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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data Driven Correlated Noise Simulation for the ICEBERG LArTPC

Accurate electronic-noise simulation is essential for low-energy physics in liquid-argon TPCs. More realistic noise modeling allows us to better tune reconstruction algorithms and more reliably assess and optimize signal-detection thresholds. We present a data-driven noise simulation framework developed for the ICEBERG test stand for DUNE that generates synthetic noise waveforms that reproduce both (i) the measured per-channel magnitude of the Fast Fourier Transform (FFT) and (ii) frequency-dependent channel-to-channel correlations observed in ICEBERG noise data. Using a dedicated noise-only dataset, we build a compact noise model containing per-channel FFT-magnitude targets together with a small set of band-wise cross-wire color matrices. White noise is generated in the frequency domain by drawing circular-symmetric complex Gaussian coefficients with random phases and scaling them to match the measured FFT-magnitude targets, and cross-wire correlations are subsequently imposed using the stored color matrices. The model and algorithm were integrated into the LArSoft + Wire-Cell Toolkit simulation chain and validated by comparing waveform structure, frequency-domain spectra, and band-limited correlation matrices from simulated noise and ICEBERG data. This approach can be extended to other LArTPC operating conditions.

Ghosh, Avik [Iowa State U.]↗
DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Development of Segregated Thermal-Hydraulics Solvers in MOOSE

The simulation of fluid flows is an essential part of the design and analysis of nuclear systems. Algorithms able to simulate flows at different fidelity levels are available in the Multiphysics Object-Oriented Simulation Environment (MOOSE) and MOOSE-based applications such as Pronghorn \cite{novak2018pronghorn}, Pronghorn-Subchannel, RELAP-7, and SAM. Currently, significant effort is being invested in the development of coarse-mesh Computational Fluid Dynamics (CFD) capabilities within MOOSE and Pronghorn for the simulation of Generation IV nuclear reactors. Traditionally, the solution algorithms in MOOSE have relied on Newton or quasi-Newton methods (such as the preconditioned Jacobian-free Newton-Krylov method) where residuals and Jacobians (or approximations thereof) are constructed. Both Newton and quasi-Newton methods require the solution of a linear system at each nonlinear Newton iteration with the Jacobian as the system matrix. The Jacobian contains blocks originating from all variables in the problem (i.e., for thermal-hydraulics at least pressure, velocities, and temperature). Due to the formulation of the problem in a general multiphysics setting on unstructured mesh, creating a good preconditioner for the linear system can be challenging, thus many fluid applications have utilized direct solver-based methods such as LU factorization. However, with increasing system size and complexity in multi-dimensional problems, the direct solution of linear systems becomes computationally expensive both in execution time and and memory. For this reason, recent effort has focused on adapting segregated solution algorithms for CFD problems in MOOSE. These algorithms use fixed-point iteration between segregated systems whose assembly and preconditioning are easier those of the monolithic system. Initial results show that the segregated solution algorithm outperforms the monolithic approach in terms of memory usage and for large 3D problems in terms of CPU time as well.

42 ENGINEERING↗
DOE OSTI2024

Development of Segregated Thermal-Hydraulics Solvers in MOOSE

The simulation of fluid flows is an essential part of the design and analysis of nuclear systems. Algorithms able to simulate flows at different fidelity levels are available in the Multiphysics Object-Oriented Simulation Environment (MOOSE) and MOOSE-based applications such as Pronghorn \cite{novak2018pronghorn}, Pronghorn-Subchannel, RELAP-7, and SAM. Currently, significant effort is being invested in the development of coarse-mesh Computational Fluid Dynamics (CFD) capabilities within MOOSE and Pronghorn for the simulation of Generation IV nuclear reactors. Traditionally, the solution algorithms in MOOSE have relied on Newton or quasi-Newton methods (such as the preconditioned Jacobian-free Newton-Krylov method) where residuals and Jacobians (or approximations thereof) are constructed. Both Newton and quasi-Newton methods require the solution of a linear system at each nonlinear Newton iteration with the Jacobian as the system matrix. The Jacobian contains blocks originating from all variables in the problem (i.e., for thermal-hydraulics at least pressure, velocities, and temperature). Due to the formulation of the problem in a general multiphysics setting on unstructured mesh, creating a good preconditioner for the linear system can be challenging, thus many fluid applications have utilized direct solver-based methods such as LU factorization. However, with increasing system size and complexity in multi-dimensional problems, the direct solution of linear systems becomes computationally expensive both in execution time and and memory. For this reason, recent effort has focused on adapting segregated solution algorithms for CFD problems in MOOSE. These algorithms use fixed-point iteration between segregated systems whose assembly and preconditioning are easier those of the monolithic system. Initial results show that the segregated solution algorithm outperforms the monolithic approach in terms of memory usage and for large 3D problems in terms of CPU time as well.

42 ENGINEERING↗
DOE OSTI2025

An improved guess for the variational calculation of charge-transfer excitations in large systems

Ab initio quantum-chemical methods that perform well for computing the electronic ground state are not straightforwardly transferable to electronically excited states, particularly in large molecular systems. Wave function theory offers high accuracy, but is often prohibitively expensive. Methods based on time-dependent density functional theory (TD-DFT) are crucially sensitive to the chosen exchange-correlation functional (XCF) parameterization, and system-specific tuning protocols were therefore proposed to address the method's robustness. Methods based on the variational relaxation of the excited-state electron density showcased promising results for the calculation of charge-transfer excitations, but the complex shape of the electronic hypersurface makes convergence to a specific excited state much more difficult than for the ground state when standard variational techniques are applied. We address the latter aspect by providing suitable initial guesses, which we obtain by two separate constrained algorithms. Combined with the squared-gradient minimization algorithm for all-electrons relaxation in a freeze-and-release scheme (FRZ-SGM), we demonstrate that orbital-optimized density functional theory (OO-DFT) calculations can reliably converge to the charge-transfer states of interest even for large molecular systems. We test the FRZ-SGM method on a phenothiazine-anthraquinone CT excitation in a supramolecular Pd(II) coordination cage complex as a function of the cage conformation. This compound has been studied experimentally prior to our work. We compare this freeze-and-release scheme to two XCF reparameterizations, which were recently proposed as low-cost TD-DFT-based alternatives to variational methods. Two dye-semiconductor complexes, which were previously investigated in the context of photovoltaic applications, serve as a second example to investigate the convergence and stability of the FRZ-SGM approach. Our results demonstrate that FRZ-SGM provides reliable convergence for charge-transfer excited states and avoids variational collapse to lower-lying electronic states, whereas time-dependent DFT calculations with an adequate tuning procedure for the range-separation parameter provide a computationally efficient initial estimate of the corresponding energies, with a computational cost comparable to that of configuration-interaction singles (CIS) calculations.

Bogo, Nicola↗
DOE OSTI2025

The latent variable proximal point algorithm for variational problems with inequality constraints

The latent variable proximal point (LVPP) algorithm is a framework for solving infinite-dimensional variational problems with pointwise inequality constraints. The algorithm is a saddle point reformulation of the Bregman proximal point algorithm. At the continuous level, the two formulations are equivalent, but the saddle point formulation is more amenable to discretization because it introduces a structure-preserving transformation between a latent function space and the feasible set. Working in this latent space is much more convenient for enforcing inequality constraints than the feasible set, as discretizations can employ general linear combinations of suitable basis functions, and nonlinear solvers can involve general additive updates. LVPP yields numerical methods with observed mesh-independence for obstacle problems, contact, fracture, plasticity, and others besides; in many cases, for the first time. The framework also extends to more complex constraints, providing means to enforce convexity in the Monge–Ampère equation and handling quasi-variational inequalities, where the underlying constraint depends implicitly on the unknown solution. Here, in this paper, we describe the LVPP algorithm in a general form and apply it to ten problems from across mathematics.

Inequality constraints↗
DOE OSTI2025

LuGo: An enhanced quantum phase estimation implementation

Quantum Phase Estimation (QPE) is a cardinal algorithm in quantum computing that plays a crucial role in various applications, including cryptography, molecular simulation, and solving systems of linear equations. However, the standard implementation of QPE faces challenges related to time complexity and circuit depth, which limit its practicality for large-scale computations. We introduce LuGo, a novel framework designed to enhance the performance of QPE by reducing circuit duplication, as well as using parallelization techniques to achieve faster generation of the QPE circuit and gate reduction. We validate the effectiveness of our framework by generating quantum linear solver circuits, which require both QPE and inverse QPE, to solve linear systems of equations. LuGo achieves significant improvements in both computational efficiency and hardware requirements without compromising on accuracy. Compared to a standard QPE implementation, LuGo reduces time consumption to generate a circuit that solves a 2 6 × 2 6 system matrix by a factor of 50.68 and over 31× reduction of quantum gates and circuit depth, with no fidelity loss on an ideal quantum simulator. Furthermore, we demonstrated the versatility and scalability of LuGo enabled HHL algorithm by simulating a canonical Hele-Shaw fluid problem using a quantum simulator. With these advantages, LuGo paves the way for more efficient implementations of QPE, enabling broader applications across several quantum computing domains.

Quantum algorithm↗
DOE OSTI2024

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗
DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗
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 OSTI2025

Analytical Identification Method of Generalized Short‐Circuit Ratio Using Phasor Measurement Units

This paper introduces a novel analytical approach for the identification of the admittance matrix and the generalized short-circuit ratio (gSCR) in power systems integrated with renewable energy sources. The proposed method leverages voltage and current measurements from phasor measurement units (PMUs) to construct a least squares objective function, which is then solved using matrix calculus and partial derivatives. Unlike conventional optimization algorithms, this approach provides an analytical solution that substantially reduces data requirements, enabling the efficient and accurate identification of the gSCR with smaller datasets. Additionally, its fixed computational complexity allows for real-time updates as new data are collected, ensuring continuous refinement of the system of equations and enabling rapid, precise gSCR calculations. The method also exhibits strong robustness against measurement noise, making it well-suited for practical applications in dynamic power systems. The combination of reduced data requirements, real-time adaptability, noise robustness and fixed computational load establishes this method as a highly efficient and reliable tool for real-time power system stability analysis. Case studies on an EPRI 36-bus system demonstrate the method's effectiveness, highlighting its accuracy in closely matching true gSCR values, even under diverse disturbances and noisy conditions.

Han, Zelei [Hohai University, Nanjing (China)] (OR↗
DOE OSTI2026

Smart building HVAC control challenge: experience and solutions from the ADRENALIN project

A smart building HVAC control competition crowdsourced and compared algorithms on fair and equal ground using the standardized BOPTEST framework. The competition attracted 138 participants, but only 9% submitted valid solutions for the final stage, highlighting the complexity of advanced HVAC control design. The winning solutions showed significant potential to reduce energy use and cost by shifting demand, without compromising occupant comfort. Across scenarios, thermal energy cost reductions of 36–76% relative to a baseline, were achieved. In peak heat periods, the cost reduction leveraged limited energy use reduction (0–15%), but more significant energy price reduction (34–62%). This shows smart controls' ability to avoid as much as possible consumption during the morning peak hours, when spot prices are tendentially the highest. Hosting the competition has highlighted challenges in creating competitions that both are fair and promotes solutions that are transferable to real life implementation.

BOPTEST↗
DOE OSTI2024

Preparing an on-Demand Cloud Processing Workflow for NISAR Ecosystems Science Products

In preparation for the NISAR launch and data collection in 2024, the NISAR Project Science Team is building workflows for each Science Team discipline (Ecosystems, Cryosphere, and Solid Earth). This abstract focuses on the Ecosystem disciplines and the development of on-demand cloud-processing workflows for wetlands inundation, forest biomass, agricultural active crop area, and forest disturbance. The workflow simulates NISAR data using UAVSAR or ALOS-2 Single Look Complex data, which are processed to Level 2 geocoded polarimetric covariance matrix products using InSAR Scientific Computing Environment 3.0 software and to Level 3 science products using the Algorithm Theoretical Basis Documents. In this presentation, we describe these workflows and efforts to improve efficiency and data accessibility by using a cloud processing system. We present preliminary sample products from each Ecosystem discipline: inundation, forest biomass, crop area, and forest disturbance.

Christensen, Alexandra↗
DOE OSTI2024

Sentinel

Network intrusion detection systems (NIDS) are commonplace in network security but they frequently employ algorithms that are computational demanding requiring hardware and software with significant power requirements. Two examples of such resource-intensive algorithms used for network security are regular expression matching and broader signature pattern matching which are commonly used in deep packet inspection (DPI). Network security algorithms that have large power requirements may be a challenge for low-power internet-of-things (IoT) environments, which generally lack the power resources to implement complex security measures like computationally expensive DPI at the edge. Furthermore, IoT environments incorporating 5G standalone networks have network latency constraints beyond just power that make DPI at the edge even more difficult. Programmable logic is ideally suited for machine learning inference for DPI because of its deep instruction level parallelism and single-cycle memory access. Machine learning approaches for DPI have been explored before using the programmable logic of field programmable gate arrays (FPGA) as a potential solution for NIDS approaches that would be power-suitable for IoT. However, those previous programmable logic NIDS approaches utilize either a supervised or unsupervised learning model. Sentinel utilizes the ensemble of these two machine learning approaches known as a semi-supervised approach which has shown promise in NIDS implementations. Sentinel provides a programmable logic implementation of a semi-supervised approach for DPI which operates at much lower power and latency than a GPU implementation with negligible loss of accuracy due to quantization through a logistic regressor.

Anderson, MatthewW [Idaho National Laboratory (INL↗
DOE OSTI2025

Advanced System Thermal Fluids Solver Development for SAM

This work summarizes a feasibility study on testing numerical algorithms that are suitable and efficient for advanced system analysis code development under the mutli-physics framework, MOOSE. The key is the implementation of a high-order one-dimensional staggered-grid finite volume method (SG-FVM), and its direct interaction with the linear/nonlinear solver, PETSc. Leveraging the existing capabilities of the SAM code, significant code coverages were established in the finite volume method code. This in turn allows for a suite of test problems with different problem sizes and levels of complexity to be used to quantify the performance improvement of the finite volume method code. As evidently shown in this study, the implemented SG-FVM demonstrated superior performance improvement against a direct finite element method implementation through MOOSE for the wide range of selected problems. On two computer systems, the speedup was observed to be significant, with at least one order of magnitude of solving time reduction. In addition, for a complex reactor model, transient simulation was performed using the finite volume method code, the results of which agree very well with the reference results from the finite element method code. Overall, this study demonstrates a successful feasibility study on the proposed numerical algorithms and software structure to support advanced system analysis tool development. In this work, short-term priority development and testing items were identified, and long-term code adoption and integration plans were made for the eventual deployment of the finite volume method in the SAM code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Point containment algorithms for constructive solid geometry with unbounded primitives

Here, we present several algorithms for evaluating point containment in constructive solid geometry (CSG) trees with unbounded primitives. Three algorithms are presented based on postfix, prefix, and infix notations of the CSG binary expression tree. We show that prefix and infix notations enable short-circuiting logic, which reduces the number of primitives that must be checked during point containment. To evaluate the performance of the algorithms, each algorithm was implemented in the OpenMC Monte Carlo particle transport code, which relies on CSG to represent solid bodies through which subatomic particles travel. Two sets of tests were carried out. First, the execution time to generate a rasterized image of a 2D slice of three CSG models of varying complexity was measured. Use of both prefix and infix notations offered significant speedup over the postfix notation that has traditionally been used in particle transport codes, with infix resulting in a 6 x reduction in execution time relative to postfix for a model of a tokamak fusion device. We then measured the execution time of neutron transport simulations of the same three models using each of the algorithms. The results and performance improvements reveal the same trends as for the rasterization test, with a 5.52 x overall speedup using the infix notation relative to the original postfix notation in OpenMC for the tokamak model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Generalized representative structures for atomistic systems

A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.

atomic cluster expansion↗