Results for “Multiscale methods” — Page 21

DOE OSTI2020

Efficient bi-directional coupling of 3D computational fluid-particle dynamics and 1D Multiple Path Particle Dosimetry lung models for multiscale modeling of aerosol dosimetry

The development of predictive aerosol dosimetry models has been a major focus of environmental toxicology and pharmaceutical health research for decades. One-dimensional (1D) models successfully predict overall deposition averages but fail to accurately predict local deposition. Computational fluid-particle dynamics (CFPD) models provide site-specific predictions but at a computational cost that prohibits whole lung predictions. Thus, there is a need for developing multiscale strategies to provide a realistic subject-specific picture of the fate of inhaled aerosol in the lungs. CT-based 3D/CFPD models of the large airways were bidirectionally coupled with individualized 1D Navier-Stokes airflow and particle transport based upon the widely used Multiple Path Particle Dosimetry Model (MPPD). Distribution of airflows among lobes was adjusted by measured lobar volume changes observed in CT images between FRC and FRC + 1.5 L. Additionally, as a test of the effectiveness of the coupling procedures, deposition modeling of previous 1 µm aerosol exposure studies was performed. The complete coupled model was run for 3 breaths, with the computation-intense portion being the 3D CFD Lagrangian particle tracking calculation. The average deposition per breath was 11% in the combined multiscale model with site-specific doses available in the CFPD portion of the model and airway- or region-specific deposition available for the MPPD portion. In conclusion, the key methods developed in this study enable predictions of ventilation heterogeneities and aerosol deposition across the lungs that are not captured by 3D or 1D models alone. Overall, these methods can be used as the foundation for multi-scale modeling of the full respiratory system.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Expandable Li Percolation Network: The Effects of Site Distortion in Cation-Disordered Rock-Salt Cathode Material

Cation-disordered rock-salt (DRX) materials receive intensive attention as a new class of cathode candidates for high-capacity lithium-ion batteries (LIBs). Unlike traditional layered cathode materials, DRX materials have a three-dimensional (3D) percolation network for Li + transportation. The disordered structure poses a grand challenge to a thorough understanding of the percolation network due to its multiscale complexity. In this work, we introduce the large supercell modeling for DRX material Li 1.16 Ti 0.37 Ni 0.37 Nb 0.10 O 2 (LTNNO) via the reverse Monte Carlo (RMC) method combined with neutron total scattering. Here, through a quantitative statistical analysis of the material’s local atomic environment, we experimentally verified the existence of short-range ordering (SRO) and uncovered an element-dependent behavior of transition metal (TM) site distortion. A displacement from the original octahedral site for Ti 4+ cations is pervasive throughout the DRX lattice. Density functional theory (DFT) calculations revealed that site distortions quantified by the centroid offsets could alter the migration barrier for Li + diffusion through the tetrahedral channels, which can expand the previously proposed theoretical percolating network of Li. The estimated accessible Li content is highly consistent with the observed charging capacity. The newly developed characterization method here uncovers the expandable nature of the Li percolation network in DRX materials, which may provide valuable guidelines for the design of superior DRX materials.

25 ENERGY STORAGE↗

DOE OSTI2023

Advancing uncertainty characterization for understanding projected water scarcity in multi-sector, multi-actor river basins across scales.

Invited Talk at AGU Fall Meeting 2023 Modeling how human institutions and infrastructure interact with the water cycle is essential to better understand the vulnerability, and resilience of water resources systems from the local to the global scale. This is especially true when investigating multi-sector, multi-actor responses to the effects of long-term changes and short-term shocks. It is also well recognized that uncertainty present throughout the modeling cycle (e.g., in data, functional relations, and model coupling approaches) limits our ability to trace the interactive dynamics of human-water systems, as well as to quantify their implications for management and planning. Systems with large numbers of diverse stakeholders further compound this challenge, as uncertain drivers and complex dynamics might have very disparate effects on water users. The work presented is conducted through the Integrated Multisector Multiscale Modeling (IM3) Science Focus Area, which explores how human and natural systems co-evolve in response to change. Through this multi-year effort, we have developed exploratory modeling methods to better characterize how the uncertain human and natural drivers of water scarcity yield consequential vulnerabilities in institutionally complex, multi-sectoral systems. This talk will specifically present on a series of uncertainty characterization experiments performed in the Upper Colorado River Basin, a sub-basin of the Colorado with thousands of water users. These complementary and systematic experiments are aimed at understanding: How are various uncertain stressors (e.g., climate change, demand growth) affecting the diverse water users of this basin in terms of water shortage? What are the key drivers of this shortage for each user? Methods and results from this work are used to address additional questions on the ability of adaptation to modulate the effects of these uncertain drivers, and on their compounding effects across spatial scales and through sectoral interactions.

Hadjimichael, Antonia↗

DOE OSTI2025

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers

Quantification of intrahepatic covalently closed circular DNA (cccDNA) is a key for evaluating an elimination of hepatitis B virus (HBV) in infected patients. However, quantifying cccDNA requires invasive methods such as a liver biopsy, which makes it impractical to access the dynamics of cccDNA in patients. Although HBV RNA and HBV core-related antigens (HBcrAg) have been proposed as surrogate markers for evaluating cccDNA activity, they do not necessarily estimate the amount of cccDNA. Here, we employed a recently developed multiscale mathematical model describing intra- and intercellular viral propagation and applied it in HBV-infected patients under treatment. We developed a model that can predict intracellular HBV dynamics by use of extracellular viral markers, including HBsAg, HBV DNA, and HBcrAg in peripheral blood. Importantly, the model prediction of the amount of cccDNA in patients over time was confirmed to be well correlated with the data for quantified cccDNA by paired liver biopsy. Thus, our method combining classic and emerging surrogate markers enables us to predict the decay dynamics of cccDNA in patients undergoing treatment.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Frontiers in the Simulation of Dislocations

Dislocations play a vital role in the mechanical behavior of crystalline materials during deformation. To capture dislocation phenomena across all relevant scales, a multiscale modeling framework of plasticity has emerged, with the goal of reaching a quantitative understanding of microstructure–property relations, for instance, to predict the strength and toughness of metals and alloys for engineering applications. This review describes the state of the art of the major dislocation modeling techniques, and then discusses how recent progress can be leveraged to advance the frontiers in simulations of dislocations. Furthermore, the frontiers of dislocation modeling include opportunities to establish quantitative connections between the scales, validate models against experiments, and use data science methods (e.g., machine learning) to gain an understanding of and enhance the current predictive capabilities.

36 MATERIALS SCIENCE↗

DOE OSTI2021

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Robust Molecular Predictive Methods for Novel Polymer Discovery and Applications

Polymeric materials are ubiquitous in modern society and they play an instrumental role in almost all industries, undoubtedly including the energy and environment sectors. Increased demand of energy and awareness to sustainability both necessitates the development of novel polymers with enhanced properties. Unfortunately, their structural and behavioral complexity render such discovery challenging and impeded. To address this problem, scientists are developing various computational modeling techniques and leveraging their power to depict the relationship between structural characteristics of polymers and their properties (such as rheological behaviors), and use such prediction to guide the design and syntheses of novel polymeric materials with enhanced performances. Unfortunately, predicting the relationships between polymer structure and composition with rheological properties via atomistic modeling is still a major challenge because of the extended time and length scales involved. Studying dynamic shear viscosity and linear viscoelasticity using molecular models requires capabilities that have been elusive, including representation of large molecular weight chains with an effective internal scale capable of describing entanglement, shear-rates that are in the s-1 scale with accurate quantitative stresses, and chemically-realistic combinations of both homogeneous and heterogeneous systems. Motivated by these unmet challenges, the overall technical objective of this DOE-STTR Phase II project is to develop robust molecular predictive methods for advanced polymer discovery and applications and especially for designing and demonstrating the “smart” polymer-based waterflooding enhanced oil recovery (EOR) process. In particular, we apply state-of-the-art molecular modeling methods developed by our academic partner, Materials Stimulation Center (MSC) at California Institute of Technology (Caltech), to facilitate and accelerate the experimental discovery processes. During the Phase I of this project, we had focused on development and demonstration of the molecular modeling methods to describe rheological properties of non-Newtonian polymer fluids, and to improve our fundamental understandings of shear-thickening mechanism and kinetics. In Phase II, we further apply the theoretical models to guide our experimental programs to improve our design of smart rheology modifier (SRM) polymers and their optimization for EOR. Specifically, we have three objectives in the Phase II study: (1) to further improve out computational modeling methods, coupling with the advanced machine learning algorithms; (2) to develop cost-effective and efficient SRM-flooding process suitable for EOR applications under typical reservoir conditions; and (3) to further explore the application of our molecular predictive models for innovative material discovery in other industrial applications. The recent development of our multiscale predictive framework allows the successful prediction of rheological properties from the chemical structure for polymers of experimentally relevant molecular weights, and provides an in-silico machine learning engine for screening novel compositions and structures with optimized non-Newtonian response, required for both shear-thinning and shear-thickening applications. Our framework provides: (1) procedures and tools for systematic coarsening from atomistic models and reverse mapping of coarse-grain models to atomistic, (2) unique ab initio methods to characterize the atomistic origin of colloidal and interfacial interactions and phenomena, (3) systematic structure and composition builders based on practical descriptors that drive rheological changes in polymer melts and diluted polymer mixtures, (4) a rheological properties engine capable of predicting viscosity in the zero-shear limit and under realistic dynamic conditions (for shear-rates commensurate with experiments) for large heterogeneous systems, (5) coarse-grain force fields with improved non-bond descriptions based on accurate quantum mechanics, (6) an in-silico screening machine learning engine that feeds from the systematic model builders to cover the descriptors search space, computes the rheological properties from converged trajectories spanning sub-milliseconds and ranks them for each structure/composition using an automated viscosity-vs-shear rate fitness function that can be tuned for shear-thickening, shear-thinning and other rheological responses.

02 PETROLEUM↗

DOE OSTI2022

A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.

multiscale blood flow models↗

DOE OSTI2022

A concurrent irradiation-mechanics multiscale coupling model

The vast majority of our current knowledge regarding the basic mechanisms controlling irradiation effect on mechanical properties is based almost entirely on the results of post-irradiation experiments or theoretical models. However, the concurrent effects of irradiation, mechanical stress, and thermal damage on the failure phenomena of materials and components remain largely unexplored due to its internal multiscale-multiphysics coupling nature. Here, we present here a concurrent irradiation-mechanics multiscale coupling model. The concurrent evolutions of nanoscale irradiation defect clusters, microscale dislocation configurations, and mechanical responses are well captured based on coupling cluster dynamics, discrete dislocation dynamics, and the finite element methods using an effective time marching scheme. Model predictions of defect densities and size are in general agreement with experimental observations. Irradiation hardening is shown to take place also in samples undergoing concurrent irradiation-mechanical loading, similar to samples tested post-irradiation. However, the occurrence of plastic flow localization and dislocation channel formation is not accompanied with apparent yield drop (softening) under concurrent irradiation-mechanical loading conditions, which is different from the post-irradiation case.

42 ENGINEERING↗

DOE OSTI2021

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2017

In-Flight Calibration of the MMS Fluxgate Magnetometers

We present an overview of the approach to in-flight calibration, which is a coordinated effort between the University of California Los Angeles (UCLA), Space Research Institute, Graz, Austria (IWF) and the NASA Goddard Space Flight Center (GSFC). We present details of the calibration effort at GSFC. During the first dayside season of the Magnetospheric Multiscale (MMS) mission, the in-flight calibration process for the Fluxgate magnetometers (FGM) implemented an algorithm that selected a constant offset (zero-level) for each sensor on each orbit. This method was generally able to reduce the amplitude of residual spin tone to less than 0.2 nT within the region of interest. However, there are times when the offsets do show significant short-term variations. These variations are most prominent in the nighttime season (phase 1X), when eclipses are accompanied by offset changes as large as 1 nT. Eclipses are followed by a recovery period as long as 12 hours where the offsets continue to change as temperatures stabilize. Understanding and compensating for these changes will become critical during Phase 2 of the mission in 2017, when the nightside will become the focus of MMS science. Although there is no direct correlation between offset and temperature, the offsets are seen for the period of any given week to be well-characterized as function of instrument temperature. Using this property, a new calibration method has been developed that has proven effective in compensating for temperature-dependent offsets during phase 1X of the MMS mission and also promises to further refine calibration quality during the dayside season.

Magnetic field reconnection↗

NASA NTRSDate not supplied

A Dynamic PCA and Machine Learning Tool for Automated Identification of Solar Wind Disturbances Impacting Earth’s Magnetosphere

Earth’s magnetosphere is continuously impacted by solar wind and interplanetary magnetic field (IMF) disturbances, such as shocks, discontinuities, magnetic clouds and more. Understanding how such disturbances propagate from the Sun and what is their impact on the different magnetospheric domains is key to understanding and forecasting energy transfer from the solar wind to Earth. The large number of overlapping solar wind and magnetospheric missions carrying magnetometers and the recent advances in communications and data storage technologies have enabled an unprecedented quantity of high-fidelity magnetic field data captured by in-situ spacecraft to be available at the click of a button. However, this massive quantity of available data can prove unwieldy for researchers, limiting the identification of interesting phenomena and disturbances to a relatively small percentage of the total dataset. Several techniques have been previously developed for automated identification of specific types of magnetic anomalies, but these methods are typically mission-specific and can be difficult to generalize. We present initial results for a generic method of automated anomaly detection in magnetic field measurements based on dimensionality reduction and unsupervised clustering via machine learning. The benefit of our technique is its high degree of generalizability and flexibility which make it a most useful data survey tool for a wide range of magnetic field datasets. This method can also be applied simultaneously to other observed time-series properties like plasma density, pressure, and velocity for more accurate event identification. Additionally, the application of this method to data captured by multiple spacecraft enables the simultaneous identification of disturbances and the determination of their propagation characteristics. Initial evaluation of this technique has been performed using data from Magnetospheric MultiScale (MMS) and THEMIS-ARTEMIS missions, providing a testbed scenario for the future Heliophysics Environmental and Radiation Measurement Experiment Suite (HERMES) platform instruments that will measure solar wind and IMF properties from lunar orbit onboard the Gateway station.

Miguel Martinez-Ledesma↗

NASA NTRSDate not supplied

A Dynamic PCA and Machine Learning Tool for Automated Identification of Solar Wind Disturbances Impacting Earth’s Magnetosphere

Earth’s magnetosphere is continuously impacted by solar wind and interplanetary magnetic field (IMF) disturbances, such as shocks, discontinuities, magnetic clouds and more. Understanding how such disturbances propagate from the Sun and what is their impact on the different magnetospheric domains is key to understanding and forecasting energy transfer from the solar wind to Earth. The large number of overlapping solar wind and magnetospheric missions carrying magnetometers and the recent advances in communications and data storage technologies have enabled an unprecedented quantity of high-fidelity magnetic field data captured by in-situ spacecraft to be available at the click of a button. However, this massive quantity of available data can prove unwieldy for researchers, limiting the identification of interesting phenomena and disturbances to a relatively small percentage of the total dataset. Several techniques have been previously developed for automated identification of specific types of magnetic anomalies, but these methods are typically mission-specific and can be difficult to generalize. We present initial results for a generic method of automated anomaly detection in magnetic field measurements based on dimensionality reduction and unsupervised clustering via machine learning. The benefit of our technique is its high degree of generalizability and flexibility which make it a most useful data survey tool for a wide range of magnetic field datasets. This method can also be applied simultaneously to other observed time-series properties like plasma density, pressure, and velocity for more accurate event identification. Additionally, the application of this method to data captured by multiple spacecraft enables the simultaneous identification of disturbances and the determination of their propagation characteristics. Initial evaluation of this technique has been performed using data from Magnetospheric MultiScale (MMS) and THEMIS-ARTEMIS missions, providing a testbed scenario for the future Heliophysics Environmental and Radiation Measurement Experiment Suite (HERMES) platform instruments that will measure solar wind and IMF properties from lunar orbit onboard the Gateway station.

Miguel Martinez-Ledesma↗

DOE OSTI2021

Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)

Zeolites, an important class of 3-dimensional nanoporous materials, have been widely explored for a variety of applications including gas storage, separations, and catalysis. As the properties of these aluminosilicate materials depend on a number of factors (e.g., framework topology, Si/Al ratio, extra-framework cations etc.), detailed experiments (e.g., catalytic properties, adsorption capacities etc.) are often limited to only a handful of materials. Computational methods have played an important role in (1) providing molecular level insights to rationalize experimental observations, and (2) screening large libraries of zeolites to identify promising candidates for experimental synthesis and validation. Different levels of theory and computational chemistry codes are necessary to describe the range of relevant phenomena such as adsorption (e.g., grand canonical Monte Carlo), diffusion (e.g., molecular dynamics), and chemical reactions (e.g., density functional theory). Manipulation of atomic structures, handling of input files, and developing robust workflows becomes quite cumbersome. To mitigate these challenges, we describe the development of the Multiscale Atomic Zeolite Simulation Environment (MAZE) – a Python package that simplifies zeolite-specific calculation workflows by providing a user-friendly interface for systematically manipulating zeolite structures

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Assessing Two Approaches for Enhancing the Range of Simulated Scales in the E3SMv1 and the Impact on the Character of Hourly US Precipitation

Abstract Improving the representation of precipitation in Earth system models is essential for understanding and projecting water cycle changes across scales. Progress has been hampered by persistent deficiencies in representing precipitation frequency, intensity, and timing in current models. Here, we analyze simulated US precipitation in the low‐resolution (LR) configuration of the Energy Exascale Earth System Model (E3SMv1) and assess the effect of two approaches to enhance the range of explicitly resolved scales: high‐resolution (HR) and multiscale modeling framework (MMF), which incur similar computational expense. Both E3SMv1‐MMF and E3SMv1‐HR capture more intense and less frequent precipitation on hourly and daily timescales relative to E3SMv1‐LR. E3SMv1‐HR improves the intensity over the Eastern and Northwestern US during winter, while E3SMv1‐MMF improves the intensity over the Eastern US and summer diurnal timing over the Central US. These results indicate that both methods may be needed to improve simulations of different storm types, seasons, and regions.

58 GEOSCIENCES↗

NASA NTRS1975

Turbulent Chemically Reacting Flows According to a Kinetic Theory

A review of various methods of calculating turbulent chemically reacting flow such as the Green Function, Navier-Stokes equation, and others is presented. Nonequilibrium degrees of freedom were employed to study the mixing behavior of a multiscale turbulence field. Classical and modern theories are discussed.

Hong, Z. C.↗

NASA NTRS2000

Formation Flying In Highly Elliptical Orbits Initializing the Formation

In this paper several methods are examined for initializing formations in which all spacecraft start in a common elliptical orbit subsequent to separation from the launch vehicle. The tetrahedron formation used on missions such as the Magnetospheric Multiscale (MMS), Auroral Multiscale Midex (AMM), and Cluster is used as a test bed Such a formation provides full three degrees-of-freedom in the relative motion about the reference orbit and is germane to several missions. The type of maneuver strategy that can be employed depends on the specific initial conditions of each member of the formation. Single-impulse maneuvers based on a Gaussian variation-of-parameters (VOP) approach, while operationally simple and intuitively-based, work only in a limited sense for a special class of initial conditions. These 'tailored' initial conditions are characterized as having only a few of the Keplerian elements different from the reference orbit. Attempts to achieve more generic initial conditions exceed the capabilities of the single impulse VOP. For these cases, multiple-impulse implementations are always possible but are generally less intuitive than the single-impulse case. The four-impulse VOP formalism discussed by Schaub is examined but smaller delta-V costs are achieved in our test problem by optimizing a Lambert solution.

Mailhe, Laurie↗