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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Analytic quasi-steady evolution of marginally unstable kinetic plasma instabilities in the presence of drag and scattering

The 1D bump-on-tail problem is studied in order to determine the influence of drag on quasi-steady solutions near marginal stability (1-γ d /γ L << 1) when effective collisions are much larger than the instability growth rate (ν>>γ). In this common tokamak regime, it is rigorously shown that the paradigmatic Berk–Breizman cubic equation for the nonlinear mode evolution reduces to a much simpler differential equation, dubbed the time-local cubic equation, which can be solved directly. It is found that in addition to increasing the saturation amplitude, drag introduces a shift in the apparent oscillation frequency by modulating the saturated wave envelope. Furthermore, excellent agreement is found between the analytic solution for the mode evolution and both the numerically integrated Berk–Breizman cubic equation and fully nonlinear 1D Vlasov simulations. Experimentally isolating the contribution of drag to the saturated mode amplitude for verification purposes is explored but complicated by the reality that the amount of drag cannot be varied independently of other key parameters in realistic scenarios. While the influence of drag is modest when the ratio of effective drag to effective scattering α/ν is very small, it can become substantial when α/ν ≳ 0.5, suggesting that drag should be accounted for in quantitative models of fast-ion-driven instabilities in fusion plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

A new form of the Saint-Venant equations for variable topography

The solution stability of river models using the one-dimensional (1D) Saint-Venant equations can be easily undermined when source terms in the discrete equations do not satisfy the Lipschitz smoothness condition for partial differential equations. Although instability issues have been previously noted, they are typically treated as model implementation issues rather than as underlying problems associated with the form of the governing equations. This study proposes a new reference slope form of the Saint-Venant equations to ensure smooth slope source terms and eliminate one source of potential numerical oscillations. It is shown that a simple algebraic transformation of channel geometry provides a smooth reference slope while preserving the correct cross-section flow area and the total Piezometric pressure gradient that drives the flow. The reference slope method ensures the slope source term in the governing equations is Lipschitz continuous while maintaining all the underlying complexity of the real-world geometry. The validity of the mathematical concept is demonstrated with the open-source Simulation Program for River Networks (SPRNT) model in a series of artificial test cases and a simulation of a small urban creek. Validation comparisons are made with analytical solutions and the Hydrologic Engineering Center's River Analysis System (HEC-RAS) model. The new method reduces numerical oscillations and instabilities without requiring ad hoc smoothing algorithms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Gradient-enhanced physics-informed neural networks for forward and inverse PDE problems

Deep learning has been shown to be an effective tool in solving partial differential equations (PDEs) through physics-informed neural networks (PINNs). PINNs embed the PDE residual into the loss function of the neural network, and have been successfully employed to solve diverse forward and inverse PDE problems. However, one disadvantage of the first generation of PINNs is that they usually have limited accuracy even with many training points. Here, we propose a new method, gradient-enhanced physics-informed neural networks (gPINNs), for improving the accuracy of PINNs. gPINNs leverage gradient information of the PDE residual and embed the gradient into the loss function. We tested gPINNs extensively and demonstrated the effectiveness of gPINNs in both forward and inverse PDE problems. Our numerical results show that gPINN performs better than PINN with fewer training points. Additionally, we combined gPINN with the method of residual-based adaptive refinement (RAR), a method for improving the distribution of training points adaptively during training, to further improve the performance of gPINN, especially in PDEs with solutions that have steep gradients.

42 ENGINEERING↗
DOE OSTI2024

Stochastic modeling of x-ray superfluorescence

An approach to modeling the dynamics of x-ray amplified spontaneous emission and superfluorescence, the phenomenon of collective x-ray emission initiated by intense pulses of x-ray free-electron lasers, is developed based on stochastic partial differential equations. The equations are derived from first principles, and the relevant approximations, derivation steps, and extensions specific to stimulated x-ray emission are presented. The resulting equations take the form of three-dimensional generalized Maxwell-Bloch equations augmented with noise terms for both field and atomic variables. The derived noise terms possess specific correlation properties that enable the correct reconstruction of spontaneous emission. Consequently, the developed theoretical formalism is universally suitable for describing all stages of stimulated x-ray emission: spontaneous emission, amplified spontaneous emission, and superfluorescence. Here, we present numerical examples that illustrate various properties of the emitted field, including spatiotemporal coherence and spectral-angular and polarization characteristics. We anticipate that the proposed theoretical framework will establish a robust foundation for interpreting measurements in stimulated x-ray emission spectroscopy, modeling x-ray laser oscillators, and describing other experiments leveraging x-ray superfluorescence.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Mixing Cell Model: A One-Dimensional Numerical Model for Assessment of Water Flow and Contaminant Transport in the Unsaturated Zone

This report describes the Mixing Cell Model code, a one dimensional model for water flow and solute transport in the unsaturated zone under steady state or transient flow conditions. The model is based on the principles and assumptions underlying mixing-cell model formulations. The unsaturated zone is discretized into a series of independent mixing cells. Each cell may have unique hydrologic, lithologic, and sorptive properties. Ordinary differential equations describe the material (water and solute) balance within each cell. Water-flow equations are derived from the continuity equation, assuming that unit gradient conditions exist at all times in each cell. Pressure gradients are considered implicitly through model discretization. Unsaturated hydraulic conductivity and moisture contents are determined by the material specific moisture-characteristic curves. Solute-transport processes include explicit treatment of advective processes, first order chain decay, and linear sorption reactions. Dispersion is addressed through implicit and explicit dispersion. Implicit dispersion is an inherent feature of all mixing-cell models and originates from the formulation of the problem in terms of mass balance around fully mixed volume elements. Expressions are provided that relate implicit dispersion to the physical dispersion of the system. Two FORTRAN codes were developed to solve the water flow and solute-transport equations: (1) the Mixing Cell Model for Flow (MCMF) solves transient water-flow problems and (2) the Mixing Cell Model for Transport (MCMT) solves the solute-transport problem. The transient water-flow problem is typically solved first by estimating the water flux through each cell in the model domain as a function of time using the MCMF code. These data are stored in either ASCII or binary files that are later read by the solute transport code (MCMT). Code output includes solute pore water concentrations, water and solute inventories in each cell and at each specified output time, and water and solute fluxes through each cell and specified output time. Computer run times for coupled transient water flow and solute transport were typically several seconds on a 2 GHz Intel Pentium IV desktop computer. The model was benchmarked against analytical solutions and finite element approximations to the partial differential equations (PDE) describing unsaturated flow and transport. Differences between the maximum solute flux estimated by the mixing cell model and the PDE models were typically less than two percent. This revision includes an option for a fixed concentration lower boundary condition for diffusive fluxes for versions 020321 and later.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Bayesian differential programming for robust systems identification under uncertainty

This paper presents a machine learning framework for Bayesian systems identification from noisy, sparse and irregular observations of nonlinear dynamical systems. The proposed method takes advantage of recent developments in differentiable programming to propagate gradient information through ordinary differential equation solvers and perform Bayesian inference with respect to unknown model parameters using Hamiltonian Monte Carlo sampling. This allows an efficient inference of the posterior distributions over plausible models with quantified uncertainty, while the use of sparsity-promoting priors enables the discovery of interpretable and parsimonious representations for the underlying latent dynamics. A series of numerical studies is presented to demonstrate the effectiveness of the proposed methods, including nonlinear oscillators, predator–prey systems and examples from systems biology. Taken together, our findings put forth a flexible and robust workflow for data-driven model discovery under uncertainty. All codes and data accompanying this article are available at https://bit.ly/34FOJMj .

Science & Technology - Other Topics↗
DOE OSTI2023

Osmotic Pressure Gradient Effects on Water Diffusion in Porous Rock: Can They Pervert Permeability Tests?

Abstract Generation of a large network of hydraulic cracks is of key importance not only for the success of fracking of shale but also for the recent scheme of sequestration of CO2 in deep formations of basalt and peridotite, which are mafic and ultramafic rocks that combine chemically with CO2. In numerical simulation of the creation of a fracture network in porous rock, an important goal is to enhance the rock permeability. The objective of this article is to calculate the effect of osmotic pressure gradients caused by gradients of concentration of the ions of Ca, Mg, Na, etc. on the effective permeability of the rock. The basic differential equations are formulated, and their explicit solutions for appropriate initial and boundary conditions are obtained under certain plausible simplifications. The main result is explicit approximate formulas for the critical time before which no water permeation through a test specimen can be observed. Depending on various parameters, this time can be unacceptably long, which is manifested as a zero water outflow. The solution may also explain the unreasonably small permeability values reported for some shales.

Mechanics↗
DOE OSTI2024

Speeding up and reducing memory usage for scientific machine learning via mixed precision

Scientific machine learning (SciML) has emerged as a versatile approach to address complex computational science and engineering problems. Within this field, physics-informed neural networks (PINNs) and deep operator networks (DeepONets) stand out as the leading techniques for solving partial differential equations by incorporating both physical equations and experimental data. However, training PINNs and DeepONets require significant computational resources, including long computational times and large amounts of memory. In search of computational efficiency, training neural networks using half precision (float16) rather than the conventional single (float32) or double (float64) precision has gained substantial interest, given the inherent benefits of reduced computational time and memory consumed. However, we find that float16 cannot be applied to SciML methods, because of gradient divergence at the start of training, weight updates going to zero, and the inability to converge to a local minima. To overcome these limitations, we explore mixed precision, which is an approach that combines the float16 and float32 numerical formats to reduce memory usage and increase computational speed. Our experiments showcase that mixed precision training not only substantially decreases training times and memory demands but also maintains model accuracy. Here, we also reinforce our empirical observations with a theoretical analysis. The research has broad implications for SciML in various computational applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Parallel-in-Time Simulation of Lindblad's Equation

Constructing fast quantum logic gates is critical to building a scalable quantum computer. We consider a qudit, a quantum version of a bit that can take an arbitrary number of states, coupled with a cavity. In this project, we wish to force the qudit to reach the 0-state, for any possible initial state. The coupled system changes in time according to Lindblad’s equation, an ordinary differential equation on the density matrix of the quantum system. Lindblad’s equation contains some parameters that we can control, so-called control functions. We seek control functions which force the qudit to the 0-state within 2 microseconds, which is much faster than what is currently done in practice. The search method is gradient descent, a numerical optimization method that uses gradient information to iteratively improve the control parameters. My contribution to this project is an attempt to speed up the computation of the gradient. It currently takes about 40 seconds to compute the gradient which involves solving a set of ODEs sequentially. Current supercomputers have thousands of cores, but sequential computations can only make use of 1 core at a time. We wish to divide up the work better, so that we can use many more cores at once. To this end, we have implemented the Multigrid Reduction in Time (MGRIT) algorithm. We perform a systematic parameter search on how to best apply this algorithm. Results indicate a 25 percent speed up for solving Lindblad’s equation and determining how close the final state is the 0-state.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Identifying stochastic dynamics via finite expression methods

Modeling stochastic differential equations (SDEs) is crucial for understanding complex dynamical systems in various scientific fields. Recent methods often employ neural network-based models, which typically represent SDEs through a combination of deterministic and stochastic terms. However, these models usually lack interpretability and have difficulty in generalizing beyond their training domain. Here, this paper introduces the Finite Expression Method (FEX), a symbolic learning approach designed to derive interpretable mathematical representations of the deterministic component of SDEs. For the stochastic component, we integrate FEX with advanced generative modeling techniques to provide a comprehensive representation of SDEs. The numerical experiments on linear, nonlinear, and multidimensional SDEs demonstrate that FEX generalizes well beyond the training domain and delivers more accurate long-term predictions compared to neural network-based methods. The symbolic expressions identified by FEX not only improve prediction accuracy but also offer valuable scientific insights into the underlying dynamics of the systems.

Complex dynamical systems↗
DOE OSTI2026

Energy-efficient scientific computing using chemical reservoirs

The rapid growth of computing demands driven by scientific computing, data analytics, and artificial intelligence (AI) advancements has exposed the limitations of traditional digital processing systems. These systems are nearing physical energy barriers, making significant gains in energy efficiency increasingly unattainable. As we advance toward post-exascale computing, disruptive approaches are critical to overcoming these limitations. Among emerging analog solutions, biochemical computing offers a transformative path for achieving orders-of-magnitude improvements in energy efficiency. By leveraging the natural optimization capabilities of chemical reaction networks (CRNs), biochemical systems have the potential to meet high-performance computing needs through natural scalability. However, numerous challenges remain, including theoretical limitations in mapping computational problems to CRNs and practical barriers in implementing biochemical computing devices. In this paper, we present a framework for chemical computation using biochemical systems and introduce key components of our approach for energy-efficient scientific computing. We showcase the feasibility of this framework by solving a system of ordinary differential equations by emulating a chemical reservoir device, demonstrating its potential for addressing modern computing challenges. This work lays a foundational step toward harnessing the computational power of chemistry to design energy-efficient, scalable, high-performance next-generation computing systems.

Johnson, Connah G. M. [Pacific Northwest National ↗
DOE OSTI2022

An improved framework for the dynamic likelihood filtering approach to data assimilation

Here, we propose improvements to the Dynamic Likelihood Filter (DLF), a Bayesian data assimilation filtering approach, specifically tailored to wave problems. The DLF approach was developed to address the common challenge in the application of data assimilation to hyperbolic problems in the geosciences and in engineering, where observation systems are sparse in space and time. When these observations have low uncertainties, as compared to model uncertainties, the DLF exploits the inherent nature of information and uncertainties to propagate along characteristics to produce estimates that are phase aware as well as amplitude aware, as would be the case in the traditional data assimilation approach. Along characteristics, the stochastic partial differential equations underlying the linear or nonlinear stochastic dynamics are differential equations. This study focuses on developing the explicit challenges of relating dynamics and uncertainties in the Eulerian and Lagrangian frames via dynamic Gaussian processes. It also implements the approach using the ensemble Kalman filter (EnKF) and compares the DLF approach to the conventional one with respect to wave amplitude and phase estimates in linear and nonlinear wave problems. Numerical comparisons show that the DLF/EnKF outperforms the EnKF estimates, when applied to linear and nonlinear wave problems. This advantage is particularly noticeable when sparse, low uncertainty observations are used.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A mixed-integer PDE-constrained optimization formulation for constructing electromagnetic cloaks with multiple materials

We study the design of an electromagnetic cloak from multiple materials with an additional constraint on the mass of the cloak. Our problem is an example of a topology optimization problem, and we formulate this problem as a mixed-integer partial-differential equation constrained optimization (MIPDECO) problem, where Maxwell’s equation models the propagation of the wave through the cloak and surrounding medium. We use binary variables to model the assignment of the different materials, and their relevant properties (permittivity and density). The mass constraint adds a nontrivial constraint to this problem. We propose a two-phase strategy to solve this problem. In the first phase, we solve a continuous relaxation, and then propose a new variant of the feasibility pump that exploits the structure of the PDE to obtain an initial integral solution candidate. In the second phase, we use a trust-region approach to improve this incumbent. We also consider a continuation or mesh-sequencing approach to find better solutions faster on consecutively finer meshes. We present detailed numerical results to illustrate the effectiveness of our approaches for constructing multi-material cloaks with a mass constraint.

Calculus of Variations and Optimization↗
DOE OSTI2023

A multifidelity deep operator network approach to closure for multiscale systems

Projection-based reduced order models (PROMs) have shown promise in representing the behavior of multiscale systems using a small set of generalized (or latent) variables. Despite their success, PROMs can be susceptible to inaccuracies, even instabilities, due to the improper accounting of the interaction between the resolved and unresolved scales of the multiscale system (known as the closure problem). In the current work, we interpret closure as a multifidelity problem and use a multifidelity deep operator network (DeepONet) framework to address it. In addition, to enhance the stability and/or accuracy of the multifidelity-based closure, we employ the recently developed ``in-the-loop" training approach from the literature on coupling physics and machine learning models. The resulting approach is tested on shock advection for the one-dimensional viscous Burgers equation and vortex merging for the two-dimensional Navier-Stokes equations. Furthermore, the numerical experiments show significant improvement of the predictive ability of the closure-corrected PROM over the un-corrected one both in the interpolative and the extrapolative regimes.

42 ENGINEERING↗
DOE OSTI2023

Dynamics of electrified liquid metal surface using shallow water model

A shallow water model that incorporates surface tension and electric field effects is developed to investigate the dynamics of an electrified liquid surface. The computational model is verified against the Zakharov–Kuznetsov equation and is applied to study the growth and damping of the electrified liquid surface. A linear wave analysis is performed under a shallow water theory assuming an analytic solution of the electric field, similar to the Tonks–Frenkel instability. The electrified liquid surface grows or dampens based on the balance of the electric field, surface tension, and gravitational forces. As a result, the numerical results obtained from the electrified shallow water solver are in good agreement with the theoretical analysis.

Computational models↗
DOE OSTI2020

A mathematical model of asynchronous data flow in parallel computers *

Abstract We present a simplified model of data flow on processors in a high-performance computing framework involving computations necessitating inter-processor communications. From this ordinary differential model, we take its asymptotic limit, resulting in a model which treats the computer as a continuum of processors and data flow as an Eulerian fluid governed by a conservation law. We derive a Hamilton–Jacobi equation associated with this conservation law for which the existence and uniqueness of solutions can be proven. We then present the results of numerical experiments for both discrete and continuum models; these show a qualitative agreement between the two and the effect of variations in the computing environment’s processing capabilities on the progress of the modelled computation.

Barnard, Richard C.↗
DOE OSTI2024

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗
DOE OSTI2023

Higher-Order Corrections to Optimisers based on Newton's Method

The Newton, Gauss–Newton and Levenberg–Marquardt methods all use the first derivative of a vector function (the Jacobian) to minimise its sum of squares. When the Jacobian matrix is ill-conditioned, the function varies much faster in some directions than others and the space of possible improvement in sum of squares becomes a long narrow ellipsoid in the linear model. This means that even a small amount of nonlinearity in the problem parameters can cause a proposed point far down the long axis of the ellipsoid to fall outside of the actual curved valley of improved values, even though it is quite nearby. This paper presents a differential equation that ‘follows’ these valleys, based on the technique of geodesic acceleration, which itself provides a 2 nd order improvement to the Levenberg–Marquardt iteration step. Higher derivatives of this equation are computed that allow n th order improvements to the optimisation methods to be derived. These higher-order accelerated methods up to 4 th order are tested numerically and shown to provide substantial reduction of both number of steps and computation time.

43 PARTICLE ACCELERATORS↗