results illustrating improvements in sparse coding and denoising on canonical datasets using both learned and structured dictionaries. The two methods of constructing a path are investigated for each dictionary type: the Euclidean geodesic formed by a linear combination of the two atoms and the 2-Wasserstein geodesic corresponding to the optimal transport map between the atoms. We prove here the existence of a higher-correlation atom in the Euclidean case under assumptions on the two bracketing atoms and introduce algorithmic modifications to improve the likelihood that the bracketing atoms meet those conditions. Although, we demonstrate our augmentation on OMP alone, in general it may be applied to any reconstruction algorithm that relies on the selection and sorting of high-similarity atoms during an analysis or identification phase.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Comparing Mapper Graphs of Artificial Neuron Activations

The mapper graph is a popular tool from topological data analysis that provides a graphical summary of point cloud data. It has been used to study data from cancer research, sports analytics, neurosciences, and machine learning. In particular, mapper graphs have been used recently to visualize the topology of high-dimensional artificial neural activations from convolutional neural networks and large language models. However, a key question that arises from using mapper graphs across applications is how to compare mapper graphs to study their structural differences. In this paper, we introduce a distance between mapper graphs using tools from optimal transport. We demonstrate the utility of such a distance by studying the topological changes of neural activations across convolutional layers in deep learning, as well as by capturing the loss of structural information for multiscale mapper.

mapper graphs, computational topology, machine lea↗