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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Localization dynamics in a centrally coupled system

In systems in which interactions couple a central degree of freedom and a bath, one would expect signatures of the bath's phase to be reflected in the dynamics of the central degree of freedom. This has been recently explored in connection with many-body localized baths coupled with a central qubit or a single-cavity mode - systems with growing experimental relevance in various platforms. Such models also have an interesting connection with Floquet many-body localization via quantizing the external drive, although this has been relatively unexplored. Here we adapt the multilayer multiconfigurational time-dependent Hartree (ML-MCTDH) method, a well-known tree tensor network algorithm, to numerically simulate the dynamics of a central degree of freedom, represented by a d-level system (qudit), coupled to a disordered interacting one-dimensional spin bath. ML-MCTDH allows us to reach ≈10 2 lattice sites, a far larger system size than what is feasible with exact diagonalization or kernel polynomial methods. From the intermediate time dynamics, we find a well-defined thermodynamic limit for the qudit dynamics upon appropriate rescaling of the system-bath coupling. The spin system shows similar scaling collapse in the Edward-Anderson spin-glass order parameter or entanglement entropy at relatively short times. At longer timescales, we see slow growth of the entanglement, which may arise from dephasing mechanisms in the localized system or long-range interactions mediated by the central degree of freedom. Similar signs of localization are shown to appear as well with unscaled system-bath coupling.

1-dimensional spin chains↗
DOE OSTI2026

elm-diagnostics

elm-diagnostics is a Python package for computing diagnostic analyses and visualizations for the E3SM Land Model (ELM) component and is meant to support new feature development in ELM. The tool reads model history files and performs quantitative analyses including budget-closure checking, variable transformations, temporal aggregations, and statistical summaries to support model evaluation, validation, and scientific interpretation. The framework is designed for extensibility, with modular architecture enabling straightforward addition of new diagnostic methods, derived variables, analysis types, visualization approaches, and model-specific adaptations

Hoffman, Matt [Los Alamos National Laboratory]↗
DOE OSTI2020

Multitask Recommender Systems for Cancer Drug Response

The problem we are currently trying to address is that there are many types of cancer drugs and many types of cancers and there is not always experimental data for a specific cancer type and cancer drug interaction. While there is a large possible set of feasible drug and cancer combinations, testing each pair is not realistic due to the high monetary cost of cell-based assays. Thus, this leaves researchers with a difficult choice of what drugs they should test on specific cancer types. This issue is known as the cold-start problem. Our focus is on developing recommender systems capable of addressing the cold-start problem as it relates to interaction between cancer types and cancer drugs. One of the most effective ways to address the cold-start problem is through large data analysis, however due to the cost prohibitive nature of cancer research the largest available data set size is the Genomics of Drug Sensitivity in Cancer with 494,973 genomic associations. To achieve optimal model performance on the cold-start problem, it is advantageous to employ multitask algorithms that are capable of transferring information between cancer datasets. The aim of this report is to draw from adaptations and state of the art developments in both algorithms for recommender systems and multitask learning to model the interaction between cancer cell lines and cancer drugs. Cancer cell lines are defined by the US National Cancer Institute as "cancer cells that keep dividing and growing over time, under certain conditions in a laboratory". This paper will focus on evaluating the performance of Neural Collaborative Filtering and Gaussian Processes, as well as their multitask adaptations, on cancer datasets from CCLE, NCI60, GDSC and CTRP. These methods will be evaluated on model performance in regression prediction but also in interpretability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum

Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Efficient Synthesis and HPLC-Based Characterization for Developing Vanadium-48-Labeled Vanadyl Acetylacetonate as a Novel Cancer Radiotracer for PET Imaging

Bis(acetylacetonato)oxidovanadium(IV) [(VO(acac) 2 ], generally known as vanadyl acetylacetonate, has been shown to be preferentially sequestered in malignant tissue. Vanadium-48 ( 48 V) generated with a compact medical cyclotron has been used to label VO(acac) 2 as a potential radiotracer in positron emission tomography (PET) imaging for the detection of cancer, but requires lengthy synthesis. Current literature protocols for the characterization of VO(acac) 2 require macroscale quantities of reactants and solvents to identify products by color and to enable crystallization that are not readily adaptable to the needs of radiotracer synthesis. We present an improved method to produce vanadium-48-labeled VO(acac) 2 , [ 48 V]VO(acac) 2 , and characterize it using high-performance liquid chromatography (HPLC) with radiation detection in combination with UV detection. The approach is suitable for radiotracer-level quantities of material. These methods are readily applicable for production of [ 48 V]VO(acac) 2 . Preliminary results of preclinical, small-animal PET studies are presented.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2026

AthenaK: A Performance-portable Version of the Athena++ Adaptive Mesh Refinement Framework

We describe AthenaK: a new implementation of the Athena++ block-based adaptive mesh refinement framework using the Kokkos programming model. Finite volume methods for Newtonian, special relativistic, and general relativistic (GR) hydrodynamics and magnetohydrodynamics (MHD), and GR-radiation hydrodynamics and MHD, as well as a module for evolving Lagrangian tracer or charged test particles (e.g., cosmic rays) are implemented using the framework. In two companion papers, we describe (1) a new solver for the Einstein equations based on the Z4c formalism, and (2) a GRMHD solver in dynamical spacetimes also implemented using the framework, enabling new applications in numerical relativity. By adopting Kokkos, the code can be run on virtually any hardware, including CPUs, GPUs from multiple vendors, and emerging Advanced RISC Machine processors. AthenaK shows excellent performance and weak scaling, achieving over 1 billion cell updates per second for hydrodynamics in three dimensions on a single NVIDIA Grace Hopper processor. It does this with a typical parallel efficiency of 80% on 65,536 AMD GPUs on the OLCF Frontier system. Such performance portability enables AthenaK to leverage modern exascale computing systems for challenging applications in astrophysical fluid dynamics, numerical relativity, and multimessenger astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Modeling land use and land cover change: using a hindcast to estimate economic parameters in gcamland v2.0

Abstract. Future changes in land use and cover have important implications for agriculture, energy, water use, and climate. Estimates of future land use and land cover differ significantly across economic models as a result of differences in drivers, model structure, and model parameters; however, these models often rely on heuristics to determine model parameters. In this study, we demonstrate a more systematic and empirically based approach to estimating a few key parameters for an economic model of land use and land cover change, gcamland. Specifically, we generate a large set of model parameter perturbations for the selected parameters and run gcamland simulations with these parameter sets over the historical period in the United States to quantify land use and land cover, determine how well the model reproduces observations, and identify parameter combinations that best replicate observations, assuming other model parameters are fixed. We also test alternate methods for forming expectations about uncertain crop yields and prices, including adaptive, perfect, linear, and hybrid approaches. In particular, we estimate parameters for six parameters used in the formation of expectations and three of seven logit exponents for the USA only. We find that an adaptive expectation approach minimizes the error between simulated outputs and observations, with parameters that suggest that for most crops, landowners put a significant weight on previous information. Interestingly, for corn, where ethanol policies have led to a rapid growth in demand, the resulting parameters show that a larger weight is placed on more recent information. We examine the change in model parameters as the metric of model error changes, finding that the measure of model fitness affects the choice of parameter sets. Finally, we discuss how the methodology and results used in this study could be used for other regions or economic models to improve projections of future land use and land cover change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Concentric semi-circular split profiling for computed tomographic imaging of electronic beams

Apparatus and method for analyzing an electron beam including a circular sensor disk adapted to receive the electron beam, an inner semi-circular slit in the circular sensor disk; an outer semi-circular slit in the circular sensor disk wherein the outer semi-circular slit is spaced from the first semi-circular slit by a fixed distance; a system for sweeping the electron beam radially outward from the central axis to the inner semi-circular slit and outer second semi-circular slit; a sensor structure operatively connected to the circular sensor disk wherein the sensor structure receives the electron beam when it passes over the inner semi-circular slit and the outer semi-circular slit; and a device for measuring the electron beam that is intercepted by the inner semi-circular slit and the outer semi-circular slit.

42 ENGINEERING↗
DOE OSTI2020

Subtask 1.5 – CO2 Injection Monitoring with an Optimized Scalable, Automated, Semipermanent Seismic Array

The scalable, automated, semipermanent seismic array (SASSA) method is a flexible and relatively cost-effective surface geophysical method for regular time-lapse monitoring of the movement of injected carbon dioxide (CO2) in a reservoir for CO2 enhanced oil recovery (EOR) or geologic CO2 storage operations. It has the advantages of a low-environmental-footprint while monitoring regions of a reservoir from the surface without the need for a regular grid distribution of receivers. Automated data collection is possible. As only time-lapse amplitude changes at the reservoir level due to CO2 movement within the reservoir are monitored, the turnaround time to deliver results from the SASSA method can be short, without the need for long, time-consuming data-processing workflows. As data is collected and processed, incremental information can be provided to the field operator. The Energy & Environmental Research Center (EERC) conducted a SASSA field test from September 2018 to November 2020 in a portion of the Bell Creek Field in Montana, which implemented new CO2 EOR field activities during the study period. Lessons learned from a proof-of-concept study were incorporated to improve the data quality of the SASSA method and demonstrate the viability of the technology. The EERC implemented several enhancements to improve data quality, including 1) an iterative survey design, which allowed placing the receivers in strategic locations where the movement of the CO2 in the reservoir could be tracked with minimum interference by the cultural noise in the study area; 2) the use of powerful seismic sources in the form of surface orbital vibrators, and 3) data acquisition during optimal periods. History-matched reservoir simulation was performed to predict gas saturation and pressure response induced by CO2 injection in the study area. The results were compared with the SASSA-measured responses to CO2 injection as a partial validation technique. A match between the two methods was observed for most of the SASSA points predicted to have intersected a CO2 saturation change. The validated results provide confidence that the SASSA method can be used independently as a CO2 saturation monitoring technique. As data are collected and processed, incremental information can be provided to the field operator. The critical components of the SASSA workflow for a successful application of the method are the following: Iterative survey design with information about CO2 injection activities from the oilfield operator. A detailed CO2 injection plan is the key driver to select the strategic monitoring location of the SASSA sensors. After this information is incorporated in the initial distribution of sources and receivers in the study area, high-resolution satellite images are used to identify ground locations not affected by cultural noise sources, such as power lines, pipelines/flow lines, or roadways. In the next iteration of the survey design, a scouting trip to the study area is needed to understand more details of the noise sources identified in the previous step and the intensity of the field activities that can also generate noise during the monitoring. Integrating the information from the scouting trip into the survey design to select the optimum source and receiver locations is the final step. Noise attenuation. The variety of noise types during seismic monitoring of an oil field is enormous. Tailored noise characterization and processing at a node-by-node level can enhance the performance and sensitivity of the SASSA technique. Future advancements that could improve the efficiency and application of the SASSA technology include: Gaining a better understanding of the noise field produced by the seismic source to aid the choice of receiver location. Surface noise from the source can overwhelm the small signal changes due to CO2 that the SASSA method measures. Improved data-processing workflow to automatically analyze and adapt to dynamic noise conditions associated with industrial settings. This subtask was funded through the EERC–DOE Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE- FE0024233.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Adaptive Urban Traffic Signal Control for Multiple Intersections: An LQR Approach

Traffic congestion leads to severe problems especially in urban traffic networks. It increases the chance of accidents, energy waste, and social costs. In order to address these problems, an adaptive linear quadratic regulator (LQR) approach is developed for traffic signal control at multiple intersections in an urban area. The proposed method controls the green time of the traffic signals to reduce traffic congestion and smooth traffic flow. Real-world data from vision-based traffic sensors are used to build the traffic network model, which mimics the real-world traffic behavior. In addition, the proposed control utilizes recursive least square parameter estimation, which is capable of tracking dynamic changes in traffic conditions. Simulation of Urban MObility (SUMO) is used to analyze the efficacy of the proposed method. Results of the simulation show that the proposed method outperforms pretimed control in various aspects.

adaptive LQR control↗
DOE OSTI2024

Haar-Like Wavelets on Hierarchical Trees

Here, discrete wavelet methods, originally formulated in the setting of regularly sampled signals, can be adapted to data defined on a point cloud if some multiresolution structure is imposed on the cloud. A wide variety of hierarchical clustering algorithms can be used for this purpose, and the multiresolution structure obtained can be encoded by a hierarchical tree of subsets of the cloud. Prior work introduced the use of Haar-like bases defined with respect to such trees for approximation and learning tasks on unstructured data. This paper builds on that work in two directions. First, we present an algorithm for constructing Haar-like bases on general discrete hierarchical trees. Second, with an eye towards data compression, we present thresholding techniques for data defined on a point cloud with error controlled in the $L$ $\infty$ norm and in a Hölder-type norm. In a concluding trio of numerical examples, we apply our methods to compress a point cloud dataset, study the tightness of the $L$ $\infty$ error bound, and use thresholding to identify MNIST classifiers with good generalizability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Flux Upcycling of Degraded Layered Cathodes to LiNi x Mn y Co z O 2 (NMCs) with Gradient Transition Metal Distribution

The rising demand for lithium-ion batteries (LIBs) has intensified the need for efficient recycling methods to address both supply chain constraints and environmental impacts. Direct upcycling, distinguished by its ability to achieve both the structural and compositional integrity of cathode materials, has gained prominence as a sustainable alternative to conventional pyrometallurgical and hydrometallurgical processes. However, the current direct upcycling methods are typically limited by incorporating Li and/or Ni, significantly constraining the adaptability across diverse LiNi x Mn y Co z O 2 (NMCs). Here, in this study, a versatile molten salt approach is reported that expands the scope of direct upcycling by enabling simultaneous incorporation of Li, Ni, and Mn. This methodology facilitates flexible conversion among diverse NMC compositions, including non-stoichiometric Co/Mn systems such as upcycling degraded LiCoO 2 (D-LCO), LiNi 1/3 Mn 1/3 Co 1/3 O 2 (D-NMC111), LiNi 0.8 Mn 0.1 Co 0.1 O 2 (D-NMC811) to surface Mn enriched NMC111, LiNi 0.5 Mn 0.3 Co 0.2 O 2 (NMC532), and NMC811, respectively. The gradient transition metal distribution in upcycled products, characterized by Mn-enriched outer layers and Co/Ni-enriched cores enhances the interfacial stability of NMC cathodes, addressing critical challenges in long-term performance and structural integrity. These results highlight the potential of flux methods for advancing the upcycling of spent cathodes and producing high-performance materials for next-generation LIBs applications.

lithium -ion batteries↗
DOE OSTI2024

Self-assembled elastomers with molecularly encoded tissue-like softness, strain-adaptive stiffening and coloration

The invention generally relates to linear-bottlebrush-linear copolymer blocks and methods of making and using same. The disclosed copolymer blocks can be useful in, for example, the formation of polymer networks that replicate biological stress-strain behavior. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present invention.

Sheiko, Sergei↗
DOE OSTI2020

Methods, systems and computer program products for determining systems re-tasking

Methods, systems and computer program products to measure system re-taskability are disclosed. The methods, systems and computer program products may be used in the design of a new or redesign of an existing System of Systems (SoS). Systems re-tasking (aka substitutability or stand-in redundancy) is the process of using different systems to substitute for non-operational systems to meet required functionality, or using multi-function systems to fulfill higher-priority tasks. This ability can increase the overall operational availability of the SoS; it can also increase the adaptability and resilience of the SoS to unknown or changing conditions. The disclosed methods, systems and computer products include simulating an SoS over time, replacing systems that become non-operational (or damaged) with systems that can fulfill the same capability in order to maximize the SoS availability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Synthetic hybrids of six yeast species

Abstract Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantum simulations of nuclear resonances with variational methods

Background: The many-body nature of nuclear physics problems poses significant computational challenges. These challenges become even more pronounced when studying the resonance states of nuclear systems, which are governed by the non-Hermitian Hamiltonian. Quantum computing, particularly for quantum many-body systems, offers a promising alternative, especially within the constraints of current noisy intermediate-scale quantum (NISQ) devices. Purpose: This work aims to simulate nuclear resonances using quantum algorithms by developing a variational framework compatible with non-Hermitian Hamiltonians and implementing it fully on a quantum simulator. Methods: We employ the complex scaling technique to extract resonance positions classically and adapt it for quantum simulations using a two-step algorithm. First, we transform the non-Hermitian Hamiltonian into a Hermitian form by using the energy variance as a cost function within a variational framework. Second, we perform 𝜃-trajectory calculations to determine optimal resonance positions in the complex energy plane. To address resource constraints on NISQ devices, we utilize Gray code (GC) encoding to reduce qubit requirements. Results: We first validate our approach using a schematic potential model that mimics a nuclear potential, successfully reproducing known resonance energies with high fidelity. We then extend the method to a more realistic 𝛼−𝛼 nuclear potential and compute the 𝐷- and 𝐺-wave resonance energies with a basis size of 𝑁=16, using only four qubits. The quantum simulation results closely match the classical values, demonstrating the feasibility of our approach. Conclusions: This study demonstrates, for the first time, that the complete 𝜃-trajectory method can be implemented on a quantum computer without relying on any classical input beyond the Hamiltonian. The results establish a scalable and efficient quantum framework for simulating resonance phenomena in nuclear systems. This work represents a significant step toward quantum simulations of open quantum systems and lays the foundation for future investigations into resonance structures in nuclear, atomic, and molecular physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Meshfree Methods

Meshfree methods have undergone substantial development and have received much attention in the last two decades. This new family of numerical methods is designed to inherit the main advantages of the finite element method such as compact supports of shape functions and good approximation properties while, at the same time, overcome the main disadvantages of the finite element method caused by the mesh dependence. The meshfree methods share a common feature that no mesh is needed and shape functions are constructed from sets of points, thus eliminating the need for time consuming mesh generation. The most significant advantage of meshfree methods is the flexibility in customizing approximation functions for desired regularity and for capturing essential physics and features of the particular problems of interest. Adaptivity formulation and multiple-scale solution strategies also can be implemented with relative ease. It has become clear that the meshfree methods provide considerable advantages over the conventional finite element methods in solving problems involving moving discontinuities, evolving material interfaces, multiple-scale phenomena, large material distortion and structural deformation, and fracture and damage processes. This Chapter gives an overview of many classes of meshfree methods, with more detailed discussions on Smoothed Particle Hydrodynamics (SPH), the Reproducing Kernel Particle Method (RKPM), Peridynamics (PD), the Material Point Method (MPM), as well as their applications in various challenging engineering problems.2

Chen, Jiun-Shyan↗
DOE OSTI2024

Sequential Kalman tuning of the t -preconditioned Crank-Nicolson algorithm: efficient, adaptive and gradient-free inference for Bayesian inverse problems

Ensemble Kalman Inversion (EKI) has been proposed as an efficient method for the approximate solution of Bayesian inverse problems with expensive forward models. However, when applied to the Bayesian inverse problem EKI is only exact in the regime of Gaussian target measures and linear forward models. Here, in this work we propose embedding EKI and Flow Annealed Kalman Inversion, its normalizing flow (NF) preconditioned variant, within a Bayesian annealing scheme as part of an adaptive implementation of the t-preconditioned Crank-Nicolson (tpCN) sampler. The tpCN sampler differs from standard pCN in that its proposal is reversible with respect to the multivariate t-distribution. The more flexible tail behaviour allows for better adaptation to sampling from non-Gaussian targets. Within our Sequential Kalman Tuning (SKT) adaptation scheme, EKI is used to initialize and precondition the tpCN sampler for each annealed target. The subsequent tpCN iterations ensure particles are correctly distributed according to each annealed target, avoiding the accumulation of errors that would otherwise impact EKI. We demonstrate the performance of SKT for tpCN on three challenging numerical benchmarks, showing significant improvements in the rate of convergence compared to adaptation within standard SMC with importance weighted resampling at each temperature level, and compared to similar adaptive implementations of standard pCN. The SKT scheme applied to tpCN offers an efficient, practical solution for solving the Bayesian inverse problem when gradients of the forward model are not available. Code implementing the SKT schemes for tpCN is available at https://github.com/RichardGrumitt/KalmanMC.

97 MATHEMATICS AND COMPUTING↗