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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light

As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Finite element formulation of fluctuating hydrodynamics for fluids filled with rigid particles using boundary fitted meshes

In this paper, we present a finite element implementation of fluctuating hydrodynamics with a moving boundary fitted mesh for treating the suspended particles. The thermal fluctuations are incorporated into the continuum equations using the Landau and Lifshitz approach [1]. The proposed implementation fulfills the fluctuation–dissipation theorem exactly at the discrete level. Since we restrict the equations to the creeping flow case, this takes the form of a relation between the diffusion coefficient matrix and friction matrix both at the particle and nodal level of the finite elements. Brownian motion of arbitrarily shaped particles in complex confinements can be considered within the present formulation. A multi-step time integration scheme is developed to correctly capture the drift term required in the stochastic differential equation (SDE) describing the evolution of the positions of the particles. The proposed approach is validated by simulating the Brownian motion of a sphere between two parallel plates and the motion of a spherical particle in a cylindrical cavity. The time integration algorithm and the fluctuating hydrodynamics implementation are then applied to study the diffusion and the equilibrium probability distribution of a confined circle under an external harmonic potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Alignment of the CLAS12 central hybrid tracker with a Kalman Filter

Several factors can contribute to the difficulty of aligning the sensors of tracking detectors, including a large number of modules, multiple types of detector technologies, and non-linear strip patterns on the sensors. All three of these factors apply to the CLAS12 CVT, which is a hybrid detector consisting of planar silicon sensors with non-parallel strips, and cylindrical micromegas sensors with longitudinal and arc-shaped strips located within a 5 T superconducting solenoid. To align this detector, we used the Kalman Alignment Algorithm, which accounts for correlations between the alignment parameters without requiring the time-consuming inversion of large matrices. This is the first time that this algorithm has been adapted for use with hybrid technologies, non-parallel strips, and curved sensors. We present the results for the first alignment of the CLAS12 CVT using straight tracks from cosmic rays and from a target with the magnetic field turned off. After running this procedure, we achieved alignment at the level of 10 µm, and the widths of the residual spectra were greatly reduced. These results attest to the flexibility of this algorithm and its applicability to future use in the CLAS12 CVT and other hybrid or curved trackers, such as those proposed for the future Electron-Ion Collider.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Advanced Shuttle Strategies for Parallel QCCD Architectures

Trapped ions (TIs) are at the forefront of quantum computing implementation, offering unparalleled coherence, fidelity, and connectivity. However, the scalability of TI systems is hampered by the limited capacity of individual ion traps, necessitating intricate ion shuttling for advanced computational tasks. The quantum charge-coupled device (QCCD) framework has emerged as a promising solution, facilitating ion mobility for universal quantum computation. Current QCCD architectures predominantly feature a linear topology, which is increasingly recognized as inefficient for complex quantum operations. Anticipating the shift toward more efficacious designs, this article introduces an innovative quantum scheduling strategy optimized for parallel QCCD topologies. Our strategy proposes a probabilistic formula for ion movement, alongside ingenious methods for local layer generation and layer compression, yielding a significant reduction in ion shuttle times. Through simulations, we demonstrate that our strategy not only substantially outstrips the linear model but also exhibits better performance over other parallel strategies that employ greedy algorithms. This is achieved through our nuanced resolution of complexities, such as traffic blocks and trap capacity limitations. The consequent reduction in shuttle operations leads to lower energy consumption and an enhancement in the quantum computer's fidelity, ultimately accelerating program execution times.

43 PARTICLE ACCELERATORS↗
DOE OSTI2018

Single-pass parallel prefix scan with dynamic look back

One embodiment of the present invention performs a parallel prefix scan in a single pass that incorporates variable look-back. A parallel processing unit (PPU) subdivides a list of inputs into sequentially-ordered segments and assigns each segment to a streaming multiprocessor (SM) included in the PPU. Notably, the SMs may operate in parallel. Each SM executes write operations on a segment descriptor that includes the status, aggregate, and inclusive-prefix associated with the assigned segment. Further, each SM may execute read operations on segment descriptors associated with other segments. In operation, each SM may perform reduction operations to determine a segment-wide aggregate, may perform look-back operations across multiple preceding segments to determine an exclusive-prefix, and may perform a scan seeded with the exclusive prefix to generate output data. Advantageously, the PPU performs one read operation per input, thereby reducing the time required to execute the prefix scan relative to prior-art parallel implementations.

Merrill, Duane↗
DOE OSTI2017

A performance spectrum for parallel computational frameworks that solve PDEs

Summary Important computational physics problems are often large‐scale in nature, and it is highly desirable to have robust and high performing computational frameworks that can quickly address these problems. However, it is no trivial task to determine whether a computational framework is performing efficiently or is scalable. The aim of this paper is to present various strategies for better understanding the performance of any parallel computational frameworks for solving PDEs. Important performance issues that negatively impact time‐to‐solution are discussed, and we propose a performance spectrum analysis that can enhance one's understanding of critical aforementioned performance issues. As proof of concept, we examine commonly used finite element simulation packages and software and apply the performance spectrum to quickly analyze the performance and scalability across various hardware platforms, software implementations, and numerical discretizations. It is shown that the proposed performance spectrum is a versatile performance model that is not only extendable to more complex PDEs such as hydrostatic ice sheet flow equations but also useful for understanding hardware performance in a massively parallel computing environment. Potential applications and future extensions of this work are also discussed.

Chang, J.↗
DOE OSTI2020

Efficient Treatment of Large Active Spaces through Multi-GPU Parallel Implementation of Direct Configuration Interaction

In this study, we have extended our graphical processing unit (GPU)-accelerated direct configuration interaction program to multiple devices, reducing iteration times for configuration spaces of 165 million determinants to only 3 s using NVIDIA P100 GPUs. Similar improvements in the one- and two-particle reduced density matrix formation allow for fast analytical energy gradients and electronic properties. Our parallel algorithm enables the calculation of arbitrarily large configuration spaces (limited only by available system memory), with iteration times of 13 min for an active space of 18 electrons in 18 orbitals (2.4 billion determinants) using six consumer grade NVIDIA 1080Ti GPUs. These advances enable routine molecular dynamics simulations, geometry optimizations, and absorption spectrum calculations for molecules with large configuration spaces, a task that has heretofore required massive computational effort. In this work, we demonstrate the utility of our program by generating the absorption spectrum for diphenyl acetylene at the floating occupation molecular orbital complete active space configuration interaction level of theory. Lastly, several active spaces were investigated to assess the dependence of spectral features on orbital space dimension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Dynamical electron vortices in attosecond double photoionization of H 2

We study electron momentum vortices in single-photon double ionization of H 2 by time-delayed, counter-rotating, elliptically polarized attosecond pulses propagating along kˆ either parallel or perpendicular to the molecular axis R. For ˆk∥R, kinematical vortices occur similar to those found for He. For kˆ⊥R, we find dynamical vortex structures originating from an ellipticity-dependent interplay of 1 Σ$^{+}_{u}$ and 1 Π$^{+}_{u}$ continuum amplitudes. Furthermore, we propose a complete experiment to determine the magnitudes and relative phase of these amplitudes by varying pulse ellipticities and time delays.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Parallel multiple-chain DRAM MCMC for large-scale geosteering inversion and uncertainty quantification

Geosteering is the proactive control of a wellbore placement based on the downhole measurements, aiming at maximizing economic production from the well. We report the recent development of azimuthal resistivity logging-whiledrilling (LWD) tools have a much larger depth of detection, thus sets higher demands for geosteering inversion as more unknown parameters need to be taken into account in the earth model to be inverted. For complicated nonlinear problems, traditional deterministic inversion methods are more likely to be trapped near local optima. In general, Markov chain Monte Carlo (MCMC) inversion methods are more capable of finding the global optimal solution and providing additional uncertainty analyses by sampling from the target distribution. However, MCMC methods usually have the problem of slow convergence. Even though optimization methods like delayed rejection (DR) and adaptive Metropolis (AM) were proposed to speed up the convergence, using MCMC methods to solve geosteering inversion problems may still incur unacceptable time cost. To reduce the sampling cost of MCMC methods, we use parallel multiple-chain DRAM MCMC methods to solve geosteering inverse problems and estimate the corresponding uncertainty. A clustering method, density-based spatial clustering of applications with noise (DBSCAN), is applied to select the best solution among many results. Lastly, the simulation results show that running many relatively short MCMC chains for one problem can obtain a similar result as running a long single chain. Besides, avoiding communications between multiple Markov chains during the sampling process yields almost linear scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Parallel Algorithms for Efficient Computation of High-Order Line Graphs of Hypergraphs

This paper considers structures of systems beyond dyadic (pairwise) interactions and investigates mathematical modeling of multi-way interactions and connections as hypergraphs, where captured relationships among system entities are set-valued. To date, in most situations, entities in a hypergraph are considered connected as long as there is at least one common ``neighbor''. However, minimal commonality sometimes discards the ``strength'' of connections and interactions among groups. To this end, considering the ``width'' of a connection, referred to as the \emph{$s$-overlap} of neighbors, provides more meaningful insights into how closely the communities or entities interact with each other. In addition, $s$-overlap computation is the fundamental kernel to construct the line graph of a hypergraph, a low-order approximation of the hypergraph which can carry significant information about the original hypergraph. Subsequent stages of a data analytics pipeline then can apply highly-tuned graph algorithms on the line graph to reveal important features. Given a hypergraph, computing the $s$-overlaps by exhaustively considering all pairwise entities can be computationally prohibitive. To tackle this challenge, we develop efficient algorithms to compute $s$-overlaps and the corresponding line graph of a hypergraph. We propose several heuristics to avoid execution of redundant work and improve performance of the $s$-overlap computation. Our parallel algorithm, combined with these heuristics, is orders of magnitude (more than $10\times$) faster than the naive algorithm in all cases and the SpGEMM algorithm with filtration in most cases (especially with large $s$ value).

hypergraph algorithms, graph algorithms, parallel ↗
DOE OSTI2019

Parallel point defect identification in molecular dynamics simulations without post-processing: A compute and dump style for LAMMPS

Two classes for the molecular dynamics program LAMMPS – one compute style and one dump style – are presented that are designed to identify, count, and output point defects in cascade damage and related molecular dynamics simulations. The calculations are done in parallel across multiple MPI processes, and can be done at the same time as the original simulation. This drastically reduces storage requirements by eliminating the need to post-process every atom in the system. Non-cubic lattices, free surfaces, and large voids can be eliminated from the output by suitable choices of the reference lattice. The classes are derived from LAMMPS’s Dump and Compute classes, and pose no additional overhead to LAMMPS if they are not used.

42 ENGINEERING↗
DOE OSTI2018

Pseudo-dynamic Aspen Plus{sup R} Model of the Defense Waste Processing Facility - 18475

The Defense Waste Processing Facility (DWPF) at the Savannah River Site converts legacy high-level waste from the Cold War into borosilicate glass for permanent disposal in a geological repository. The waste sludge is chemically adjusted by the addition of acid, mixed with frit, and concentrated in the DWPF Chemical Process Cell (CPC) to ensure that the final glass has the desired properties. The resulting mixture is fed into the melter where the waste is melted and poured into stainless steel storage canisters. We present an Aspen Plus{sup R} model of the DWPF CPC, which is being developed to aid chemical processing decisions pertaining to the current flowsheet and to aid decisions regarding optimizing future processing. Given a waste feed composition with acid and frit additions, the model will predict the sludge and off-gas compositions throughout the processing, as well as the final melter feed composition. This allows different processing scenarios to be investigated easily, reducing the reliance on experimental testing, and hence saving time and money. The model has multiple potential applications, including calculating the acid and frit additions required to give acceptable glass properties, off-gas permitting, tracking mercury steam-stripped from the waste in the off-gas system, tracking flammable gases in the offgas system, investigating the effect of reducing air purges in the condensers, and general process optimization. The waste is processed in the CPC in batches, requiring dynamic simulation to track the time-dependent operations. Accurate modeling of the processing also requires calculations of phase and electrolyte chemical equilibria and parallel rate-dependent reactions. Due to existing technical limitations with dynamic simulation of the complex chemical system, we have adopted a pseudo-dynamic approach in which time intervals are treated as consecutive steady-state operations in Aspen Plus{sup R}. Thus, the model consists of ∼100 replicas of the processing vessel and its off-gas system, with the sludge output by one replica (representing one time interval) becoming the feed to the next (representing the next time interval). By examining the results from these replicas in sequence, one can see the time evolution of the model. This general approach can be used wherever simultaneous calculation of phase and electrolyte chemical equilibria in a dynamically evolving system is needed. In addition to describing the general structure and chemistry of the model, we present results from tests of the model against experimental data. These data are from laboratory-scale process simulations of the CPC with a nonradioactive waste sludge simulant. These tests include the model's predictions of the offgas composition, the sludge pH, and the final sludge composition. We will also discuss planned future developments of the model. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Highly interactive, steered scientific workflows on HPC systems: optimizing design solutions

Scientific workflows are becoming increasingly important in high performance computing (HPC) settings, as the feasibility and appeal of many simultaneous heterogeneous tasks increases with increasing hardware capabilities. Currently no HPC-based workflow platform supports a dynamically adaptable workflow with interactive steering and analysis at run-time. Furthermore, for most workflow programs, compute resources are fixed for a given instance, resulting in a possible waste of expensive allocation resources when tasks are spawned and killed. Here we describe the design and testing of a run-time-interactive, adaptable, steered workflow tool capable of executing thousands of parallel tasks without an MPI programming model, using a database management system to facilitate task management through multiple live connections. We find that on the Oak Ridge Leadership Computing Facility pre-exascale Summit supercomputer it is possible to launch and interactively steer workflows with thousands of simultaneous tasks with negligible latency. For the case of particle simulation and analysis tasks that run for minutes to hours, this paradigm offers the prospect of a robust and efficient means to perform simulation-space exploration with on-the-fly analysis and adaptation.

Ossyra, John R↗
DOE OSTI2016

Hydroxy double salts loaded with bioactive ions: Synthesis, intercalation mechanisms, and functional performance

The intercalation of the anions of diclofenac (Dic), naproxen (Nap), and valproic acid (Val) into three hydroxy double salts (HDSs) has been explored in this work. Experiments were performed with [Co{sub 1.2}Zn{sub 3.8}(OH){sub 8}](NO{sub 3}){sub 2}·2H{sub 2}O (CoZn-NO{sub 3}), [Ni{sub 2}Zn{sub 3}(OH){sub 8}](NO{sub 3}){sub 2}·2H{sub 2}O (NiZn-NO{sub 3}) and [Zn{sub 5}(OH){sub 8}](NO{sub 3}){sub 2}·2H{sub 2}O (Zn-NO{sub 3}). It proved possible to intercalate diclofenac and naproxen into all three HDSs. In contrast, Val could be intercalated into CoZn-NO{sub 3} but when it was reacted with Zn-NO{sub 3} the HDS structure was destroyed, and the product comprised ZnO. Successful intercalation was verified by X-ray diffraction, IR spectroscopy, and elemental microanalysis. Molecular dynamics simulations showed the Dic and Nap ions to arrange themselves in an “X” shape in the interlayer space, forming a bilayer. Val was found to adopt a position with its aliphatic groups parallel to the HDS layer, again in a bilayer. In situ time resolved X-ray diffraction experiments revealed that intercalation of Dic and Nap into CoZn-NO{sub 3} and Zn-NO{sub 3} is mechanistically complex, with a number of intermediate phases observed. In contrast, the intercalation of all three guests into NiZn-NO{sub 3} and of Val into CoZn-NO{sub 3} are simple one step reactions proceeding directly from the starting material to the product. The HDS-drug composites were found to have sustained release profiles. - Graphical abstract: Seven new drug intercalates of hydroxy double salts (HDSs) have been prepared and characterised. The intercalation mechanisms have been explored, and the drug release properties of the HDS/drug composites quantified. Display Omitted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Ab Initio Reactive Computer Aided Molecular Design

Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Critical Factors Driving the High Volumetric Uptake of Methane in Cu 3 (btc) 2

We report a thorough experimental and computational study has been carried out to elucidate the mechanistic reasons for the high volumetric uptake of methane in the metal–organic framework Cu 3 (btc) 2 (btc 3– = 1,3,5-benzenetricarboxylate; HKUST-1). Methane adsorption data measured at several temperatures for Cu 3 (btc) 2 , and its isostructural analogue Cr 3 (btc) 2 , show that there is little difference in volumetric adsorption capacity when the metal center is changed. In situ neutron powder diffraction data obtained for both materials were used to locate four CD 4 adsorption sites that fill sequentially. This data unequivocally shows that primary adsorption sites around, and within, the small octahedral cage in the structure are favored over the exposed Cu 2+ or Cr 2+ cations. These results are supported by an exhaustive parallel computational study, and contradict results recently reported using a time-resolved diffraction structure envelope (TRDSE) method. Moreover, the computational study reveals that strong methane binding at the open metal sites is largely due to methane–methane interactions with adjacent molecules adsorbed at the primary sites instead of an electronic interaction with the metal center. Simulated methane adsorption isotherms for Cu 3 (btc) 2 are shown to exhibit excellent agreement with experimental isotherms, allowing for additional simulations that show that modifications to the metal center, ligand, or even tuning the overall binding enthalpy would not improve the working capacity for methane storage over that measured for Cu 3 (btc) 2 itself.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Intrinsic flow and tearing mode rotation in the RFP during improved confinement

We use charge exchange recombination spectroscopy to make the first localized measurements of impurity ion flow velocity profiles in the reversed field pinch. Measurements in improved confinement plasmas reveal an intrinsic flow profile that is peaked on axis and mostly parallel to the equilibrium magnetic field. The toroidal flow decreases in time at off-axis locations where tearing modes are resonant, giving rise to a highly sheared flow profile near the axis. The tearing mode phase velocity correlates strongly with toroidal flow near the resonant surface and weakly with flow in other locations, providing an opportunity to verify the commonly held assumption that the plasma and mode move together at the resonant surface. Mechanisms for the observed momentum loss during the improved confinement period are evaluated and it is found that eddy currents in the conducting shell caused by the rotation of the dominant tearing mode dominate over other losses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗