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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Toward Evaluating High-Level Synthesis Portability and Performance between Intel and Xilinx FPGAs

Offloading computation from a CPU to a hardware accelerator is becoming a more common solution for improving performance because traditional gains enabled by Moore’s law and Dennard scaling have slowed. GPUs are often used as hardware accelerators, but field-programmable gate arrays (FPGAs) are gaining traction. FPGAs are beneficial because they allow hardware specific to a particular application to be created. However, they are notoriously difficult to program. To this end, two of the main FPGA manufacturers, Intel and Xilinx, have created tools and frameworks that enable the use of higher level languages to design FPGA hardware. Although Xilinx kernels can be designed by using C/C++, both Intel and Xilinx support the use of OpenCL C to architect FPGA hardware. However, not much is known about the portability and performance between these two device families other than the fact that it is theoretically possible to synthesize a kernel meant for Intel to Xilinx and vice versa.In this work, we evaluate the portability and performance of Intel and Xilinx kernels. We use OpenCL C implementations of a subset of the Rodinia benchmarking suite that were designed for an Intel FPGA and make the necessary modifications to create synthesizable OpenCL C kernels for a Xilinx FPGA. We find that the difficulty of porting certain kernel optimizations varies, depending on the construct. Once the minimum amount of modifications is made to create synthesizable hardware for the Xilinx platform, more nontrivial work is needed to improve performance. However, we find that constructs that are known to be performant for an FPGA should improve performance regardless of the platform; the difficulty comes in deciding how to invoke certain kernel optimizations while also abiding by the constraints enforced by a given platform’s hardware compiler.

Cabrera, Anthony↗
DOE OSTI2021

ArborX

ArborX library tackles a problem of efficiently finding geometric objects that are close in space. Variations of this problem, such as finding the nearest neighbors of a point, or finding all objects within a certain distance, are inherent components of applications in many fields. The data may be large so that solving the problem efficiently may require significant computational resources, such as multiple processors or accelerators such as general purpose GPUs. ArborX' main advantage in its ability to solve large problems efficiently utilizing a combination of distributed and on-node parallelism. ArborX can be run efficiently on a wide variety of hardware, including GPUs from different vendors, which distinguishes it from other available libraries which typically choose only few of these. The other advantage is that it supports both types of user problems: spatial problems (useful for intersections and finding objects within certain distance), and nearest neighbor problems. ArborX also supports flexible interface in its interaction with a user. Particularly, it allows a user to call user's own function on a positive match, a functionality not rarely available in other libraries. ArborX implements construction and traversal algorithms using efficient tree structures, such as bounding volume hierarchy (BVH). At its core, it uses linear BVH for its low construction cost and sufficient quality. ArborX is written using C++, and is parallelized using the message passing interface (MPI) for the distributed communication, and the Kokkos library for on-node parallelism. This approach allows ArborX to be run on a wide variety of hardware, from common laptops and desktops to supercomputers while using the same codebase. ArborX also implements several advanced algorithms using geometric search, such as density-based clustering algorithm DBSCAN.

ECP↗
DOE OSTI2025

ArborX 2.0

ArborX library tackles a problem of efficiently finding geometric objects that are close in space. Variations of this problem, such as finding the nearest neighbors of a point, or finding all objects within a certain distance, are inherent components of applications in many fields. The data may be large so that solving the problem efficiently may require significant computational resources, such as multiple processors or accelerators such as general purpose GPUs. ArborX' main advantage in its ability to solve large problems efficiently utilizing a combination of distributed and on-node parallelism. ArborX can be run efficiently on a wide variety of hardware, including GPUs from different vendors, which distinguishes it from other available libraries which typically choose only few of these. The other advantage is that it supports both types of user problems: spatial problems (useful for intersections and finding objects within certain distance), and nearest neighbor problems. ArborX also supports flexible interface in its interaction with a user. Particularly, it allows a user to call user's own function on a positive match, a functionality not rarely available in other libraries. ArborX implements construction and traversal algorithms using efficient tree structures, such as bounding volume hierarchy (BVH). At its core, ArborX uses linear BVH for its low construction cost and sufficient quality. ArborX implements both spatial and nearest-neighbor traversal algorithms. ArborX also provides several clustering algorithms (minimum spanning tree, DBSCAN, HDBSCAN*), interpolation using minimum least squares and ray tracing. ArborX is written using C++, and is parallelized using the message passing interface (MPI) for the distributed communication, and the Kokkos library for on-node parallelism. This approach allows ArborX to be run on a wide variety of hardware, from common laptops and desktops to supercomputers while using the same codebase.

Prokopenko, Andrey [Oak Ridge National Laboratory ↗
DOE OSTI2023

Active Learning Framework

Machine learning (ML) of interatomic potentials show great promise to accelerate scientific simulation, e.g., by emulating expensive computations at a high accuracy but much reduced computational cost. Training datasets are calculated from computationally expensive ab initio quantum mechanics methods, density functional theory (DFT). Trained on this data, an ML model can be very successful in predicting energy and forces for new atomic configurations. A critical factor is the quality and diversity of the training dataset. Thus, a highly automated approach to dataset construction based on active learning framework is designed suitable for material physics. The active learning scheme begins with fully randomized atomic configurations. Then, many Molecular Dynamics (MD) trajectories are simulated using current ML potentials, where each MD trajectory is initialized to a random disordered configuration. The temperature is varied in order to diversify the sampled configuration during these simulations. The variance of predictions for eight neural networks within an ensemble is analyzed to determine whether the model is operating as expected. This helps in determining whether collecting more data would be helpful to the model by checking the ensemble variance is greater than the threshold. In this case, the MD trajectory is terminated and the final atomic configuration is placed on a queue (SQL database) for DFT calculations and added to training dataset. Periodically, ML model is retrained to the updated training model. This Active Learning loop is iterated until the cost of MD simulations becomes prohibitively expensive. The MD simulations will hopefully be sufficiently robust to support nucleation after many active learning iterations. In this sense, active learning scheme must automatically discover the important low energy and nonequilibrium physics.

Nebgen, Benjamin↗
DOE OSTI2024

Searching for Strongly Coupled Dark Sectors with Unsupervised and Generative Learning

Recipient of the URA Early Career Award for groundbreaking searches for dark matter arising from strongly coupled dark sectors with the CMS detector, pioneering work in ML-based model-independent anomaly detection for collider and astrophysics experiments, and leadership in the development of new AI/ML techniques to improve event reconstruction and detector simulation in particle physics, as well as novel strategies to accelerate AI inference and throughput with heterogeneous computing using coprocessors as a service.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses

Plants produce a diverse range of specialized metabolites that play pivotal roles in mediating environmental interactions and stress adaptation. These unique chemical compounds also hold significant agricultural, medicinal, and industrial values. Despite the expanding knowledge of their functions in plant stress interactions, understanding the intricate biosynthetic pathways of these natural products remains challenging due to gene and pathway redundancy, multifunctionality of proteins, and the activity of enzymes with broad substrate specificity. In the past decade, substantial progress in genomics, transcriptomics, metabolomics, and proteomics has made the exploration of plant specialized metabolism more feasible than ever before. Notably, recent advances in integrative multi-omics and computational approaches, along with other technologies, are accelerating the discovery of plant specialized metabolism. In this review, we present a summary of the recent progress in the discovery of plant stress-related specialized metabolites. Emphasis is placed on the application of advanced omics-based approaches and other techniques in studying plant stress-related specialized metabolism. Additionally, we discuss the high-throughput methods for gene functional characterization. These advances hold great promise for harnessing the potential of specialized metabolites to enhance plant stress resilience in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

deeprob/ThioesteraseEnzymeSpecificity: EnZymClass-first-release

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

Banerjee, Deepro↗
DOE OSTI2023

Higher-Order Corrections to Optimisers based on Newton's Method

The Newton, Gauss–Newton and Levenberg–Marquardt methods all use the first derivative of a vector function (the Jacobian) to minimise its sum of squares. When the Jacobian matrix is ill-conditioned, the function varies much faster in some directions than others and the space of possible improvement in sum of squares becomes a long narrow ellipsoid in the linear model. This means that even a small amount of nonlinearity in the problem parameters can cause a proposed point far down the long axis of the ellipsoid to fall outside of the actual curved valley of improved values, even though it is quite nearby. This paper presents a differential equation that ‘follows’ these valleys, based on the technique of geodesic acceleration, which itself provides a 2 nd order improvement to the Levenberg–Marquardt iteration step. Higher derivatives of this equation are computed that allow n th order improvements to the optimisation methods to be derived. These higher-order accelerated methods up to 4 th order are tested numerically and shown to provide substantial reduction of both number of steps and computation time.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Accelerating scientific discoveries through data-driven innovations

Developing artificial intelligence (AI) and machine learning (ML) methods that can accelerate scientific discoveries and advance science has become one of the important research directions for the AI/ML research community. It has been gaining increasing attention from researchers in diverse scientific areas, including biomedical science, materials science, climate science, physics, chemistry, and many others. Data-driven AI/ML innovations to enable reliable predictions and optimal decision making for scientific discoveries face several critical challenges, among which are high system complexity, large search space, incomplete knowledge, and small data, all of which demand novel strategies to effectively address them. Meeting these challenges and thereby accelerating scientific discoveries and industrial innovations, calls for research that can take full advantage of the latest advances in AI/ML to integrate data-driven techniques with scientific knowledge and is able to execute them in modern high-performance computing (HPC) environments at scale. This Patterns special collection "Accelerating scientific discoveries through data-driven innovations" features articles that showcase the promising roles of AI/ML and data-driven modeling in accelerating scientific discoveries and may inspire the next wave of data-driven innovations in various scientific domains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Optimizing $\mathrm{ACRT}$ to reduce inclusion formation during the $\mathrm{VGF}$ growth of cadmium zinc telluride: II. Application to experiments

Here two different accelerated crucible rotation technique (ACRT) rotation schedules are assessed, via theoretical computations and growth experiments, according to their ability to reduce tellurium-rich inclusions during the vertical gradient freeze (VGF) of cadmium zinc telluride (CZT). A vigorous rotation schedule based on classical ACRT guidelines produces a well-mixed melt that is expected to reduce tellurium inclusions compared to growth without crucible rotation. In contrast, a new ACRT schedule, derived from model-based optimization for interface stability, employs slower rotation with longer periods and is predicted to further reduce inclusions. Growth experiments corroborate these expectations. Namely, both ACRT schedules result in crystals with inclusion size and volume significantly decreased from levels found in material grown with no rotation, and material grown using the computationally optimized ACRT parameters exhibits a median inclusion size that is smaller and with a sharper distribution than in material grown via classical ACRT.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A numerical solver for investigating the space charge effect on the electric field in liquid argon time projection chambers

This paper reports the development of a numerical solver aimed to simulate the interaction between the space charge (i.e. ions) distribution and the electric field in liquid argon time projection chamber (LArTPC) detectors. The ion transport equation is solved by a time-accurate, cell-centered finite volume method and the electric potential equation by a continuous finite element method. The electric potential equation updates the electric field which provides the drift velocity to the ion transport equation. The ion transport equation updates the space charge density distribution which appears as the source term in the electric potential equation. The interaction between the space charge distribution and the electric field is numerically simulated within each physical time step. The convective velocity in the ion transport equation can include the background flow velocity in addition to the electric drift velocity. The numerical solver has been parallelized using the Message Passing Interface (MPI) library. Numerical tests show and verify the capability and accuracy of the current numerical solver. It is planned that the developed numerical solver, together with a Computational Fluid Dynamics (CFD) package which provides the flow velocity field, can be used to investigate the space charge effect on the electric field in large-scale particle detectors.

42 ENGINEERING↗
DOE OSTI2023

An ICME Modeling Framework for Metal Matrix Composites Focusing on Ultrahigh Temperature Matrix Material and Tungsten Carbide Reinforcement Particulate (Final CRADA Report)

Ultra High Temperature Metal Matrix Composites (UHT-MMCs) are of interest to the due to their potential defense and aerospace applications. These materials consist of a metal matrix reinforced with a stiff ceramic or cermet. Based on a preliminary literature survey, this project will focused on a pure titanium (Ti) matrix reinforced with tungsten carbide-cobalt (WC-Co). UHT-MMC technology is still at a nascent stage of development and requires extensive experimental work to optimize the structure and resulting material properties of a particular UHT-MMC material system. An accurate and complete high-performance computing (HPC) model of the Ti/WC-Co material system could greatly accelerate the development and deployment Ti/WC-Co materials by connecting processing parameters to material properties. This type of model could then be used in an integrated computational materials engineering approach to optimize the material structure to achieve a targeted level of performance.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Distinct Mechanisms and Hydricities of Cp*Ir-Based CO 2 Hydrogenation Catalysts in Basic Water

Transition metal-catalyzed reversible hydrogenation of CO 2 to formate in aqueous solutions under ambient conditions is an attractive environmentally friendly strategy for the storage and transportation of H 2 in a liquid chemical form. Here, mechanistic details for the CO 2 hydrogenation by a series of pentamethylcyclopentadienyl iridium(III) (Cp*Ir) complexes with picolinamidate ligands are investigated through density functional theory and kinetic isotope effects (KIEs) calculations. Additionally, adopting a speciation approach at a pH of 8.2, CO 2 hydrogenation mechanisms of 37 distinct protonation states and conformers of Cp*Ir type complexes are investigated. This imposes a challenging test for the computational modeling in terms of providing a consistent correlation with experimental kinetics and KIE studies of multiple catalysts instead of a single complex. Overall, H 2 heterolysis to generate an iridium hydride intermediate was demonstrated to be the rate determining step, which proceeds via distinct pathways depending on the stereoelectronic properties of the ligand. A peculiar iridium dihydride route was also uncovered, which could be optimized to accelerate the H 2 heterolysis. We have further computed the thermodynamic and kinetic hydricities of 74 complexes with [Cp*Ir(L)(H)] q ( q = -1, 0, 1 depending on the ligand charge by deprotonation or protonation events) general formula. Hydricity values do not show any noticeable correlation with the thermodynamics (Δ G ) of [Cp*Ir(L)(HCO 2 – )] formation but exhibit linear correlation with the kinetics (Δ G ‡ ) of electrophilic CO 2 attack to iridium hydride species, especially when the charges and local structural effects of the metal hydrides are considered. Insights gained in this study on (i) the factors determining the preferred pathway for the rate-limiting H 2 heterolysis step, (ii) the correlation between thermodynamic hydricity and the kinetics of CO 2 insertion to iridium hydride species, and (iii) mechanistic analysis via combination of free energy profiles and KIE studies for a series of iridium catalysts will provide guidelines for the design of next-generation catalysts for the reversible H 2 storage through CO 2 utilization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Analysis of GPU Data Access Patterns on Complex Geometries for the D3Q19 Lattice Boltzmann Algorithm

GPU performance of the lattice Boltzmann method (LBM) depends heavily on memory access patterns. When implemented with GPUs on complex domains, typically, geometric data is accessed indirectly and lattice data is accessed lexicographically. Although there are a variety of other options, no study has examined the relative efficacy between them. Here, we examine a suite of memory access schemes via empirical testing and performance modeling. We find strong evidence that semi-direct is often better suited than the more common indirect addressing, providing increased computational speed and reducing memory consumption. For the layout, we find that the Collected Structure of Arrays (CSoA) and bundling layouts outperform the common Structure of Array layout; on V100 and P100 devices, CSoA consistently outperforms bundling, however the relationship is more complicated on K40 devices. When compared to state-of-the-art practices, our recommendations lead to speedups of 10–40 percent and reduce memory consumption up to 17 percent. Using performance modeling and computational experimentation, we determine the mechanisms behind the accelerations. We demonstrate that our results hold across multiple GPUs on two leadership class systems, and present the first near-optimal strong results for LBM with arterial geometries run on GPUs.

42 ENGINEERING↗
DOE OSTI2022

A hybrid nodal-staggered pseudo-spectral electromagnetic particle-in-cell method with finite-order centering

Electromagnetic particle-in-cell (PIC) codes are widely used to perform computer simulations of a variety of physical systems, including fusion plasmas, astrophysical plasmas, plasma wakefield particle accelerators, and secondary photon sources driven by ultra-intense lasers. In a PIC code, Maxwell's equations are solved on a grid with a numerical method of choice. This article focuses on pseudo-spectral analytical time-domain (PSATD) algorithms and presents a novel hybrid PSATD PIC scheme that combines the respective advantages of standard nodal and staggered methods. The novelty of the hybrid scheme consists in using finite-order centering of grid quantities between nodal and staggered grids, in order to combine the solution of Maxwell's equations on a staggered grid with the deposition of charges and currents and the gathering of electromagnetic forces on a nodal grid. The correctness and performance of the novel hybrid scheme are assessed by means of numerical tests that employ different classes of PSATD equations in a variety of physical scenarios, ranging from the modeling of electron-positron pair creation in vacuum to the simulation of laser-driven and particle beam-driven plasma wakefield acceleration. It is shown that the novel hybrid scheme offers significant numerical and computational advantages, compared to purely nodal or staggered methods, for all the test cases presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Machine learning accelerated turbulence modeling of transient flashing jets

We report modeling the sudden depressurization of superheated liquids through nozzles is a challenge because the pressure drop causes rapid flash boiling of the liquid. The resulting jet usually demonstrates a wide range of structures, including ligaments and droplets, due to both mechanical and thermodynamic effects. As the simulation comprises increasingly numerous phenomena, the computational cost begins to increase. One way to moderate the additional cost is to use machine learning surrogacy for specific elements of the calculation. This study presents a machine learning-assisted computational fluid dynamics approach for simulating the atomization of flashing liquids accounting for distinct stages, from primary atomization to secondary breakup to small droplets using the Σ - Y model coupled with the homogeneous relaxation model. Notably, the models for thermodynamic non-equilibrium (HRM) and Σ - Y are coupled, for the first time, with a deep neural network that simulates the turbulence quantities, which are then used in the prediction of superheated liquid jet atomization. The data-driven component of this method is used for turbulence modeling, avoiding the solution of the two-equation turbulence model typically used for Reynolds-averaged Navier-Stokes simulations for these problems. Both the accuracy and speed of the hybrid approach are evaluated, demonstrating adequate accuracy and at least 25% faster computational fluid dynamics simulations than the traditional approach. This acceleration suggests that perhaps additional components of the calculation could be replaced for even further benefit. Published under an exclusive license by AIP Publishing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗