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At least 487 records · Page 27

EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix

Stable isotope based metabolic flux analysis is currently the unique methodology that allows the experimental study of the integrated responses of metabolic networks. This method primarily relies on isotope labeling and modeling, which could be a challenge in both experimental and computational biology. Specifically, the algorithm implementation for isotope simulation is a critical step, limiting extensive usage of this powerful approach. In this work, we introduce EMUlator a Python-based isotope simulator which is developed on Elementary Metabolite Unit (EMU) algorithm, an efficient and powerful algorithm for isotope modeling. We propose a novel adjacency matrix method to implement EMU modeling and exemplify it stepwise. This method is intuitively straightforward and can be conveniently mastered for various customized purposes. We apply this arithmetic pipeline to understand the phosphoketolase flux in the metabolic network of an industrial microbe Clostridium acetobutylicum . The resulting design enables a high-throughput and non-invasive approach for estimating phosphoketolase flux in vivo . Our computational insights allow the systematic design and prediction of isotope-based metabolic models and yield a comprehensive understanding of their limitations and potentials.

09 BIOMASS FUELS↗

Performance Results on CPU/GPU Exascale Architectures for OMEGA: The Ocean Model for E3SM Global Applications

The US Department of Energy (DOE) conducts climate simulations on some of the world’s largest supercomputers. These exascale machines use heterogeneous architectures with both CPUs and GPUs, and scientific codes must adapt to make full use of this computing power. Los Alamos National Lab is developing Omega: The Ocean Model for E3SM Global Applications, which is specifically designed for modern exascale computers. It uses external libraries that have been optimized for a variety of architectures to run on different supercomputers. Omega is an unstructured-mesh ocean model based on TRiSK numerical methods. It will be the new ocean component of the DOE’s Energy Exascale Earth System Model (E3SM). The algorithms in Omega follow those of the current ocean component, MPAS-Ocean, but it will be written in C++ rather than Fortran to take advantage of the Kokkos performance portability library. Omega spatial operators are written as Kokkos kernels to run efficiently on both CPUs and GPUs. Work on Omega began in 2023 with a new C++ framework for unstructured mesh partitioning, halo exchanges, parallel IO, and Kokkos interfaces. The current version, Omega-0, is being developed to solve the shallow water equations and at present includes all of the tendency terms but not time stepping. Here we share the results of Omega-0 verification and performance testing. Verification includes unit tests implemented with CTest as well as convergence tests in Polaris, an in-house python package with a large suite of test problems. Performance tests compare simulations conducted on CPUs versus GPUs and across different architectures: tests are run on Frontier, which has AMD “Optimized 3rd Gen EPYC” CPUs and AMD MI250X GPUs, as well as Perlmutter, which is composed of AMD EPYC 7763 CPUs and NVIDIA A100 GPUs.

58 GEOSCIENCES↗

ASC FY2023 Implementation Plan Revision 0

The DOE National Nuclear Security Administration (NNSA) Stockpile Stewardship Program (SSP) is an integrated technical program for maintaining the safety, security, and reliability of the U.S. nuclear stockpile. The SSP incorporates nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. The suite of data analyzed comes from activities including previous nuclear tests, stockpile surveillance, experimental research, and development and engineering programs. This integrated national program requires the continued use of experimental facilities and the computational capabilities to support the SSP missions. These component parts, in addition to an appropriately scaled production capability, enable NNSA to support stockpile requirements. The ultimate goal of the SSP, and thus of the Advanced Simulation and Computing (ASC) Program, is to ensure that the U.S. maintains a safe, secure, and effective strategic deterrent.

97 MATHEMATICS AND COMPUTING↗

Advanced Simulation and Computing: FY25 Implementation Plan

The DOE National Nuclear Security Administration (NNSA) Stockpile Stewardship Program (SSP) is an integrated technical program for maintaining the safety, security, and reliability of the U.S. nuclear stockpile. The SSP incorporates nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. The suite of data analyzed comes from activities including previous nuclear tests, stockpile surveillance, experimental research, and development and engineering programs. This integrated national program requires the continued use of experimental facilities and the computational capabilities to support the SSP missions. These component parts, in addition to an appropriately scaled production capability, enable NNSA to support stockpile requirements. The ultimate goal of the SSP, and thus of the Advanced Simulation and Computing (ASC) program, is to ensure that the U.S. maintains a safe, secure, and effective strategic deterrent.

97 MATHEMATICS AND COMPUTING↗

Urban building energy modeling (UBEM) tools: A state-of-the-art review of bottom-up physics-based approaches

Regulations corroborate the importance of retrofitting existing building stocks or constructing new energy-efficient districts. There is, thus, a need for modeling tools to evaluate energy scenarios to better manage and design cities, and numerous methodologies and tools have been developed. Among them, Urban Building Energy Modelling (UBEM) tools allow the energy simulation of buildings at large scales. Choosing an appropriate UBEM tool, balancing the level of complexity, accuracy, usability, and computing needs, remains a challenge for users. The review focuses on the main bottom-up physics-based UBEM tools, comparing them from a user-oriented perspective. Five categories are used: (i) the required inputs, (ii) the reported outputs, (iii) the exploited workflow, (iv) the applicability of each tool, and (v) the potential users. Moreover, a critical discussion is proposed, focusing on interests and trends in research and development. The results highlighted major differences between UBEM tools that must be considered to choose the proper one for an application. Finally, barriers of adoption of UBEM tools include the needs of a standardized ontology, a common three-dimensional city model, a standard procedure to collect data, and a standard set of test cases. This feeds into future development of UBEM tools to support cities’ sustainability goals.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Machine Learning Algorithms for Matching Theories, Simulations, and Observations in Cosmology (Final Project)

The search for simple and elegant equations to explain and predict observable natural phenomena has been a driving force in scientific theory for several centuries. The great successes of Newton's laws, Maxwell's equations, the Schrodinger equation, and the theory of General Relativity have encouraged this perspective, and perhaps a beautiful equation comprising a “theory of everything” remains to be discovered. But now scientists are grappling with systems of ever-increasing complexity, fraught with nonlinearity, and with the quantities of interest often only indirectly observed. Nature may resist a simple description, and the most important discoveries of the next century may be complex theories with countless variables and parameters. The era of big data opens up a promising new approach to scientific discovery in this setting. The predictions of modern theories, even if complex or nonlinear, can be examined through detailed and computationally-intensive simulations that take days or weeks to run and fill petabytes of disk space. The upcoming generation of scientific instruments will provide petabytes of observations at unprecedented resolution and depth. The challenge is to compare data to simulations so as to test theories and identify those that best match the observations. The data are numerous and rich but are subject to noise and various systematic biases. The simulations are large and detailed but are so costly that the effective sample size is small. Moreover, the mapping from data to simulation to the parameters of interest is typically complicated and ill-conditioned. Although these challenges, and the solutions we propose, apply across the sciences, we will ground our efforts by focusing on cosmology. Here, we are truly entering the era of big data in several senses. Ever larger experiments survey larger and larger cosmological volumes, resulting in enormous amounts of pixel data to process and extract the information of cosmological interest. These include large imaging surveys, which collect all the light in broad wavelength ranges over significant fractions of the sky, and spectroscopic surveys, which measure the light as a function of wavelength to map out 3D distances. These experiments are designed to shed light on the big unanswered questions in cosmology. Distilling the petabytes of data into observed quantities for comparison with theory is a daunting task. But these large experiments do not only result in large amounts of data to analyze: if we wish to compare to theories of physics, then we need increasingly extensive predictions for the observed quantities as well, which requires ever-larger cosmological simulations that take substantial -- and at times prohibitive -- computational resources to produce. Our goal is to develop statistical and machine learning methods for using observed and simulated data to advance machine learning with applications cosmology. In particular, we focus our research efforts on the following tasks: The challenge for automated science is that it is computationally impossible and statistically dangerous to consider every possible model in order to find the best one. We will develop Bayesian Optimization based active-learning methods that accelerate both the execution of the simulations and the search for best-fitting parameters. The key idea is to make the simulations adaptive -- across resolutions, time, and parameters -- using the data to search as the simulation runs; Most ML methods operate on simple finite dimensional feature vectors. However, many cosmology and other science applications require ML methods that can operate on more complex objects as inputs or outputs such as functions, distributions, or sets and point clouds. Our goal is to develop efficient ML methods for this problem and demonstrate their applicability in Cosmology, Astrophysics, and other science problems.

79 ASTRONOMY AND ASTROPHYSICS↗

Development of a Computational Framework for Multiphysics Multiphase Species Tracking using NEAMS Tools

This report implements a high-fidelity multiphysics modeling framework using the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program tools to track isotopic species in Molten Salt Reactors (MSRs), with a specific focus on the 91-depletion chain within the Molten Salt Reactor Experiment (MSRE). The model integrates neutronics, thermal-hydraulics, depletion, and thermochemistry to simulate the production, transport, and phase transitions of isotopes under steady-state and transient conditions. The main findings reveal that isotopes such as bromine-91 largely remain in the liquid phase, while others, including krypton-91and yttrium-91, transition to the gas phase, significantly influencing the reactor’s radiological source term. The study also shows that during transients, like a reactivity insertion transient, rapid void formation and the expansion of the liquid-gas interface led to substantial transfers of dissolved isotopes into the gas phase, altering isotope distribution and largely increasing the source term in the off-gas system. Additionally, the research highlights that short-lived isotopes dominate the initial off-gas response during transients, while longer-lived isotopes determine the equilibrium state, underscoring the necessity of dynamic simulations for accurate species tracking and reactor safety analysis. The developed methodology will be applied in the future to the tracking of a larger number of species and introduce other species tracking mechanisms, such as deposition and plating.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Transferability of data-driven, many-body models for CO 2 simulations in the vapor and liquid phases

Here, extending on the previous work by Riera et al. [J. Chem. Theory Comput. 16, 2246–2257 (2020)], we introduce a second generation family of data-driven many-body MB-nrg models for CO 2 and systematically assess how the strength and anisotropy of the CO 2 –CO 2 interactions affect the models’ ability to predict vapor, liquid, and vapor–liquid equilibrium properties. Building upon the many-body expansion formalism, we construct a series of MB-nrg models by fitting one-body and two-body reference energies calculated at the coupled cluster level of theory for large monomer and dimer training sets. Advancing from the first generation models, we employ the charge model 5 scheme to determine the atomic charges and systematically scale the two-body energies to obtain more accurate descriptions of vapor, liquid, and vapor–liquid equilibrium properties. Challenges in model construction arise due to the anisotropic nature and small magnitude of the interaction energies in CO 2 , calling for the necessity of highly accurate descriptions of the multidimensional energy landscape of liquid CO 2 . These findings emphasize the key role played by the training set quality in the development of transferable, data-driven models, which, accurately representing high-dimensional many-body effects, can enable predictive computer simulations of molecular fluids across the entire phase diagram.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulating Catalysis with Realistic Pellet Geometries Using Mesoflow: A Case Study of Catalytic Propane Dehydrogenation

We present a case study of catalytic propane dehydrogenation with our open-source multiphysics solver, Mesoflow. The solver was developed to simulate reactive flow coupled to heterogeneous catalytic reactions and deactivation in the context of complex, mesoscale geometry. The method leverages cartesian block-structured adaptive mesh refinement to capture realistic catalyst microstructural features acquired directly from X-ray computed tomography data. A kinetic model for propane dehydrogenation and catalyst deactivation was developed based on temporal analysis of products (TAP) reactor experiments. The TAP reactor experiments allow for precise characterization of intrinsic kinetic reaction steps which are implemented into Mesoflow simulations to model the spatial and temporal evolution of reactants, products, and catalyst active sites. The short-term and long-term deactivation behavior is studied by using XCT data collected from fresh and aged catalyst pellets, which exhibit different microstructural features. This study employs time-splitting algorithms to connect disparate reaction and flow timescales, enabling the simulations to achieve realistic deactivation timescales on the order of minutes while the flow time-scales for small particles (100 microns) are several milliseconds. We also introduce a flexible automated python script that writes the necessary files to construct a Mesoflow simulation from user-created chemical mechanisms. We will also introduce a few new features that are added to Mesoflow such as higher order schemes, implicit chemistry integrators and the ability to run on AMD and NVIDIA graphics-processing-units.

AMReX↗

Insight into the deformation features and capacity loss mechanisms of lithium-ion pouch cells under spherical indentation conditions

Mechanical deformation under extreme conditions is one of the important reasons for the failure of lithium-ion batteries in automotive application. However, the deformation features and component failure of lithium-ion cells to external loading has never been a design consideration. Here, in this study, we conduct spherical indentation tests on a dozen of lithium-ion cells with different capacities under different control mode conditions to investigate their deformation features and capacity loss mechanisms. The experimental results show that, under mechanical deformation conditions, internal faults of cells occur in stages, and energy accumulation and sudden release are two key processes of cell's mechanical failure. The cells' state of charge is the main factor affecting their thermal runaway behaviors. In addition, a finite element model is developed to simulate the deformation features and the failure mechanism of key components of lithium-ion pouch cells; the 3D x-ray computed tomography is employed to demonstrate its internal configuration. With this model, the force-strain response, the deformation features as well as the size of the failure area of lithium-ion cells under spherical indentation conditions are accurately predicted. In 3D x-ray computed tomography images, unique mud cracks in cooper current collector are observed, and the influence mechanisms of the isolated fragments on the cell capacities are revealed. These results may provide useful information for the mechanical structure design of the components of lithium-ion pouch cells.

25 ENERGY STORAGE↗

Evaluation of a thermomechanical model for prediction of residual stress during laser powder bed fusion of Ti-6Al-4V

The build-up of residual stresses in a part during laser powder bed fusion provides a significant limitation to the adoption of this process. These residuals stresses may cause a part to fail during a build or fall outside the specified tolerances after fabrication. In the present work a thermomechanical model is used to simulate the build process and calculate the residual stress state for Ti–6Al–4V specimens built with continuous and island scan strategies. A layer agglomeration, or lumping, approach is used to speed up the computations. A material model is developed to naturally capture the strain-rate dependence and annealing behavior of Ti–6Al–4V at elevated temperatures. Conclusions from the thermomechanical simulations showed good agreement with synchrotron X-ray diffraction measurements used to determine the residual elastic strains in these parts. Yet, the experimental measurements showed higher residual strains for the specimen built with an island scan strategy; a trend not fully captured by the simulations. Parameter studies were performed to fully understand the advantages and limitations of the current simulation methodology. Reasons for both the computational and experimental findings are discussed.

36 MATERIALS SCIENCE↗

An efficient hybrid downscaling framework to estimate high-resolution river hydrodynamics

Flow depth and velocity are the most important hydrodynamic variables that govern various river functions, including water resources, navigation, sediment transport, and biogeochemical cycling. Existing high-resolution flow depth simulations rely on either computationally expensive river hydrodynamic models (RHMs) or data-driven models with formidable training costs, whereas data-driven modeling of flow velocity has rarely been explored. Here, using the hybrid Low-fidelity, Spatial analysis, and Gaussian process learning (LSG) model, we developed a downscaling approach to construct high-resolution flow depth and velocity from a two-dimensional (2-D) RHM simulation at coarse resolution. The LSG models were trained and tested in an urban watershed in Houston using two different hurricane-driven flood events. The high-resolution (as fine as 30 m resolution) and low-resolution (mostly 1000 m resolution) meshes include 664 724 and 14 536 grid cells, respectively. The results showed that through downscaling, the simulation errors were reduced to less than one-fourth and one-third of the errors of the low-resolution 2-D RHM for flow depth and velocity, respectively. Our analysis further revealed that the dominant uncertainty sources of the downscaled hydrodynamics are different, with flow velocity dominated by the dimensionality reduction error, which we reduced by using a regionalized training procedure. The downscaling approach achieves an 84-fold acceleration in computational time compared to the high-resolution 2-D RHM, making high-fidelity ensemble flood modeling feasible. More importantly, the developed method provides an opportunity to couple large-scale hydrodynamical processes with local physical, chemical, and biological processes in river models.

Tan, Zeli [Pacific Northwest National Laboratory (↗

Identifying Entangled Physics Relationships Through Sparse Matrix Decomposition to Inform Plasma Fusion Design

We report a sustainable burn platform through inertial confinement fusion (ICF) has been an ongoing challenge for over 50 years. Mitigating engineering limitations and improving the current design involves an understanding of the complex coupling of physical processes. While sophisticated simulation codes are used to model ICF implosions, these tools contain necessary numerical approximation but miss physical processes that limit predictive capability. Identification of relationships between controllable design inputs to ICF experiments and measurable outcomes (e.g., neutron yield, neutron velocity, areal density) from performed experiments can help guide the future design of experiments and development of simulation codes, to potentially improve the accuracy of the computational models used to simulate ICF experiments. We use sparse matrix decomposition methods to identify clusters of a few related design variables. Sparse principal component analysis (SPCA) identifies groupings that are related to the physical origin of the variables (laser, hohlraum, and capsule). A variable importance analysis finds that in addition to variables highly correlated with neutron yield, such as picket power and laser energy, variables that represent a dramatic change of the ICF design, such as number of pulse steps, are also very important. The obtained sparse components are then used to train a random forest (RF) regression surrogate for predicting total yield. The RF performance on the training and testing data compares with the performance of the RF trained using all the design variables considered. This work is intended to inform design changes in future ICF experiments by augmenting the expert intuition and simulation results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A simplified parameterization of isoprene-epoxydiol-derived secondary organic aerosol (IEPOX-SOA) for global chemistry and climate models: a case study with GEOS-Chem v11-02-rc

Secondary organic aerosol derived from isoprene epoxydiols (IEPOX-SOA) is thought to contribute the dominant fraction of total isoprene SOA, but the current volatility-based lumped SOA parameterizations are not appropriate to represent the reactive uptake of IEPOX onto acidified aerosols. A full explicit modeling of this chemistry is however computationally expensive owing to the many species and reactions tracked, which makes it difficult to include it in chemistry–climate models for long-term studies. Here we present three simplified parameterizations (version 1.0) for IEPOX-SOA simulation, based on an approximate analytical/fitting solution of the IEPOX-SOA yield and formation timescale. The yield and timescale can then be directly calculated using the global model fields of oxidants, NO, aerosol pH and other key properties, and dry deposition rates. The advantage of the proposed parameterizations is that they do not require the simulation of the intermediates while retaining the key physicochemical dependencies. We have implemented the new parameterizations into the GEOS-Chem v11-02-rc chemical transport model, which has two empirical treatments for isoprene SOA (the volatility-basis-set, VBS, approach and a fixed 3% yield parameterization), and compared all of them to the case with detailed fully explicit chemistry. The best parameterization (PAR3) captures the global tropospheric burden of IEPOX-SOA and its spatiotemporal distribution ( R 2 =0.94 ) vs. those simulated by the full chemistry, while being more computationally efficient ( ~5 times faster), and accurately captures the response to changes in NO x and SO 2 emissions. On the other hand, the constant 3 % yield that is now the default in GEOS-Chem deviates strongly ( R 2 =0.66 ), as does the VBS ( R 2 =0.47 , 49% underestimation), with neither parameterization capturing the response to emission changes. With the advent of new mass spectrometry instrumentation, many detailed SOA mechanisms are being developed, which will challenge global and especially climate models with their computational cost. The methods developed in this study can be applied to other SOA pathways, which can allow including accurate SOA simulations in climate and global modeling studies in the future.

58 GEOSCIENCES↗

Advancing Catalytic Fast Pyrolysis Through Integrated Experimentation and Multi-Scale Computational Modeling

This webinar will highlight recent results from a multi-disciplinary research effort in which integrated reaction testing was coupled with particle- and reactor-scale computational modeling to advance catalytic fast pyrolysis (CFP) for the production of renewable hydrocarbon fuels. Data will be presented from a series of ex situ CFP experiments in which a fixed bed of Pt/TiO2 was utilized with co-fed H2 to upgrade woody biomass pyrolysis vapors. Further discussion will include the application of these data towards the development of (1) a multiscale simulation framework to de-couple apparent kinetics from both intraparticle and reactor-scale transport phenomena and (2) a finite element computational model to understand and predict thermal excursions during catalyst regeneration. Throughout the presentation, the speakers will emphasize synergistic outcomes derived from the collaborative approach and highlight ongoing research efforts to accelerate technology maturation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

The Influence of Environment on Post-Detonation Chemistry and Debris Formation (Abbreviated Final Report: 20-SI-006)

Predicting, responding to, or interpreting the chemical record preserved in debris derived from nuclear events can be challenging due to chemical fractionation. Chemical fractionation is where different species of the evolving radionuclide inventory segregate and/or are lost from the system over the timescales of debris formation. Both historic data and recent research suggest that the interaction and character of the local environment may exert controls on chemical fractionation by influencing the cooling and evolution of the associated fireball as well as the composition of the vapor term and resultant speciation. Prior to this work, an integrated platform permitting dynamic and concurrent consideration of physical and chemical evolution of early time post-detonation event environments did not exist. Our work merged historic data and experimental approaches to support development of a computational framework able to simulate fundamental processes (e.g., entrainment of local environment, oxidation chemistry, and cooling time scales) that may perturb the radionuclide inventory captured in post-detonation debris. Work with historic debris confirmed that entrained environmental material affect debris composition, structure, and radionuclide incorporation. Complementary work utilizing a readily controllable and tunable benchtop setup (a plasma flow reactor) simulated the late cooling of a nuclear fireball (e.g., T < 6000 K) and bounded the sensitivity of actinide speciation and particle size distribution to variations in oxygen concentration and cooling rates. Concurrent laser ablation and laser heating experiments were used to investigate the chemistry and physics of processes occurring in vaporized and/or rapidly heated actinides and other elements in the presence of oxygen. A more computationally efficient microphysical model was developed for predicting and evolving size distributions of particles forming from mixed vapor terms and simulating particle formation processes under a variety of extreme conditions. Continued study of historic nuclear event film confirmed that shockwave data and physics codes agree to within the uncertainty of the data. Good agreement was achieved for thermal emission from an airburst, however the paucity of low-temperature molecular opacity data for mixtures of air, bomb debris, entrained dirt, and water vapor complicate agreement for more elaborate scenarios. A multiphysics code (ALE3D) was modified to bring the necessary physics and chemistry, including these new data and insights, onto a single platform. Code development included improved initialization of large physical systems, modernization of chemistry capabilities, and modifications to enable inclusion of particle transport.

07 ISOTOPE AND RADIATION SOURCES↗

CFD Simulation of the Dosing Behavior within the Atomic Layer Deposition Feeding System

The effective operation of atomic layer deposition (ALD) feeding system is the premise of realizing specific ALD processes. In the present work, a detailed computational fluid dynamics (CFD) model of the feeding system has been developed and validated, which accounts for the roles of ALD valves and manifolds. A numerical simulation of the compressible fluid flow and heat/mass transfer within the feeding system was conducted. The dosing amounts and the spatiotemporal distributions of the precursors can be accurately predicted using the CFD model, as validated by experimental results. Different precursors, operating conditions, and structures of the feeding system were simulated and analyzed to examine the operating flexibility of the feeding system. The simulation results can be adopted as the upstream boundary conditions for simulations of the ALD process in the reaction chamber. The substrate-scale simulation indicates that the effect of the feeding system on the film deposition is highly related to the surface kinetics of ALD. The present work can serve as a guide for the development and optimization of different ALD-based processes via proper operation and even the design of the feeding system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗