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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism

Background As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. Methods In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. Results In 30 of 115 patients (26.1%), we identified four novel genes ( ARSH , DMD , MAGEA4 and SHROOM2 ) affecting at least five unrelated patients and four known genes ( USP9Y , UBA1 , BCORL1 and KDM6A ) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10 −6 ) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. Conclusion Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.

Chen, Jianhai (ORCID:0000000300932003)↗
DOE OSTI2020

Sampling and resolution characteristics in reduced order models of shallow water equations: Intrusive vs nonintrusive

We investigate the sensitivity of reduced order models (ROMs) to training data spatial resolution as well as sampling rate. In particular, we consider proper orthogonal decomposition (POD), coupled with Galerkin projection (POD-GP), as an intrusive reduced order modeling technique. For non-intrusive ROMs, we consider two frameworks. The first is using dynamic mode decomposition (DMD), and the second is based on artificial neural networks (ANNs). For ANN, we utilized a residual deep neural network, and for DMD we have studied two versions of DMD approaches; one with hard thresholding and the other with sorted bases selection. Also, we highlight the differences between mean-subtracting the data (centering) and using the data without mean-subtraction. We tested these ROMs using a system of 2D shallow water equations for four different numerical experiments, adopting combinations of sampling rates and spatial resolutions. For these cases, we found that the DMD basis obtained with hard threshodling is sensitive to sampling rate. The sorted DMD algorithm helps to mitigate this problem and yields more stabilized and converging solution. Furthermore, we demonstrate that both DMD approaches without mean subtraction provide significantly more accurate results than DMD with mean-subtracting the data. On the other hand, POD is relatively insensitive to sampling rate and yields better representation of the flow field. Meanwhile, spatial resolution has little effect on both POD and DMD performances. Here, the numerical results reveal that an ANN on POD subspace (POD-ANN) performs remarkably better than POD-GP and DMD in capturing system dynamics, even with a small number of modes.

42 ENGINEERING↗
DOE OSTI2022

Parametric dynamic mode decomposition for reduced order modeling

Dynamic Mode Decomposition (DMD) is a model-order reduction approach, whereby spatial modes of fixed temporal frequencies are extracted from numerical or experimental data sets. The DMD low-rank or reduced operator is typically obtained by singular value decomposition of the temporal data sets. For parameter-dependent models, as found in many multi-query applications such as uncertainty quantification or design optimization, the only parametric DMD technique developed was a stacked approach, with data sets at multiple parameter values were aggregated together, increasing the computational work needed to devise low-rank dynamical reduced-order models. Here in this paper, we present two novel approach to carry out parametric DMD: one based on the interpolation of the reduced-order DMD eigen-pair and the other based on the interpolation of the reduced DMD (Koopman) operator. Numerical results are presented for diffusion-dominated nonlinear dynamical problems, including a multiphysics radiative transfer example. All three parametric DMD approaches are compared.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Characterizing magnetized plasmas with dynamic mode decomposition

Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear and computationally intensive and can be difficult to interpret, while often only approximating the true dynamics. In this work, data-driven techniques recently developed in the field of fluid dynamics are leveraged to develop interpretable reduced-order models of plasmas that strike a balance between accuracy and efficiency. In particular, dynamic mode decomposition (DMD) is used to extract spatio-temporal magnetic coherent structures from the experimental and simulation datasets of the helicity injected torus with steady inductive (HIT-SI) experiment. Three-dimensional magnetic surface probes from the HIT-SI experiment are analyzed, along with companion simulations with synthetic internal magnetic probes. A number of leading variants of the DMD algorithm are compared, including the sparsity-promoting and optimized DMD. Optimized DMD results in the highest overall prediction accuracy, while sparsity-promoting DMD yields physically interpretable models that avoid overfitting. These DMD algorithms uncover several coherent magnetic modes that provide new physical insights into the inner plasma structure. These modes were subsequently used to discover a previously unobserved three-dimensional structure in the simulation, rotating at the second injector harmonic. Finally, using data from probes at experimentally accessible locations, DMD identifies a resistive kink mode, a ubiquitous instability seen in magnetized plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Dynamic mode decomposition for gyrokinetic eigenmode analysis

Dynamic mode decomposition (DMD) is a post-processing approach to decompose a complex time series into a set of modes via spectral analysis. DMD provides a new and powerful method to recover gyrokinetic drift-wave eigenfrequencies and eigenfunctions based only on the solution of the gyrokinetic-Maxwell initial value problem with almost no added cost to the initial value solver. In the present paper, DMD is applied to the CGYRO gyrokinetic code using a newly-developed CGYRO-DMD post-processor. CGYRO-DMD is numerically efficient, even on a single CPU. It does not set any restrictions on the plasma shape, beta (ratio of the plasma pressure to the magnetic field pressure), collisionality or number of species, and allows one to resolve numerous eigenmodes, even of comparable growth rates. In addition, DMD is not limited to unstable modes, but rather can capture stable and unstable branches simultaneously. In this work, we illustrate the accuracy of DMD through gyrokinetic analysis of mode transition for electromagnetic drift wave instabilities.

drift-wave eigenmodes↗
DOE OSTI2020

Survey of Dynamic Mode Decomposition Methods

Dynamic mode decomposition (DMD) is a data-driven reduced order modeling (ROM) technique used for dynamic systems. The widely adopted algorithm was first introduced and demonstrated on fluid flow data by Schmid. In recent years, various other fields, such as nuclear engineering, have begun to adopt this method. For example, DMD has been used for estimating α-eigenvalues, as an ROM for pulsed neutron problems, for predicting isotopic composition in burnup calculations, as acceleration techniques for iterative methods, and in capturing dynamic behaviors in molten salt reactor transients. This report seeks to demonstrate the capabilities and limits of the standard DMD algorithm, and identify problem spaces where variants may be better suited. The primary variant this report considers is Multi-Resolution DMD (mrDMD). Because this serves as a survey, synthetically produced data is used in lieu of simulation results. The remainder of this report will go into detail on the DMD theory, outline the standard DMD and mrDMD algorithms, present test cases highlighting the applicability of each, and finally present a discussion on how to determine the best suited algorithm for a given problem. All calculations performed in this report are carried out using the open source DMD library, PyDMD.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Data-Driven Analysis of Multipactor Dynamics via Dynamic Mode Decomposition

Multipactor effect is a performance-limiting kinetic plasma effect that can occur in high-power microwave and radio frequency (RF) devices. Multipactor effect is of special concern in vacuum or near-vacuum conditions such as those in particle accelerators and spaceborne devices. In this work, we present a data-driven reduced-order model (ROM) based on dynamic mode decomposition (DMD) for modeling of multipactor effects. We study multipactor effects and the resulting nonlinear harmonic generation by processing high-fidelity data generated from electromagnetic particle-in-cell (EMPIC) simulations using the DMD algorithm. We also investigate time-delay embedding extensions of DMD with improved generalizability and accuracy for modeling the electron plasma current density behavior. Here, the results show that DMD provides valuable insights into multipactor phenomena by extracting relevant modal spatiotemporal patterns and frequencies. In addition, DMD offers the potential to time extrapolate EMPIC simulations at a minimal cost, thereby reducing overall simulation time.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Reduced-order modeling on a near-term quantum computer

Quantum computing is an advancing area of research in which computer hardware and algorithms are developed to take advantage of quantum mechanical phenomena. In recent studies, quantum algorithms have shown promise in solving linear systems of equations as well as systems of linear ordinary differential equations (ODEs) and partial differential equations (PDEs). Reducedorder modeling (ROM) algorithms for studying fluid dynamics have shown success in identifying linear operators that can describe flowfields, where dynamic mode decomposition (DMD) is a particularly useful method in which a linear operator is identified from data. In this work, DMD is reformulated as an optimization problem to propagate the state of the linearized dynamical system on a quantum computer. This reformulation was chosen as a means of facilitating implementation on a near-term quantum computer. Quadratic unconstrained binary optimization (QUBO), a technique for optimizing quadratic polynomials in binary variables, allows for quantum annealing algorithms to be applied. A quantum circuit model (quantum approximation optimization algorithm, QAOA) is utilized to obtain predictions of the state trajectories. Results are shown for the quantum-ROM predictions for flow over a 2D cylinder at Re = 220 and flow over a NACA0009 airfoil at Re = 500 and α = 15°. The quantum-ROM predictions are found to depend on the number of bits utilized for a fixed point representation and the truncation level of the DMD model. Comparisons with DMD predictions from a classical computer algorithm are made, as well as an analysis of the computational complexity and prospects for future, more fault-tolerant quantum computers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Using dynamic mode decomposition to predict the dynamics of a two-time non-equilibrium Green’s function

Computing the numerical solution of the Kadanoff–Baym equations, a set of nonlinear integral differential equations satisfied by the two-time Green's functions derived from many-body perturbation theory for a quantum many-body system away from equilibrium, is a challenging task. Recently, we have successfully applied dynamic mode decomposition (DMD) to construct a data driven reduced order model that can be used to extrapolate the time-diagonal of a two-time Green's function from numerical solutions of the KBE within a small time window. In this paper, we extend the previous work and use DMD to predict off-diagonal elements of the two-time Green's function. We partition the two-time Green's function into a number of one-time functions along the diagonal and subdiagonals of the two-time window as well as in horizontal and vertical directions. We use DMD to construct separate reduced order models to predict the dynamics of these one-time functions in a two-step procedure. We extrapolate along diagonal and several subdiagonals within a subdiagonal band of a two-time window in the first step. In the second step, we use DMD to extrapolate the Green's function outside of the sub-diagonal band. In conclusion, we demonstrate the efficiency and accuracy of this approach by applying it to a two-band Hubbard model problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Dynamic mode decomposition of nonequilibrium electron-phonon dynamics: accelerating the first-principles real-time Boltzmann equation

Abstract Nonequilibrium dynamics governed by electron–phonon ( e -ph) interactions plays a key role in electronic devices and spectroscopies and is central to understanding electronic excitations in materials. The real-time Boltzmann transport equation (rt-BTE) with collision processes computed from first principles can describe the coupled dynamics of electrons and atomic vibrations (phonons). Yet, a bottleneck of these simulations is the calculation of e –ph scattering integrals on dense momentum grids at each time step. Here we show a data-driven approach based on dynamic mode decomposition (DMD) that can accelerate the time propagation of the rt-BTE and identify dominant electronic processes. We apply this approach to two case studies, high-field charge transport and ultrafast excited electron relaxation. In both cases, simulating only a short time window of ~10% of the dynamics suffices to predict the dynamics from initial excitation to steady state using DMD extrapolation. Analysis of the momentum-space modes extracted from DMD sheds light on the microscopic mechanisms governing electron relaxation to a steady state or equilibrium. The combination of accuracy and efficiency makes our DMD-based method a valuable tool for investigating ultrafast dynamics in a wide range of materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Dynamic mode decomposition with core sketch

With the increase in collected data volumes, either from experimental measurements or high fidelity simulations, there is an ever-growing need to develop computationally efficient tools to process, analyze, and interpret these datasets. Modal analysis techniques have gained great interest due to their ability to identify patterns in the data and extract valuable information about the system being considered. Dynamic mode decomposition (DMD) relies on elements of the Koopman approximation theory to compute a set of modes, each associated with a fixed oscillation frequency and a decay/growth rate. Extracting these details from large datasets can be computationally expensive due to the need to implement singular value decomposition of the input data matrix. Sketching algorithms have become popular in numerical linear algebra where statistical theoretic approaches are utilized to reduce the cost of major operations. A sketch of a matrix is another matrix, which is significantly smaller, but still sufficiently approximates the original system. We put forth an efficient DMD framework, SketchyDMD, based on a core sketching algorithm that captures information about the range and corange (their mutual relationship) of input data. The proposed sketching-based framework can accelerate various portions of the DMD routines, compared to classical methods that operate directly on the raw input data. We conduct numerical experiments using the spherical shallow water equations as a prototypical model in the context of geophysical flows. In conclusion, we show that the proposed SketchyDMD is superior to existing randomized DMD methods that are based on capturing only the range of the input data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Accelerating particle-in-cell kinetic plasma simulations via reduced-order modeling of space-charge dynamics using dynamic mode decomposition

We present a data-driven reduced-order modeling of the space-charge dynamics for electromagnetic particle-in-cell (EMPIC) plasma simulations based on dynamic mode decomposition (DMD). The dynamics of the charged particles in kinetic plasma simulations such as EMPIC is manifested through the plasma current density defined along the edges of the spatial mesh. We showcase the efficacy of DMD in modeling the time evolution of current density through a low-dimensional feature space. Not only do such DMD based predictive reduced-order models help accelerate EMPIC simulations, they also have the potential to facilitate investigative analysis and control applications. Here, we demonstrate the proposed DMD-EMPIC scheme for reduced-order modeling of current density and speedup in EMPIC simulations involving electron beam under the influence of magnetic field, virtual cathode oscillations, and backward wave oscillator.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Granger Causality for prediction in Dynamic Mode Decomposition: Application to power systems

Here, the dynamic mode decomposition (DMD) technique extracts the dominant modes characterizing the innate dynamical behavior of the system within the measurement data. For appropriate identification of dominant modes from the measurement data, the DMD algorithm necessitates ensuring the quality of the input measurement data sequences. On that account, for validating the usability of the dataset for the DMD algorithm, the paper proposed two conditions: Persistence of excitation (PE) and the Granger Causality Test (GCT). The virtual data sequences are designed with the hankel matrix representation such that the dimensions of the subspace spanning the essential system modes are increased with the addition of new state variables. The PE condition provides the lower bound for the trajectory length, and the GCT provides the order of the model. Satisfying the PE condition enables estimating an approximate linear model, but the predictability with the identified model is only assured with the temporal causation among data searched with GCT. The proposed methodology is validated with the application for coherency identification (CI) in a multi-machine power system (MMPS), an essential phenomenon in transient stability analysis. The significance of PE condition and GCT is demonstrated through various case studies implemented on 22 bus six generator system.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Data-driven acceleration of thermal radiation transfer calculations with the dynamic mode decomposition and a sequential singular value decomposition

In this work, we present a method for accelerating discrete ordinates radiative transfer calculations for radiative transfer. Our method works with nonlinear positivity fixes, in contrast to most acceleration schemes. The method is based on the dynamic mode decomposition (DMD) and using a sequence of rank-one updates to compute the singular value decomposition needed for DMD. Using a sequential method allows us to automatically determine the number of solution vectors to include in the DMD acceleration. We present results for slab geometry discrete ordinates calculations with the standard temperature linearization. Compared with positive source iteration, our results demonstrate that our acceleration method reduces the number of transport sweeps required to solve the problem by a factor of about 3 on a standard diffusive Marshak wave problem, a factor of several thousand on a cooling problem where the effective scattering ratio approaches unity, and a factor of 20 improvement in a realistic, multimaterial radiating shock problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

AMOC Variability in Climate Models and Its Dependence on the Mean State

Abstract Understanding internal variability of the climate system is critical when isolating internal and anthropogenically forced signals. Here, we investigate the modes of Atlantic Meridional Overturning Circulation ( AMOC ) variability using perturbation experiments with the Institut Pierre‐Simon Laplace's (IPSL) coupled model and compare them to Coupled Model Intercomparison Project Phase 6 (CMIP6) pre‐industrial control simulations. We identify two characteristic modes of variability—decadal‐to‐multidecadal ( DMD var ) and centennial ( CEN var ). The former is driven largely by temperature anomalies in the subpolar North Atlantic, while the latter is driven by salinity in the western subpolar North Atlantic. The amplitude of each mode scales linearly with the mean AMOC strength in the IPSL experiments. The DMD var amplitude correlates well with the AMOC mean strength across CMIP6 models, while the CEN var mode does not. These findings suggest that the strength of DMD var depends robustly on the North Atlantic mean state, while the CEN var mode may be model‐dependent.

Ferster, Brady S. [LOCEAN‐IPSL Sorbonne Université↗