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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 505 records · Page 28

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↗

Performance Analysis of a Hybrid Overset Multi-Block Application on Multiple Architectures

This paper presents a detailed performance analysis of a multi-block overset grid compu- tational fluid dynamics app!ication on multiple state-of-the-art computer architectures. The application is implemented using a hybrid MPI+OpenMP programming paradigm that exploits both coarse and fine-grain parallelism; the former via MPI message passing and the latter via OpenMP directives. The hybrid model also extends the applicability of multi-block programs to large clusters of SNIP nodes by overcoming the restriction that the number of processors be less than the number of grid blocks. A key kernel of the application, namely the LU-SGS linear solver, had to be modified to enhance the performance of the hybrid approach on the target machines. Investigations were conducted on cacheless Cray SX6 vector processors, cache-based IBM Power3 and Power4 architectures, and single system image SGI Origin3000 platforms. Overall results for complex vortex dynamics simulations demonstrate that the SX6 achieves the highest performance and outperforms the RISC-based architectures; however, the best scaling performance was achieved on the Power3.

Djomehri, M. Jahed↗

Understanding the Influence of Chain Architecture on the Transport Quantities of Polymer Electrolytes with Covalently Bonded Anions

Here, we use a combination of experiments and coarse-grained molecular dynamics simulations to elucidate the structure–property relationships in polymer electrolytes obtained by the copolymerization of poly(vinyl ethylene carbonate─lithium styrene bis(trifluoromethanesulfonyl)imide) or p(VEC-LiSTFSI). Experiments show that the conductivity reduces with increasing anion (i.e., STFSI) fraction on the chain, and the cation transference number (t + ) is found to be dependent on the anion fraction. Furthermore, a significant fraction of unpolymerized VEC monomers are observed. Since it is inherently difficult to experimentally control the chain architecture and the amount of unpolymerized VEC in these systems, we perform coarse-grained molecular dynamics simulations on model polymer systems with different chain architectures to mimic the plausible experimental systems. Specifically, we look at the differences in transference numbers arising from (i) a random copolymer of VEC and STFSI monomers; (ii) a blend of VEC-STFSI copolymer with VEC monomers; and (iii) a ternary blend of the VEC homopolymer, STFSI homopolymers, and VEC monomers. The ternary blend model demonstrates the closest resemblance with the experimental transference numbers and diffusivities. The lithium diffusivity obtained from the coarse-grained models with VEC monomers (plasticizers) is about 1.5 times that of the model without VEC monomers, showing that the plasticizing effect of VEC monomers is modest. We rationalize the experimental observations based on aggregate and cluster analyses obtained from molecular simulations. This work reveals that polymer electrolyte chain architecture and plasticizers can critically influence the transport properties, and these parameters should be considered when designing single ion conducting polymeric electrolytes.

cluster distribution↗

Maximizing the impact of the Vera Rubin Observatory LSST, and DESI and CMB-S4 experiments in constraining gravity and dark sector physics

The work in this award has addressed our objectives on a number of fronts: Current graduate student Chris Wilson and Bean are determining how cosmic voids can be used to test the properties of gravity, leveraging simulations from DESI collaborator Baojiu Li and refining theoretical Gaussian Streaming Model approaches to predict galaxy dynamics in voids when the cosmology is not GR. This work is still underway, including analyses of the efficacy of void quadrupole correlation statistics and void size functions when studying dark matter halo statistics or the expected galaxy distributions from upcoming galaxy surveys; Current graduate student Yulin Gong, Bean with collaborators are refining techniques to extract out the kinetic Sunyaev Zel’dovich effect from galaxy cluster survey data and CMB temperature anisotropies, with the intent to further ready this pipeline development in readiness for spectroscopic data from DESI and LSST along with CMB-S4 measurements.

79 ASTRONOMY AND ASTROPHYSICS↗

Critical magnetic Reynolds number of the turbulent dynamo in collisionless plasmas

The intracluster medium of galaxy clusters is an extremely hot and diffuse, nearly collisionless plasma, which hosts dynamically important magnetic fields of ~μG strength. Seed magnetic fields of much weaker strength of astrophysical or primordial origin can be present in the intracluster medium. In collisional plasmas, which can be approximated in the magnetohydrodynamical (MHD) limit, the turbulent dynamo mechanism can amplify weak seed fields to strong dynamical levels efficiently by converting turbulent kinetic energy into magnetic energy. However, the viability of this mechanism in weakly collisional or completely collisionless plasma is much less understood. In this study, we explore the properties of the collisionless turbulent dynamo using three-dimensional hybrid-kinetic particle-in-cell simulations. We explore the properties of the collisionless turbulent dynamo in the kinematic regime for different values of the magnetic Reynolds number, Rm, initial magnetic-to-kinetic energy ratio, (E mag /E kin ) i , and initial Larmor ratio, (r Larmor /L box ) i , i.e. the ratio of the Larmor radius to the size of the turbulent system. We find that in the ‘un-magnetized’ regime, (r Larmor /L box ) i > 1, the critical magnetic Reynolds number for the dynamo action Rm crit ≈ 107 ± 3. In the ‘magnetized’ regime, (r Larmor /L box ) i ≲ 1, we find a marginally higher Rm crit = 124 ± 8. We find that the growth rate of the magnetic energy does not depend on the strength of the seed magnetic field when the initial magnetization is fixed. We also study the distribution and evolution of the pressure anisotropy in the collisionless plasma and compare our results with the MHD turbulent dynamo.

79 ASTRONOMY AND ASTROPHYSICS↗

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

The Impact of Horizontal and Temporal Resolution on Convection and Precipitation with High-Resolution GEOS-5

Using a high-resolution non-hydrostatic version of GEOS-5 with the cubed-sphere finite-volume dynamical core, the impact of spatial and temporal resolution on cloud properties will be evaluated. There are indications from examining convective cluster development in high resolution GEOS-5 forecasts that the temporal resolution within the model may playas significant a role as horizontal resolution. Comparing modeled convective cloud clusters versus satellite observations of brightness temperature, we have found that improved. temporal resolution in GEOS-S accounts for a significant portion of the improvements in the statistical distribution of convective cloud clusters. Using satellite simulators in GEOS-S we will compare the cloud optical properties of GEOS-S at various spatial and temporal resolutions with those observed from MODIS. The potential impact of these results on tropical cyclone formation and intensity will be examined as well.

Putman, William P.↗

Active and Transfer Learning of High-Dimensional Neural Network Potentials for Transition Metals

Classical molecular dynamics (MD) simulations represent a very popular and powerful tool for materials modeling and design. The predictive power of MD hinges on the ability of the interatomic potential to capture the underlying physics and chemistry. There have been decades of seminal work on developing interatomic potentials, albeit with a focus predominantly on capturing the properties of bulk materials. Such physics-based models, while extensively deployed for predicting the dynamics and properties of nanoscale systems over the past two decades, tend to perform poorly in predicting nanoscale potential energy surfaces (PESs) when compared to high-fidelity first-principles calculations. These limitations stem from the lack of flexibility in such models, which rely on a predefined functional form. Machine learning (ML) models and approaches have emerged as a viable alternative to capture the diverse size-dependent cluster geometries, nanoscale dynamics, and the complex nanoscale PESs, without sacrificing the bulk properties. Here, in this study, we introduce an ML workflow that combines transfer and active learning strategies to develop high-dimensional neural networks (NNs) for capturing the cluster and bulk properties for several different transition metals with applications in catalysis, microelectronics, and energy storage, to name a few. Our NN first learns the bulk PES from the high-quality physics-based models in literature and subsequently augments this learning via retraining with a higher-fidelity first-principles training data set to concurrently capture both the nanoscale and bulk PES. Our workflow departs from status-quo in its ability to learn from a sparsely sampled data set that nonetheless covers a diverse range of cluster configurations from near-equilibrium to highly nonequilibrium as well as learning strategies that iteratively improve the fingerprinting depending on model fidelity. All the developed models are rigorously tested against an extensive first-principles data set of energies and forces of cluster configurations as well as several properties of bulk configurations for 10 different transition metals. Our approach is material agnostic and provides a methodology to transfer and build upon the learnings from decades of seminal work in molecular simulations on to a new generation of ML-trained potentials to accelerate materials discovery and design.

36 MATERIALS SCIENCE↗

Intermittent cluster dynamics and temporal fractional diffusion in a bulk metallic glass

Glassy solids evolve towards lower-energy structural states by physical aging. This can be characterized by structural relaxation times, the assessment of which is essential for understanding the glass’ time-dependent property changes. Conducted over short times, a continuous increase of relaxation times with time is seen, suggesting a time-dependent dissipative transport mechanism. By focusing on micro-structural rearrangements at the atomic-scale, we demonstrate the emergence of sub-diffusive anomalous transport and therefore temporal fractional diffusion in a metallic glass, which we track via coherent x-ray scattering conducted over more than 300,000 s. At the longest probed decorrelation times, a transition from classical stretched exponential to a power-law behavior occurs, which in concert with atomistic simulations reveals collective and intermittent atomic motion. Our observations give a physical basis for classical stretched exponential relaxation behavior, uncover a new power-law governed collective transport regime for metallic glasses at long and practically relevant time-scales, and demonstrate a rich and highly non-monotonous aging response in a glassy solid, thereby challenging the common framework of homogeneous aging and atomic scale diffusion.

42 ENGINEERING↗

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Abstract There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

54 ENVIRONMENTAL SCIENCES↗

Ferroelectric phase transition in group-IV monochalcogenides from an equivariant machine learned force field

Group-IV monochalcogenides are a class of layered ferroelectric semiconductors that have demonstrated spontaneous intrinsic polarization above room temperature. Here, in this study, we use the multi-atomic cluster expansion (MACE) machine learning architecture to train and test a force field capable of modeling the structural properties and second-order ferroelectric-to-paraelectric phase transition in a Group-IV monochalcogenide, GeSe. The model captures the double-well potential energy surface associated with the onset of macroscopic polarization in bulk GeSe within 12.5 meV/atom, as well as near-equilibrium properties like the phonon dispersion. The development of this quantitatively accurate force field enables long-time molecular dynamics simulations, which predict the critical temperature of the ferroelectric-to-paraelectric phase transition in bulk GeSe to be T c = 600 K. This study demonstrates the capabilities of equivariant force-fields to accurately describe phenomena associated with structural symmetry breaking.

ferroelectricity↗

Computational Fluid Dynamics Modeling to Simulate a Combined Reforming Process for Syngas and Hydrogen Production

An Oxygen Transport Membrane (OTM) combined reforming technology for producing syngas and hydrogen integrates the advantages of multiple processes—steam methane reforming (SMR), autothermal reforming (ATR), an air separation unit (ASU)—into a single integrated technology. The OTM consists of a primary reforming tube, in which desulfurized natural gas is partially reformed by steam at high pressure in the presence of a metal catalyst. This process is followed in series by a ceramic OTM with a secondary reformer, in which residual methane reforms and O 2 - ions react with a portion of the CO and H 2 fuel to provide the heat to support both primary and secondary reforming. Although the OTM combined reformer technology for syngas and H 2 production has been substantially developed in the last decade, several challenges that affect the overall production efficiency and reliability are yet to be fully understood, addressed, and resolved. Therefore, developing Computational Fluid Dynamics (CFD) models that incorporate fluid dynamics, mass transport, kinetics, heat transport, and structural mechanics is critical to understanding and minimizing the probability of tube failures during the startup and operation. In this report, an exhaustive literature review was performed to survey the current state of technology for producing syngas and H 2 using either conventional or renewable energy sources. The feedstocks reviewed include natural gas and coal for the conventional technologies, whereas biomass, solar, wind, and nuclear energy for the renewable technologies. The existing industry-grade COMSOL multiphysics models of OTM were upgraded for the latest software release. In addition, they were improved to help achieve grid and solver independence and were successfully ported on the ORNL high-performance computing clusters to speed up their run times. A 42% reduction in the simulation run time was achieved. A new higher-fidelity CFD model of an OTM tube was developed in the StarCCM+ simulation platform. This new model was designed to simulate various physics using first principles, e.g., turbulent flow, heat transfer, and chemical reactions while avoiding unnecessary simplifications. The resulting predictions were qualitatively assessed and provided useful insights into the multiphysics complexity of an OTM tube.

08 HYDROGEN↗

The void spectrum in two-dimensional numerical simulations of gravitational clustering

An algorithm for deriving a spectrum of void sizes from two-dimensional high-resolution numerical simulations of gravitational clustering is tested, and it is verified that it produces the correct results where those results can be anticipated. The method is used to study the growth of voids as clustering proceeds. It is found that the most stable indicator of the characteristic void 'size' in the simulations is the mean fractional area covered by voids of diameter d, in a density field smoothed at its correlation length. Very accurate scaling behavior is found in power-law numerical models as they evolve. Eventually, this scaling breaks down as the nonlinearity reaches larger scales. It is shown that this breakdown is a manifestation of the undesirable effect of boundary conditions on simulations, even with the very large dynamic range possible here. A simple criterion is suggested for deciding when simulations with modest large-scale power may systematically underestimate the frequency of larger voids.

Kauffmann, Guinevere↗

GenomeFace v1.0

GenomeFace is meta-genome binning software. Metagenomic binning, the process of grouping DNA sequences into taxonomic units, is critical for understanding the functions, interactions, and evolutionary dynamics of microbial communities. We propose a deep learning approach to binning using two neural networks, one based on composition and another on environmental abundance, dynamically weighting the contribution of each based on characteristics of the input data. Trained on over 43,000 prokaryotic genomes, our network for composition-based binning is inspired by metric learning techniques used for facial recognition. Using a task-specific, multi-GPU accelerated algorithm to cluster the embeddings produced by our network, our binner leverages marker genes observed to be universally present in nearly all taxa to grade and select optimal clusters of sequences from a hierarchy of candidates. We evaluate our approach on four simulated datasets with known ground truth. Our linear time integration of marker genes recovers more near complete genomes than state of the art but computationally infeasible solutions using them, while being over an order of magnitude faster. Finally, we demonstrate the scalability and acuity of our approach by testing it on three of the largest metagenome assemblies ever performed. Compared to other binners, we produced 47%-183% more near complete genomes. From these datasets, we find over the genomes of over 3000 new candidate species which have never been previously cataloged, representing a potential 4% expansion of the known bacterial tree of life.

Lettich, Richard [Lawrence Berkeley National Labor↗

Evolutionary Models of Cold, Magnetized, Interstellar Clouds

We modeled the long-term and small-scale evolution of molecular clouds using direct 2D and 3D magnetohydrodynamic (MHD) simulations. This work followed up on previous research by our group under auspices of the ATP in which we studied the energetics of turbulent, magnetized clouds and their internal structure on intermediate scales. Our new work focused on both global and smallscale aspects of the evolution of turbulent, magnetized clouds, and in particular studied the response of turbulent proto-cloud material to passage through the Galactic spiral potential, and the dynamical collapse of turbulent, magnetized (supercritical) clouds into fragments to initiate the formation of a stellar cluster. Technical advances under this program include developing an adaptive-mesh MHD code as a successor to ZEUS (ATHENA) in order to follow cloud fragmentation, developing a shearing-sheet MHD code which includes self-gravity and externally-imposed gravity to follow the evolution of clouds in the Galactic potential, and developing radiative transfer models to evaluate the internal ionization of clumpy clouds exposed to external photoionizing UV and CR radiation. Gammie's work at UIUC focused on the radiative transfer aspects of this program.

Gammie, Charles F.↗

SV-Sim: Scalable PGAS-based State Vector Simulation of Quantum Circuits

High-performance quantum circuit simulation in a classic HPC is still imperative in the NISQ era. Observing that the major obstacle of scalable state-vector quantum simulation arises from the massively fine-grained irregular data-exchange with remote nodes, in this paper we present SV-Sim to apply the emerging PGAS-based communication models (i.e., direct peer access for intra-node CPUs/GPUs and SHMEM for inter-node CPU/GPU clusters) for efficient scalable quantum circuit simulation. Through an orchestrated device functional pointer design, SV-Sim is able to abstract the quantum gate sets across various heterogeneous backends, including IBM/Intel/AMD CPUs, NVIDIA /AMD GPUs, and Intel MIC, in a unified framework, but still asserting outstanding performance and tractable interface to higher-level quantum programming environments, such as IBM Qiskit, Microsoft Q\# and Google Cirq. Circumventing the disability of polymorphism in GPUs and leveraging the device-initiated one-sided communication, SV-Sim can process dynamically synthesized quantum circuit in a single GPU/CPU kernel without the need of expensive JIT or runtime branching, significantly improving the performance and simplifying the programming complexity for the emerging variational quantum algorithms. Evaluations on NVIDIA A100-DGX-1, V100-DGX-2, AMD MI100, ALCF Theta, and OLCF Summit HPCs show that SV-Sim can delivery scalable performance on various state-of-the-art HPC platforms, offering a useful tool for quantum algorithm validation and verification.

Li, Ang↗

Regional and Model-Specific Response Types in A Global Gridded Crop Model Ensemble

Crop models are often employed to project crop yields under changing conditions such as global warming and associated management change for adaptation. Multi-model ensembles are promoted to enhance the robustness of projections, but questions remain on what causes often large differences between projections of individual models. Global Gridded Crop Models (GGCMs) are especially exposed to this question when applied for assessing climate change impacts, adaptation, environmental impacts of agricultural production, because their results are used in downstream analyses, such as in integrated assessment or economic modeling for projecting future land-use change. Even though global gridded crop models are often based on detailed field-scale models or have implemented similar modeling principles in other ecosystem models, global-scale models are subject to substantial uncertainties from both model structure and parametrization as well as from calibration and input data quality. AgMIP’s Global Gridded Crop Model Intercomparison (GGCMI) has thus set out to intercompare GGCMs in order to evaluate model performance, describe model uncertainties, identify inconsistencies within the ensemble and underlying reasons, and to ultimately improve models and modeling capacities. In phase 2 of the GGCMI activities, 12 modeling groups followed a modeling protocol that asked for up to 1404 31-year global simulations at 0.5 arc-degree spatial resolution to assess models’ sensitivities to changes in carbon dioxide (C; 4 different levels) temperature (T; 7 different offset levels), water supply (W; 9 levels), and nitrogen (N; 3 levels), the so-called CTWN experiment (Franke et al. 2020; http://dx.doi.org/10.5194/gmd-13-2315-2020). We here present analyses of model response types using impact response surfaces along the C, T, W, and N dimensions, respectively and collectively. Doing so, we can understand differences in simulated responses per driver rather than aggregated changes in yields. We find that models’ sensitivities to the individual driver dimensions are substantially different and often more different across models than across regions. A cluster analysis finds regional and model-specific patterns. There is some agreement across models with respect to the spatial patterns of response types but strong differences in the distribution of response type clusters across models suggests that models need to undergo further scrutiny. We suggest establishing standards in model process evaluation not only against historical dynamics but also against dedicated experiments across the CTWN dimensions.

crop models↗

Scalable, In-situ Data Clustering Data Analysis for Extreme Scale Scientific Computing (Final Report)

The objective of this project is to address challenges in the design and development of scalable in-situ data clustering and analytics algorithms and software. Our goal is to develop parallel software consisting of a set of spatio-temporal data clustering and anomaly detection functions, both of which are very important for large-scale analysis and have wide applicability for in-situ runs as well as post-processing analysis. Our design principles for in-situ analysis consider the following: (1) identify parts of the computation can be done close to the data within the nodes, while it is still in memory; (2) extract analysis components can (and should) be performed in remote staging and analysis nodes; (3) develop error-bound approximation methods for applications tolerable for small errors; (4) identify the type of derived distributions and statistics, for spatio-temporal data, that can be kept locally in order to both accelerate computations and meet energy constraints in subsequent iterations and phases; (5) use a self-describing data format so that data can be consistent and understood among local storage (memory and SSDs) and at staging and analysis nodes, thereby providing portability and flexibility; (6) develop service-oriented functions that can schedule in-situ and post-hoc analysis tasks based on the dynamic requirements of applications. Our development focus is to produce the parallel data analysis software/library that will be scalable, reusable, extensible, and generic for applications in different disciplines. The software will be able to run in-situ with the simulations as well as post-hoc analysis. This approach will satisfy many synergistic requirements for data intensive applications executed on data coming from instruments and experiments. In particular, the proposed multilevel approach is directly applicable to perform design tradeoffs for running part of the algorithms near the instruments and the rest on remote (analysis) systems.

97 MATHEMATICS AND COMPUTING↗