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At least 775 records · Page 43

A tightly-coupled domain-decomposition approach for highly nonlinear stochastic multiphysics systems

Multiphysics simulations often involve nonlinear components that are driven by internally generated or externally imposed random fluctuations. When used with a domain-decomposition (DD) algorithm, such components have to be coupled in a way that both accurately propagates the noise between the subdomains and lends itself to a stable and cost-effective temporal integration. We develop a conservative DD approach in which tight coupling is obtained by using a Jacobian-free Newton–Krylov (JfNK) method with a generalized minimum residual iterative linear solver. This strategy is tested on a coupled nonlinear diffusion system forced by a truncated Gaussian noise at the boundary. Enforcement of path-wise continuity of the state variable and its flux, as opposed to continuity in the mean, at interfaces between subdomains enables the DD algorithm to correctly propagate boundary fluctuations throughout the computational domain. Reliance on a single Newton iteration (explicit coupling), rather than on the fully converged JfNK (implicit) coupling, may increase the solution error by an order of magnitude. Increase in communication frequency between the DD components reduces the explicit coupling's error, but makes it less efficient than the implicit coupling at comparable error levels for all noise strengths considered. Finally, the DD algorithm with the implicit JfNK coupling resolves temporally-correlated fluctuations of the boundary noise when the correlation time of the latter exceeds some multiple of an appropriately defined characteristic diffusion time.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An analysis of the spatio-temporal resolution of the immersed boundary method with direct forcing

The immersed boundary method (IBM) with direct forcing is very popular in the simulation of rigid particulate flows. In the IBM, an interaction force is introduced at the interface between fluid and particle in order to approximate the no-slip boundary condition. The interaction force is calculated through dividing the velocity difference (or error) between fluid and particle at the interface by the time step. Here, a dynamic equation for the velocity difference is derived. Additionally, analyses on the dynamic equation provide a few new findings: (i) The interaction force is the solution of a least-squares error problem, with the direct implication that the Lagrangian marker distribution has no effect on the large scale flow structure once the distribution of Lagrangian markers become saturated along the interface (i.e., each marker remains properly correlated with all its neighbors); (ii) The Lagrangian volume-weight is a relaxation factor to control how fast the velocity error decays to the ideal value of zero; (iii) The optimal choice of the Lagrangian volume-weight is the largest value permissible by a stability condition. A comprehensive convergence analysis with regard to the spatial and temporal resolution is presented for the velocity error and also for the shear-stress and surface pressure. In three simple canonical problems, it is analytically and numerically shown that the IBM results converge to the theoretical solutions obtained with precise imposition of no-slip and no-penetration boundary conditions. It is observed that it is not necessary to match the Lagrangian marker volume-weight to that of the local Eulerian cell volume and in fact this matching leads to lower than optimal computational efficiency. However, it is found that extremely high Eulerian grid resolution and small time step have to be used to obtain high precision simulation results. Especially, the time step should be inversely proportional to the particle Reynolds number for low Reynolds number flows. For high frequency oscillation problems, the grid size needs to be reduced by a factor of the square root of the frequency, and the time step to be reduced by a factor of the frequency. The theoretical findings here can be used to alleviate the technical difficulties in simulating non-spherical particles by not requiring the Lagrangian marker distribution to match the Eulerian grids and also in the implementation of IBM on non-uniform Eulerian grids. The present work also provides simple practical guidance on the choice of temporal and spatial resolution so as to control the simulation error a priori.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Brownian dynamics of confined rigid bodies

We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the other based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advanced simulation capability for environmental management, integrated tool-sets and simulator to enhance public communication - 15186

The U.S. Department of Energy (US DOE) Office of Environmental Management (EM), Office of Soil and Groundwater Remediation, is supporting multi-laboratory development of the Advanced Simulation Capability for Environmental Management (ASCEM). ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. ASCEM facilitates transparent, efficient and integrated approaches to modeling and site characterization, and provides robust and standardized assessments of performance and risk for EM cleanup and closure activities. Site subsurface simulation modeling and performance assessments are complex and involve sensitivity evaluations and uncertainty quantification to better understand the risks at a site. The ASCEM tool-set was designed in close collaboration with the sites and other potential end-users (both the public and regulators) to allow better communication and understanding of these complex modeling efforts. ASCEM's integrated tool-sets provide a user interface and tools for managing work-flows, including conceptual model development, management of data and metadata for model input, sensitivity analysis, model calibration and uncertainty analysis, model execution on diverse computational platforms, and processing of model output, including visualization. The hierarchical and modular design of ASCEM HPC simulator Amanzi easily lends itself to translating this conceptual model of a site into a numerical model that can easily be spatially and temporally discretized to run on the HPC simulator. Together this integrated work-flow allows for a seamless and integrated analysis tracking all provenance information and modeling uncertainties. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Eulerian Applications Project - xRage: High Explosives Package [Slides]

At the most elementary level, the high explosive model in xRage (or many other hydro codes) computes the amount of material that changes from a high explosive reactant to a high explosive product during a time step and accounts for the energy added to the flow by this reaction. The actual chemical reactions that occur during this conversion are not modeled. These processes are very complicated and involve levels of spatial and temporal resolution that are generally not practical for an application code. They would also require a state variable representation that includes all of the chemical species that are produced by the reaction and account for multiple stage chemical reactions. Instead the explosive models we generally use are phenomenological and try to represent the most important physics that drive the explosive wave in a very simplified way. These models generally have a number of tunable parameters that must be calibrated to experiment.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Accurate and efficient prediction of fine-resolution hydrologic and carbon dynamic simulations from coarse-resolution models

The topography, and the biotic and abiotic parameters are typically upscaled to make watershed-scale hydrologic-biogeochemical models computationally tractable. However, upscaling procedure can produce biases when nonlinear interactions between different processes are not fully captured at coarse resolutions. Here, we applied the Proper Orthogonal Decomposition Mapping Method (PODMM) to downscale the field solutions from a coarse (7 km) resolution grid to a fine (220 m) resolution grid. PODMM trains a reduced-order model (ROM) with coarse-resolution and fine-resolution solutions, here obtained using PAWS+CLM, a quasi-3-D watershed processes model that has been validated for many temperate watersheds. Subsequent fine-resolution solutions were approximated based only on coarse-resolution solutions and the ROM. The approximation errors were efficiently quantified using an error estimator. By jointly estimating correlated variables and temporally varying the ROM parameters, we further reduced the approximation errors by up to 20%. We also improved the method's robustness by constructing multiple ROMs using different set of variables, and selecting the best approximation based on the error estimator. The ROMs produced accurate downscaling of soil moisture, latent heat flux, and net primary production with O(1000) reduction in computational cost. The subgrid distributions were also nearly indistinguishable from the ones obtained using the fine-resolution model. Compared to coarse-resolution solutions, biases in upscaled ROM solutions were reduced by up to 80%. This method has the potential to help address the long-standing spatial scaling problem in hydrology and enable long-time integration, parameter estimation, and stochastic uncertainty analysis while accurately representing the heterogeneities.

58 GEOSCIENCES↗

Higher-order temporal integration for the incompressible Navier–Stokes equations in bounded domains

Here, this paper compares and contrasts higher-order, semi-implicit temporal integration strategies for the incompressible Navier–Stokes methods based on spectral deferred corrections applied to certain gauge or auxiliary variable formulations of the equations. Particular focus is placed on the imposition of boundary conditions in the semi-implicit formulation, the accurate treatment of the pressure term, and the smoothness of the numerical solution for different formulations. The main result presented here is the formulation and numerical validation of a single-step, semi-implicit method called spectral deferred pressure corrections, which can in theory obtain arbitrary formal order of accuracy in time. Lastly, numerical results demonstrate up to eighth-order accuracy, scenarios where optimal temporal accuracy is attained, and scenarios where order reduction is observed due to time-dependent boundary conditions.

97 MATHEMATICS AND COMPUTING↗

A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection

Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs) is the formation of spherical structures, primarily in lungs, called granulomas. Infection occurs after inhalation of bacteria into lungs, where resident antigen-presenting cells (APCs), take up bacteria and initiate the immune response to Mtb infection. APCs traffic from the site of infection (lung) to lung-draining lymph nodes (LNs) where they prime T cells to recognize Mtb. These T cells, circulating back through blood, migrate back to lungs to perform their immune effector functions. We have previously developed a hybrid agent-based model (ABM, labeled GranSim) describing in silico immune cell, bacterial (Mtb) and molecular behaviors during tuberculosis infection and recently linked that model to operate across three physiological compartments: lung (infection site where granulomas form), lung draining lymph node (LN, site of generation of adaptive immunity) and blood (a measurable compartment). Granuloma formation and function is captured by a spatio-temporal model (i.e., ABM), while LN and blood compartments represent temporal dynamics of the whole body in response to infection and are captured with ordinary differential equations (ODEs). In order to have a more mechanistic representation of APC trafficking from the lung to the lymph node, and to better capture antigen presentation in a draining LN, this current study incorporates the role of dendritic cells (DCs) in a computational fashion into GranSim.

59 BASIC BIOLOGICAL SCIENCES↗

Spatiotemporal modeling of node temperatures in supercomputers

Los Alamos National Laboratory (LANL) is home to many large supercomputing clusters. These clusters require an enormous amount of power (~500-2000 kW each), and most of this energy is converted into heat. Thus, cooling the components of the supercomputer becomes a critical and expensive endeavor. Recently a project was initiated to investigate the effect that changes to the cooling system in a machine room had on three large machines that were housed there. Coupled with this goal was the aim to develop a general good-practice for characterizing the effect of cooling changes and monitoring machine node temperatures in this and other machine rooms. This paper focuses on the statistical approach used to quantify the effect that several cooling changes to the room had on the temperatures of the individual nodes of the computers. The largest cluster in the room has 1,600 nodes that run a variety of jobs during general use. Since extremes temperatures are important, a Normal distribution plus generalized Pareto distribution for the upper tail is used to model the marginal distribution, along with a Gaussian process copula to account for spatio-temporal dependence. A Gaussian Markov random field (GMRF) model is used to model the spatial effects on the node temperatures as the cooling changes take place. This model is then used to assess the condition of the node temperatures after each change to the room. The analysis approach was used to uncover the cause of a problematic episode of overheating nodes on one of the supercomputing clusters. Lastly, this same approach can easily be applied to monitor and investigate cooling systems at other data centers, as well.

97 MATHEMATICS AND COMPUTING↗

An efficient parallel simulation of unsteady blood flows in patient-specific pulmonary artery

Simulation of blood flows in the pulmonary artery provides some insight into certain diseases by examining the relationship between some continuum metrics, eg, the wall shear stress acting on the vascular endothelium, which responds to flow-induced mechanical forces by releasing vasodilators/constrictors. V. Kheyfets, in his previous work, studies numerically a patient-specific pulmonary circulation to show that decreasing wall shear stress is correlated with increasing pulmonary vascular impedance. We develop a scalable parallel algorithm based on domain decomposition methods to investigate an unsteady model with patient-specific pulsatile waveforms as the inlet boundary condition. The unsteady model offers tremendously more information about the dynamic behavior of the flow field, but computationally speaking, the simulation is a lot more expensive since a problem which is similar to the steady-state problem has to be solved many times, and therefore, the traditional sequential approach is not suitable anymore. We show computationally that simulations using the proposed parallel approach with up to 10 000 processor cores can be obtained with much reduced compute time. Finally, this makes the technology potentially usable for the routine study of the dynamic behavior of blood flows in the pulmonary artery, in particular, the changes of the blood flows and the wall shear stress in the spatial and temporal dimensions.

60 APPLIED LIFE SCIENCES↗

Synergistic cross-scale coupling of turbulence in a tokamak plasma

For the first time, nonlinear gyrokinetic simulations spanning both the ion and electron spatio-temporal scales have been performed with realistic electron mass ratio ((m D /m e ) 1/2 = 60.0), realistic geometry, and all experimental inputs, demonstrating the coexistence and synergy of ion ( ( k θ ρ s ∼ O ( 1.0 ) ) ) and electron-scale ( ( k θ ρ e ∼ O ( 1.0 ) ) ) turbulence in the core of a tokamak plasma. All multi-scale simulations utilized the GYRO code [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] to study the coupling of ion and electron-scale turbulence in the core (r/a = 0.6) of an Alcator C-Mod L-mode discharge shown previously to exhibit an under-prediction of the electron heat flux when using simulations only including ion-scale turbulence. Electron-scale turbulence is found to play a dominant role in setting the electron heat flux level and radially elongated (k r ≪ k θ ) “streamers” are found to coexist with ion-scale eddies in experimental plasma conditions. Inclusion of electron-scale turbulence in these simulations is found to increase both ion and electron heat flux levels by enhancing the transport at the ion-scale while also driving electron heat flux at sub-ρ i scales. The combined increases in the low and high-k driven electron heat flux may explain previously observed discrepancies between simulated and experimental electron heat fluxes and indicates a complex interaction of short and long wavelength turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Should Sea-Ice Modeling Tools Designed for Climate Research Be Used for Short-Term Forecasting?

In theory, the same sea-ice models could be used for both research and operations, but in practice, differences in scientific and software requirements and computational and human resources complicate the matter. Although sea-ice modeling tools developed for climate studies and other research applications produce output of interest to operational forecast users, such as ice motion, convergence, and internal ice pressure, the relevant spatial and temporal scales may not be sufficiently resolved. For instance, sea-ice research codes are typically run with horizontal resolution of more than 3 km, while mariners need information on scales less than 300 m. Certain sea-ice processes and coupled feedbacks that are critical to simulating the Earth system may not be relevant on these scales; and therefore, the most important model upgrades for improving sea-ice predictions might be made in the atmosphere and ocean components of coupled models or in their coupling mechanisms, rather than in the sea-ice model itself. This paper discusses some of the challenges in applying sea-ice modeling tools developed for research purposes for operational forecasting on short time scales, and highlights promising new directions in sea-ice modeling.

54 ENVIRONMENTAL SCIENCES↗

A transformed path integral approach for solution of the Fokker–Planck equation

A novel path integral (PI) based method for solution of the Fokker–Planck equation is presented. The proposed method, termed the transformed path integral (TPI) method, utilizes a new formulation for the underlying short-time propagator to perform the evolution of the probability density function (PDF) in a transformed computational domain where a more accurate representation of the PDF can be ensured. The new formulation, based on a dynamic transformation of the original state space with the statistics of the PDF as parameters, preserves the non-negativity of the PDF and incorporates short-time properties of the underlying stochastic process. New update equations for the state PDF in a transformed space and the parameters of the transformation (including mean and covariance) that better accommodate nonlinearities in drift and non-Gaussian behavior in distributions are proposed (based on properties of the SDE). Owing to the choice of transformation considered, the proposed method maps a fixed grid in transformed space to a dynamically adaptive grid in the original state space. The TPI method, in contrast to conventional methods such as Monte Carlo simulations and fixed grid approaches, is able to better represent the distributions (especially the tail information) and better address challenges in processes with large diffusion, large drift and large concentration of PDF. Additionally, in the proposed TPI method, error bounds on the probability in the computational domain can be obtained using the Chebyshev's inequality. The benefits of the TPI method over conventional methods are illustrated through simulations of linear and nonlinear drift processes in one-dimensional and multidimensional state spaces. The effects of spatial and temporal grid resolutions as well as that of the diffusion coefficient on the error in the PDF are also characterized.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A space-time adaptive finite element method with exponential time integrator for the phase field model of pitting corrosion

In this paper we propose a space-time adaptive finite element method for the phase field model of pitting corrosion, which is a parabolic partial differential equation system consisting of a phase variable and a concentration variable. A major challenge in solving this phase field model is that the problem is very stiff, which makes the time step size extremely small for standard temporal discretizations. Another difficulty is that a high spatial resolution is required to capture the steep gradients within the diffused interface, which results in very large number of degrees of freedom for uniform meshes. To overcome the stiffness of this model, we combine the Rosenbrock–Euler exponential integrator with Crank–Nicolson scheme for the temporal discretization. Moreover, by exploiting the fact that the speed of the corroding interface decreases with time, we derive an adaptive time stepping formula. For the spatial approximation, we propose a simple and efficient strategy to generate adaptive meshes that reduces the computational cost significantly. Thus, the proposed method utilizes local adaptivity and mesh refinement for efficient simulation of the corrosive dissolution over long times in heterogeneous media with complex microstructures. We also present an extensive set of numerical experiments in both two and three dimensional spaces to demonstrate efficiency and robustness of the proposed method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the role of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The physical chemistry of solar fuels catalysis

The demonstration of effective light-driven electrochemical water splitting at the surface of a TiO 2 electrode in the seminal 1972 Honda–Fujishima publication spurred global research efforts to understand this effect and design advanced systems for solar H 2 generation from water as a carbon-free and sustainable fuel. In the 50+ years since that discovery, research investigating approaches toward the catalytic generation of the so-called “solar fuels,” i.e., not only H 2 from water but also CO 2 reduction products and NH 3 from N 2 , has expanded dramatically in scope and scale. The development of new experimental and computational methods and construction and commissioning of large-scale facilities have paved the way for important insights into the machinery of natural photosynthesis, leading to a greater understanding of the complexity of light-to-chemical energy conversion with an exquisite temporal and spatial resolution. Finally, these studies have provided the foundation for biologically inspired molecular and hybrid designs with the goal to promote the photochemical steps critical to solar fuels generation while avoiding unproductive or unnecessary pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Excess deaths reveal the true spatial, temporal and demographic impact of COVID-19 on mortality in Ecuador

Accepted Background In early 2020, Ecuador reported one of the highest surges of per capita deaths across the globe. Methods We collected a comprehensive dataset containing individual death records between 2015 and 2020, from the Ecuadorian National Institute of Statistics and Census and the Ecuadorian Ministry of Government. We computed the number of excess deaths across time, geographical locations and demographic groups using Poisson regression methods. Results Between 1 January and 23 September 2020, the number of excess deaths in Ecuador was 36 402 [95% confidence interval (CI): 35 762–36 827] or 208 per 100 000 people, which is 171% of the expected deaths in that period in a typical year. Only 20% of the excess deaths are attributable to confirmed COVID-19 deaths. Strikingly, in provinces that were most affected by COVID-19 such as Guayas and Santa Elena, the all-cause deaths are more than double the expected number of deaths that would have occurred in a normal year. The extent of excess deaths in men is higher than in women, and the number of excess deaths increases with age. Indigenous populations had the highest level of excess deaths among all ethnic groups. Conclusions Overall, the exceptionally high level of excess deaths in Ecuador highlights the enormous burden and heterogeneous impact of COVID-19 on mortality, especially in older age groups and Indigenous populations in Ecuador, which was not fully revealed by COVID-19 death counts. Together with the limited testing in Ecuador, our results suggest that the majority of the excess deaths were likely to be undocumented COVID-19 deaths.

60 APPLIED LIFE SCIENCES↗

Ferroelectric Fractals: Switching Mechanism of Wurtzite AlN

The advent of wurtzite ferroelectrics is enabling new ferroelectric devices for computer memory that have the potential to bypass the von Neumann bottleneck due to their robust polarization and silicon compatibility. However, the atomistic switching mechanism of wurtzites is still undetermined due to the limitations of density functional theory simulation size and experimental temporal and spatial resolution. Thus, physics-informed materials engineering to reduce coercive field and breakdown in these devices has been limited. In this work, the atomistic mechanism of domain wall migration and domain growth in aluminum nitride-based wurtzites is uncovered using molecular dynamics and Monte Carlo simulations. We reveal the anomalous switching mechanism of fast 1D single columns of atoms propagating from a slow-moving 2D fractallike domain wall. We find that the critical nucleus is a single aluminum ion that breaks its bond with one nitrogen and bonds to another nitrogen; this creates a cascade that flips atoms directly only in the same column, due to the extreme locality (sharpness) of the domain walls in wurtzites. We further show how the fractallike shape of the domain wall in the 2D plane breaks assumptions in the Kolmogorov, Avrami, and Ishibashi (KAI) model and leads to the anomalously fast switching in wurtzite structured ferroelectrics.

36 MATERIALS SCIENCE↗