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At least 127 records · Page 7
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DOE OSTI2021

Entropy stable modal discontinuous Galerkin schemes and wall boundary conditions for the compressible Navier-Stokes equations

Entropy stable schemes ensure that physically meaningful numerical solutions also satisfy a semi-discrete entropy inequality under appropriate boundary conditions. Here in this work, we describe a discretization of viscous terms in the compressible Navier-Stokes equations which enables a simple and explicit imposition of entropy stable no-slip and reflective (symmetry) wall boundary conditions for discontinuous Galerkin (DG) discretizations. Specifically, we derive methods for imposing adiabatic no-slip and reflective (symmetry) boundary conditions for modal entropy stable DG formulations which preserve a semi-discrete entropy inequality. Numerical results confirm the robustness and accuracy of the proposed approaches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Conservative DG method for the micro-macro decomposition of the Vlasov–Poisson–Lenard–Bernstein model

The micro-macro (mM) decomposition approach is considered for the numerical solution of the Vlasov– Poisson–Lenard–Bernstein (VPLB) system, which is relevant for plasma physics applications. In the mM approach, the kinetic distribution function is decomposed as $f$ = $\mathscr{E}$[$ρ_f$] + g , where $\mathscr{E}$ is a local equilibrium distribution, depending on the macroscopic moments $ρ_f$ = $∫_{\mathbb{R}}$ $efdv$ = $\langle$$ef$$\rangle$$_{\mathbb{R}}$, where e = (1, $v$, $\frac{1}{2}$ $v^2$) T , and $g$, the microscopic distribution, is defined such that $\langle$$eg$$\rangle$$_{\mathbb{R}}$ = 0. We aim to design numerical methods for the mM decomposition of the VPLB system, which consists of coupled equations for $ρ_f$ and $g$. To this end, we use the discontinuous Galerkin (DG) method for phase-space discretization, and implicit-explicit (IMEX) time integration, where the phase-space advection terms are integrated explicitly and the collision operator is integrated implicitly. We give special consideration to ensure that the resulting mM method maintains the $\langle$$eg$$\rangle$$_{\mathbb{R}}$ = 0 constraint, which may be necessary for obtaining (i) satisfactory results in the collision dominated regime with coarse velocity resolution, and (ii) unambiguous conservation properties. The constraint-preserving property is achieved through a consistent discretization of the equations governing the micro and macro components. Here, we present numerical results that demonstrate the performance of the mM method. The mM method is also compared against a corresponding DG-IMEX method solving directly for $f$.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Bio‐Imaging quorum sensing signal molecules in a soil‐mimic gel

Rhizosphere, the narrow region surrounding plant roots directly influenced by root exudates and the root associated microbiome, plays an important role in plant productivity and the rhizosphere is well known for stimulating microbial metabolic activities. How microbial communities interact to form stable, metabolically interconnected functional communities is an area of intense interest. The question remains on how microbially produced secreted molecules that function as intercellular communication signals shape the structure and function of microbial communities. Our goal is to detect and quantify signal molecules produced by microbes or plants in the root‐soil environment, spatially and temporarily. As a proof‐of‐concept, we are imaging diffusible extracellular microbial metabolites involved in a bacteria‐bacteria communication process called quorum‐sensing. Quorum‐sensing relies on the accumulation of high concentrations of signal molecules in the environment to control bacterial gene expression, influencing rhizosphere colonization and plant health. Local concentration of quorum sensing molecules are determined using aptamer based sensors. Aptamers that can specifically bind the desired signal molecules are selected through SELEX and immobilized on the surface of nano‐porous membranes. Binding of the signal molecules and aptamer covered surface results in changes in surface charge distribution and steric hinderance and thus modifying the transmembrane ionic transport. Changes in transmembrane impedance can be measured through electrochemical impedance spectroscopy methods to monitor local concentrations of signal molecules. Sensor responses were determined for different concentrations of signal molecules and results showed detection of C4‐HSL in a soil‐mimic solution with K D of 10 nM. We demonstrate that the quorum‐sensing signal molecule C4‐homoserine lactone and (C4‐HSL) can rapidly diffuse in a soil‐mimic gel, providing evidence for our use of a soil‐mimic for further aptasensor development and validation. The sensors were then inserted into soil mimic gel for monitoring C4‐HSL diffusion and the resulted impedance changes were used to determine the C4‐HSL concentration at different positions in the gel. Measurements of local C4‐HSL concentrations variation and numerical solution of diffusion equation were used to create 4D images of C4‐HSL molecule diffusion in the soil‐mimic gel.

Jiang, Nianyu↗
DOE OSTI2022

A Lagrangian dual method for two-stage robust optimization with binary uncertainties

This report presents a new exact method to calculate worst-case parameter realizations in two-stage robust optimization problems with categorical or binary-valued uncertain data. Traditional exact algorithms for these problems, notably Benders decomposition and column-and-constraint generation, compute worst-case parameter realizations by solving mixed-integer bilinear optimization subproblems. However, their numerical solution can be computationally expensive not only due to their resulting large size after reformulating the bilinear terms, but also because decision-independent bounds on their variables are typically unknown. We propose an alternative Lagrangian dual method that circumvents these difficulties and is readily integrated in either algorithm. We specialize the method to problems where the binary parameters switch on or off constraints as these are commonly encountered in applications, and discuss extensions to problems that lack relatively complete recourse and to those with integer recourse. Numerical experiments provide evidence of significant computational improvements over existing methods.

42 ENGINEERING↗
DOE OSTI2024

Simplified Universal Equations for Ionic Conductivity and Transference Number

Nernst-Einstein equation can provide a reasonable estimate of the ionic conductivity of dilute solutions. For concentrated solutions, alternate methods such as Green–Kubo relations and Einstein relations are more suitable to account for ion-ion interactions. Such computations can be expensive for multicomponent systems. Simplified mathematical expressions like the Nernst-Einstein equation do not exist for concentrated multicomponent mixtures. Newman’s treatment of multicomponent concentrated solutions yields a conductivity relation in terms of species concentration and Onsager phenomenological coefficients. However, the estimation of these phenomenological coefficients is not straightforward. Here, mathematical formulations that relate the phenomenological coefficients with the friction coefficients are developed, leading to simplified, ready-to-use expressions of conductivity and transference numbers that can be used for a wide range of ionic mixtures. This approach involves spectral decomposition of the matrix of Onsager phenomenological coefficients. The general analytical expressions for conductivity and transference number are simplified for binary electrolytes, and numerical solutions are provided for ternary and quaternary mixtures with ion dissociation.

Electrochemistry↗
DOE OSTI2022

Spatial resolution of different discretizations over long-time for the Dirac equation with small potentials

In this report we compare the long-time error bounds and spatial resolution of finite difference methods with different spatial discretizations for the Dirac equation with small electromagnetic potentials characterized by $\varepsilon \in (0, 1]$ a dimensionless parameter. We begin with the simple and widely used finite difference time domain (FDTD) methods, and establish rigorous error bounds of them, which are valid up to the time at $O(1/\varepsilon)$. In the error estimates, we pay particular attention to how the errors depend explicitly on the mesh size $h$ and time step $\tau$ as well as the small parameter $\varepsilon$. Based on the results, in order to obtain "correct" numerical solutions up to the time at $O(1/\varepsilon)$, the $\varepsilon$-scalability (or meshing strategy requirement) of the FDTD methods should be taken as $h = O(\varepsilon^{1/2})$ and $\tau = O(\varepsilon^{1/2})$. To improve the spatial resolution capacity, we apply the Fourier spectral method to discretize the Dirac equation in space. Error bounds of the resulting finite difference Fourier pseudospectral (FDFP) methods show that they exhibit uniform spatial errors in the long-time regime, which are optimal in space as suggested by the Shannon's sampling theorem. Extensive numerical results are reported to confirm the error bounds and demonstrate that they are sharp.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A meshless stochastic method for Poisson–Nernst–Planck equations

A plethora of biological, physical, and chemical phenomena involve transport of charged particles (ions). Its continuum-scale description relies on the Poisson–Nernst–Planck (PNP) system, which encapsulates the conservation of mass and charge. The numerical solution of these coupled partial differential equations is challenging and suffers from both the curse of dimensionality and difficulty in efficiently parallelizing. We present a novel particle-based framework to solve the full PNP system by simulating a drift–diffusion process with time- and space-varying drift. We leverage Green’s functions, kernel-independent fast multipole methods, and kernel density estimation to solve the PNP system in a meshless manner, capable of handling discontinuous initial states. The method is embarrassingly parallel, and the computational cost scales linearly with the number of particles and dimension. We use a series of numerical experiments to demonstrate both the method’s convergence with respect to the number of particles and computational cost vis-à-vis a traditional partial differential equation solver.

Chemistry↗
DOE OSTI2020

Helicity at small x: oscillations generated by bringing back the quarks

We construct a numerical solution of the recently-derived large-N c &N f small-x helicity evolution equations with the aim to establish the small-x asymptotics of the quark helicity distribution beyond the large-N c limit explored previously in the same framework. (Here N c and N f are the numbers of quark colors and flavors.) While the large-N c helicity evolution involves gluons only, the large-N c &N f evolution includes contributions from quarks as well. We find that adding quarks to the evolution makes quark helicity distribution oscillate as a function of x. Our numerical results in the large-N c &N f limit lead to the x-dependence of the flavor-singlet quark helicity distribution which is well-approximated by $$ {\left.\Delta \Sigma \left(x,{Q}^2\right)\right|}_{\mathrm{large}\hbox{-} {N}_c\&{N}_f}\sim {\left(\frac{1}{x}\right)}^{\alpha_h^q}\cos \left[{\omega}_q\ln \left(\frac{1}{x}\right)+{\varphi}_q\right]. $$. The power $α^{q}_{h}$ exhibits a weak N f -dependence, and, for all Nf values considered, remains very close to $α^{q}_{h}$(N f =0)=$\left(4/\sqrt{3}\right)\sqrt{\alpha_s{N}_c/\left(2\pi \right)}$ obtained earlier in the large-N c limit. The novel oscillation frequency ω q and phase shift φ q depend more strongly on the number of flavors N f (with ω q = 0 in the pure-glue large-N c limit). The typical period of oscillations for ΔΣ is rather long, spanning many units of rapidity. We speculate whether the oscillations we find are related to the sign variation with x seen in the strange quark helicity distribution extracted from the data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Energy conserving and well-balanced discontinuous Galerkin methods for the Euler–Poisson equations in spherical symmetry

ABSTRACT This paper presents high-order Runge–Kutta (RK) discontinuous Galerkin methods for the Euler–Poisson equations in spherical symmetry. The scheme can preserve a general polytropic equilibrium state and achieve total energy conservation up to machine precision with carefully designed spatial and temporal discretizations. To achieve the well-balanced property, the numerical solutions are decomposed into equilibrium and fluctuation components that are treated differently in the source term approximation. One non-trivial challenge encountered in the procedure is the complexity of the equilibrium state, which is governed by the Lane–Emden equation. For total energy conservation, we present second- and third-order RK time discretization, where different source term approximations are introduced in each stage of the RK method to ensure the conservation of total energy. A carefully designed slope limiter for spherical symmetry is also introduced to eliminate oscillations near discontinuities while maintaining the well-balanced and total-energy-conserving properties. Extensive numerical examples – including a toy model of stellar core collapse with a phenomenological equation of state that results in core bounce and shock formation – are provided to demonstrate the desired properties of the proposed methods, including the well-balanced property, high-order accuracy, shock-capturing capability, and total energy conservation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Droplet formation simulation using mixed finite elements

Droplet formation happens in finite time due to the surface tension force. The linear stability analysis is useful to estimate the size of a droplet but fails to approximate the shape of the droplet. This is due to a highly nonlinear flow description near the point where the first pinch-off happens. A one-dimensional axisymmetric mathematical model was first developed by Eggers and Dupont [“Drop formation in a one-dimensional approximation of the Navier–Stokes equation,” J. Fluid Mech. 262, 205–221 (1994)] using asymptotic analysis. This asymptotic approach to the Navier–Stokes equations leads to a universal scaling explaining the self-similar nature of the solution. Numerical models for the one-dimensional model were developed using the finite difference [Eggers and Dupont, “Drop formation in a one-dimensional approximation of the Navier–Stokes equation,” J. Fluid Mech. 262, 205–221 (1994)] and finite element method [Ambravaneswaran et al., “Drop formation from a capillary tube: Comparison of one-dimensional and two-dimensional analyses and occurrence of satellite drops,” Phys. Fluids 14, 2606–2621 (2002)]. The focus of this study is to provide a robust computational model for one-dimensional axisymmetric droplet formation using the Portable, Extensible Toolkit for Scientific Computation. The code is verified using the Method of Manufactured Solutions and validated using previous experimental studies done by Zhang and Basaran [“An experimental study of dynamics of drop formation,” Phys. Fluids 7, 1184–1203 (1995)]. The present model is used for simulating pendant drops of water, glycerol, and paraffin wax, with an aspiration of extending the application to simulate more complex pinch-off phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Learning how structures form in drift-wave turbulence

Drift-wave turbulence produces anomalous transport via cross-correlations between fluctuations. This transport has profound implications for confinement, structure formation, and virtually all aspects of the non-linear turbulent dynamics. Herein, we use a data-driven method based on deep learning in order to study turbulent transport in the 2D Hasegawa–Wakatani system and infer a reduced mean-field model from numerical solution. In addition to the usual turbulent diffusion, we find an effect which couples the particle flux to the local gradient of vorticity, which tends to modulate the density profile. The direct coupling to the shear is relatively weak. In addition, the deep learning method finds a model for spontaneous zonal flow generation by negative viscosity, stabilized by non-linear and hyperviscous terms. We compare these results to analytic calculations using quasilinear theory and wave kinetics, finding qualitative agreement, though the calculations miss certain higher-order effects. A simplified, 1-D model for the evolution of the profile, flow, and intensity based on the deep learning results is solved numerically and compared to previous models for staircasing based on bistability. We see that the physics uncovered by the deep learning method provided simple explanations for the formation of zonal structures in the density, flow, and turbulence fields. We highlight the important role of symmetry in the deep learning method and speculate on the portability of the method to other applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Recurrent neural network-based multiaxial plasticity model with regularization for physics-informed constraints

We report a recurrent neural network (RNN) based model is developed as a surrogate to predict nonlinear plastic response under multiaxial loading. The RNN-based model is trained and tested on stress versus strain curves generated using a numerical solution based on the classical radial return method. Besides simply learning the basic constitutive relationship, a novel approach is taken to enforce certain physical conditions. Specifically, regularization is employed to maintain non-negative plastic power density throughout the loading history thereby ensuring monotonically increasing plastic work and thermodynamic consistency. Enforcing physics in this manner permits coupling of the data-driven RNN approach with physics-based knowledge and laws. This has the effect of reducing the necessary amount of data and ensuring known physical laws are not violated. Since, once trained, the model need not perform the expensive task of solving nonlinear equations, its efficiency is orders of magnitude greater than its numerical counterpart. The RNN-based model has been trained on varied sets of data and the accuracy on test datasets validated. The developed model is general and robust and has widespread application such as in the simulation of metal forming, large scale plasticity, and part life prediction.

42 ENGINEERING↗
DOE OSTI2025

A novel ignition model for low velocity impact of heterogeneous explosives based on interacting hot spots

While numerous studies have focused on the ignition of explosives occurring in high velocity impact and the associated shock-to-detonation transition, there has been growing interest in developing computational models focused on low-velocity impact regimes. A predictive low-velocity impact ignition model will be important for analyzing high explosive safety and potential accident scenarios. This work introduces a novel ignition model based on the concept of thermally interacting hot spots to simulate low velocity impacted heterogeneous explosives where observed ignition times are on the order of milliseconds. The model asserts that relevant hot spots are micron-sized, the typical separation between neighboring hot spots is on the order of a hundred microns, and that neighbors interact thermally through heat conduction across the interstitial region between them. To achieve tractable numerical solutions, hot spots are assumed to form a periodic array as opposed to the highly irregular positioning in an actual explosive. This idealization allows a single two hotspot system to characterize the ignition process. Consequently, the model is referred to as the two hot spot Frank-Kamenetskii ignition model. In the present study, hot spots are modeled as constant heat sources terms, but this can be extended to include grain-scale phenomena like frictional heating of micron-sized growing cracks that are confined under high pressure. Because the micron-sized features are below the scale that can be efficiently resolved at a systems level, an efficient subscale scheme based on the Method of Weighted Residuals (MWR) is used to efficiently solve the equations. In conclusion, we carry out numerical examples and analytic predictions illustrating the accuracy and the functioning of the model.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Natively Periodic Fast Multipole Method: Approximating the Optimal Green’s Function

The fast multipole method (FMM) obeys periodic boundary conditions "natively" if it uses a periodic Green's function for computing the multipole expansion in the interaction zone of each FMM oct-tree node. One can define the "optimal" Green's function for such a method that results in the numerical solution that converges to the equivalent particle-mesh (PM) solution in the limit of sufficiently high order of multipoles. A discrete functional equation for the optimal Green's function can be derived, but is not practically useful as methods for its solution are not known. Instead, this paper presents an approximation for the optimal Green's function that is accurate to better than 10 -3 in ${L}_{\mathrm{MAX}}$ norm and 10 -4 in L 2 norm for practically useful multipole counts. Such an approximately optimal Green's function offers a practical way for implementing the FMM with periodic boundary conditions natively, without the need to compute lattice sums or to rely on hybrid FMM-PM approaches.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

A randomized sketching trust-region secant method for low-memory dynamic optimization

The numerical solution of dynamic optimization problems is often limited by the memory required to store the state trajectory, which is used to evaluate the objective function and its derivatives. Recently, [R. Muthukumar et al., SIAM Journal on Optimization 31(2), pp. 1242–1275 (2021)] introduced a trust-region method for dynamic optimization that employs randomized sketching to compress the state trajectory, resulting in inexact derivative computations. By adaptively learning the sketch rank, the trust-region algorithm achieves rigorous convergence guarantees. Here, we extend this approach to use secant Hessian approximations. Due to the randomness introduced by the sketch, the traditional secant update formulae can produce poor Hessian approximations. In particular, the difference of two gradients, computed from two different sketches, may be inconsistent. To overcome this, we employ a sketched approximation of the Hessian application, in lieu of computing the gradient difference. We numerically demonstrate the improved stability of this approach on an example from PDE-constrained optimization.

dynamic optimization↗
DOE OSTI2021

Plasma heating and current sheet structure in anti-parallel magnetic reconnection

A theoretical model and an analytic theory of current sheet structure are presented for understanding anti-parallel driven magnetic reconnection in 2-1/2 dimension in collisionless plasmas. The theoretical model provides formulation to compute the current sheet y-profiles by specifying the profiles of electron and ion flow velocities V ex (x,y) and V ix (x,y). The current sheet solutions depend on the plasma density n in , merging magnetic field B 0 , ion velocity v i , and electron velocity ve in the upstream and the S evz =V ez /V dz parameter where V ez is the electron velocity accelerated by the reconnection electric field E z in the electron orbit meandering region, V dz ≃cE y /B x is the $\overrightarrow{E}$ × $\overrightarrow{B}$ drift velocity as electrons enter the orbit meandering region, B x is the merging magnetic field, and E y is the electrostatic electric field. With simplifying assumptions on the y-profiles of V ex and V ix , we have also developed an analytic theory of the current sheet structure. Analytic expressions for the anomalous resistivity, the electrostatic potential drop, and the maximum E y amplitude E max are obtained. The analytic results agree reasonably well with both the particle-in-cell simulation results and the numerical solutions of the theoretical model. The ions energy gain due to the potential drop is $∝B^2_0/n_{in}$. The electron energy gain is $∝(B^2_0 /8πn_{in})S_{evz}$. The $B^2_0/n_{in}$ scaling of the average ion and electron energy gains are consistent with laboratory experiments and space plasma observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Ameliorating the Courant-Friedrichs-Lewy condition in spherical coordinates: A double FFT filter method for general relativistic MHD in dynamical spacetimes

Numerical simulations of merging compact objects and their remnants form the theoretical foundation for gravitational wave and multimessenger astronomy. While Cartesian-coordinate-based adaptive mesh refinement is commonly used for simulations, spherical-like coordinates are more suitable for nearly spherical remnants and azimuthal flows due to lower numerical dissipation in the evolution of fluid angular momentum, as well as requiring fewer numbers of computational cells. However, the use of spherical coordinates to numerically solve hyperbolic partial differential equations can result in severe Courant-Friedrichs-Lewy (CFL) stability condition time step limitations, which can make simulations prohibitively expensive. This paper addresses this issue for the numerical solution of coupled spacetime and general relativistic magnetohydrodynamics evolutions by introducing a double fast Fourier transform (FFT) filter and implementing it within the fully message passing interface (mpi)-parallelized sphericalnr framework in the einstein toolkit. In conclusion, we demonstrate the effectiveness and robustness of the filtering algorithm by applying it to a number of challenging code tests, and show that it passes these tests effectively, demonstrating convergence while also increasing the time step significantly compared to unfiltered simulations.

79 ASTRONOMY AND ASTROPHYSICS↗