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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

HPC Molecular Simulation Tries Out a New GPU: Experiences on Early AMD Test Systems for the Frontier Supercomputer

Molecular simulation is an important tool for nu- merous efforts in physics, chemistry, and the biological sciences. Simulating molecular dynamics requires extremely rapid cal- culations to enable sufficient sampling of simulated temporal molecular processes. The Hewlett Packard Enterprise (HPE) Cray EX Frontier supercomputer installed at the Oak Ridge Leadership Computing Facility (OLCF) will provide an exascale resource for open science, and will feature graphics processing units (GPUs) from Advanced Micro Devices (AMD). The future LUMI supercomputer in Finland will be based on an HPE Cray EX platform as well. Here we test the ports of several widely used molecular dynamics packages that have each made substantial use of acceleration with NVIDIA GPUs, on Spock, the early Cray pre-Frontier testbed system at the OLCF which employs AMD GPUs. These programs are used extensively in industry for pharmaceutical and materials research, as well as academia, and are also frequently deployed on high-performance computing (HPC) systems, including national leadership HPC resources. We find that in general, performance is competitive and installation is straightforward, even at these early stages in a new GPU ecosystem. Our experiences point to an expanding arena for GPU vendors in HPC for molecular simulation.

Sedova, Ada↗
DOE OSTI2018

Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and noncovalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra-high dimensional configuration spaces, and the requirement to avoid (self-) collisions, which results in low acceptance rates. In this paper, we present two novel mechanisms to overcome these limitations. First, we introduce temporary constraints between near-colliding links. The resulting constraint varieties instantaneously redirect the search for collision-free conformations, and couple motions between distant parts of the linkage. Second, we adapt a randomized Poisson-disk motion planner, which prevents local oversampling and widens the search, to ultra-high dimensions. Tests on several model systems show that the sampling acceptance rate can increase from 16% to 70%, and that the conformational coverage in loop modeling measured as average closeness to existing loop conformations doubled. Finally, correlated protein motions identified with our algorithm agree with those from MD simulations.

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

An efficient, partitioned ensemble algorithm for simulating ensembles of evolutionary MHD flows at low magnetic Reynolds number

Studying the propagation of uncertainties in a nonlinear dynamical system usually involves generating a set of samples in the stochastic parameter space and then repeated simulations with different sampled parameters. The main difficulty faced in the process is the excessive computational cost. In this paper, we present an efficient, partitioned ensemble algorithm to determine multiple realizations of a reduced Magnetohydrodynamics (MHD) system, which models MHD flows at low magnetic Reynolds number. The algorithm decouples the fully coupled problem into two smaller subphysics problems, which reduces the size of the linear systems that to be solved and allows the use of optimized codes for each subphysics problem. Moreover, the resulting coefficient matrices are the same for all realizations at each time step, which allows faster computation of all realizations and significant savings in computational cost. We prove this algorithm is first order accurate and long time stable under a time step condition. Numerical examples are provided to verify the theoretical results and demonstrate the efficiency of the algorithm.

Jiang, Nan↗
DOE OSTI2024

The ReSWARM microgravity flight experiments: Planning, control, and model estimation for on‐orbit close proximity operations

Abstract On‐orbit close proximity operations involve robotic spacecraft maneuvering and making decisions for a growing number of mission scenarios demanding autonomy, including on‐orbit assembly, repair, and astronaut assistance. Of these scenarios, on‐orbit assembly is an enabling technology that will allow large space structures to be built in situ, using smaller building block modules. However, like many of these scenarios, robotic on‐orbit assembly involves several technical hurdles, such as changing system models. For instance, grappled modules moved by a free‐flying “assembler” robot can cause significant changes in the combined system inertia, which have cascading impacts on motion planning and control portions of the autonomy stack. Further, on‐orbit assembly and other scenarios require collision‐avoiding motion planning, particularly when operating in a “construction site” scenario of multiple assembler robots and structures. Multiple key technologies that address these complicating factors for autonomous microgravity close proximity operations are detailed in this work, in particular: (1) application of global long‐horizon planning, accomplished using offline and online sampling‐based planner options that consider the system dynamics; (2) adaptation of the recently proposed RATTLE information‐aware planning framework for on‐orbit reconfiguration model learning; and (3) connection with robust control tools to provide low‐level control robustness using current system knowledge. These approaches were demonstrated for an autonomous on‐orbit assembly use case by the RElative Satellite sWarming and Robotic Maneuvering (ReSWARM) experiments using NASA's Astrobee robots on the International Space Station. Results of the ReSWARM experiments are provided along with significant operational and implementation detail discussing the practicalities of hardware implementation and unique aspects of working with the Astrobee free‐flyer robots in microgravity. ReSWARM provides a base set of planning and control tools for robotic close proximity operations, demonstrates them in microgravity, and outlines some of the important hardware aspects that future autonomous free‐flyers will need to consider.

Robotics↗
DOE OSTI2022

Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics

Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Perturbative theoretical model of electronic transient circular dichroism spectroscopy of molecular aggregates

A chiral analog of transient absorption spectroscopy, transient circular dichroism (TCD) spectroscopy is an emerging time-resolved method. Both spectroscopic methods can probe the electronic transitions of a sample, and TCD is additionally sensitive to the dynamic aspects of chirality, such as those induced by molecular excitons. Here, we develop a theoretical description of TCD for electronic multi-level models in which the pump pulse is linearly polarized and probe pulse is alternately left- and right-circularly polarized. We derive effective response functions analogous to those often used to describe other four-wave mixing methods and then simulate and analyze TCD spectra for three representative multi-level electronic model systems. We elaborate on the presence and detection of the spectral signatures of electronic coherences.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Three-dimensional optical trapping and orientation of microparticles for coherent X-ray diffraction imaging

Optical trapping has been implemented in many areas of physics and biology as a noncontact sample manipulation technique to study the structure and dynamics of nano-andmesoscale objects. It provides a unique approach for manipulating microscopic objects without inducing undesired changes in structure. Combining optical trapping with hard X-ray microscopy techniques, such as coherent diffraction imaging and crystallography, provides a nonperturbing environment where electronic and structural dynamics of an individual particle in solution can be followed in situ. It was previously shown that optical trapping allows the manipulation of micrometer-sized objects for Xray fluorescence imaging. However, questions remain over the ability of optical trapping to position objects for X-ray diffraction measurements, which have stringent requirements for angular stability. Our work demonstrates that dynamic holographic optical tweezers are capable of manipulating single micrometer-scale anisotropic particles in a microfluidic environment with the precision and stability required for X-ray Bragg diffraction experiments-thus functioning as an "optical goniometer." The methodology can be extended to a variety of X-ray experiments and the Bragg coherent diffractive imaging of individual particles in solution, as demonstrated here, will be markedly enhanced with the advent of brighter, coherent X-ray sources.

Gao, Yuan↗
DOE OSTI2021

Standardizing reverberation-measured Mg II time-lag quasars, by using the radius–luminosity relation, and constraining cosmological model parameters

ABSTRACT We use 78 reverberation-measured Mg II time-lag quasars (QSOs) in the redshift range 0.0033 ≤ z ≤ 1.89 to constrain cosmological parameters in six different cosmological models. The basis of our method is the use of the radius–luminosity or R−L relation to standardize these 78 Mg II QSOs. In each cosmological model, we simultaneously determine R−L relation and cosmological model parameters, thus avoiding the circularity problem. We find that the R−L relation parameter values are independent of the cosmological model used in the analysis, thus, establishing that current Mg II QSOs are standardizable candles. Cosmological constraints obtained using these QSOs are significantly weaker than, but consistent with, those obtained from a joint analysis of baryon acoustic oscillation (BAO) observations and Hubble parameter [H(z)] measurements. So, we also analyse these QSOs in conjunction with the BAO + H(z) data and find cosmological constraints consistent with the standard spatially flat ΛCDM model as well as with mild dark energy dynamics and a little spatial curvature. A larger sample of higher quality reverberation-measured QSOs should have a smaller intrinsic dispersion and so should provide tighter constraints on cosmological parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Zhao, Yanyan (ORCID:0000000323021763)↗
DOE OSTI2025

Hardware-Efficient Quantum Phase Estimation via Local Control

Quantum phase estimation plays a central role in quantum simulation as it enables the study of spectral properties of many-body quantum systems. Most variants of the phase estimation algorithm require the application of the global unitary evolution conditioned on the state of one or more auxiliary qubits, posing a significant challenge for current quantum devices. In this work, we present an approach to quantum phase estimation that uses only locally controlled operations, resulting in a significantly reduced circuit depth. At the heart of our approach are efficient routines to measure the complex phase of the expectation value of the time-evolution operator, the so-called Loschmidt echo, for both circuit dynamics and Hamiltonian dynamics. By tracking changes in the phase during the dynamics, the routines trade circuit depth for increased sampling cost and classical postprocessing. Our approach does not rely on reference states and is applicable to any efficiently preparable state, regardless of its correlations. We provide a comprehensive analysis of the sample complexity and illustrate the results with numerical simulations. Our methods offer a practical pathway for measuring spectral properties in large many-body quantum systems using current quantum devices.

Schiffer, Benjamin F. [Max Planck Institute of Qua↗
DOE OSTI2021

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Neural Lyapunov Differentiable Predictive Control

We present a learning-based predictive control methodology using the differentiable programming framework with sufficient Lyapunov-based guarantees. The neural Lyapunov differentiable predictive control (NLDPC) learns the policy by constructing a computational graph encompassing the system dynamics, state, and input constraints, and the necessary Lyapunov certification constraints, and thereafter using the automatic differentiation to update the neural policy parameters. In conjunction, our approach jointly learns a Lyapunov function that certifies the regions of state-space with stable dynamics. We also provide an initial condition sampling-based statistical guarantee for the training of NLDPC. Our offline training approach provides a computationally efficient and scalable alternative to classical model predictive control solutions, which now directly comes with Lyapunov based guarantees as shown in this paper. We substantiate the advantages of the proposed approach with simulations to stabilize the double integrator model and on an example of controlling an aircraft model.

Mukherjee, Sayak↗
DOE OSTI2019

Surrogate Optimization of Computationally Expensive Black-Box Problems with Hidden Constraints (SHEBO) v1.0

SHEBO (surrogate optimization of problems with hidden constraints and expensive black-box objectives) is an efficient optimization algorithm that employs surrogate models to solve computationally expensive black-box simulation optimization problems that have hidden constraints. Hidden constraints are encountered when the objective function evaluation does not return a value for a parameter vector. These constraints are often encountered in optimization problems in which the objective function is computed by a black-box simulation code. SHEBO uses a combination of local and global search strategies together with an evaluability prediction function and a dynamically adjusted evaluability threshold to iteratively select new sample points.

Mueller, Juliane↗
DOE OSTI2024

From Fossil Fuels to Green Mines: Understanding Hydrogen-Shale Interactions for Secure Underground Storage

Hydrogen-powered mining trucks are rapidly gaining traction as a key driver of decarbonization in the mining industry. This surge necessitates a decisive shift towards renewable energy sources, primarily for hydrogen production. However, the inherent intermittency of renewables poses a challenge for continuous operations, demanding efficient storage solutions for hydrogen fuel. Hydrogen, derived from renewables, requires large-scale storage, with underground hydrogen storage (UHS) in depleted oil and gas reservoirs projected to provide this capacity. An impermeable seal (caprock) overlying depleted reservoirs is crucial for preventing leakage and ensuring secure storage. Shale, a potential caprock, has been recognized for its effectiveness in containing natural gas for geological time-periods. This study investigates the impact of hydrogen exposure on the matrix permeability of Marcellus shale, a key factor influencing its sealing capacity. A novel time-resolved approach was employed, measuring matrix permeability after each exposure to understand the dynamic interactions between hydrogen and the shale matrix. Samples were exposed to hydrogen in pressure reactions at realistic reservoir conditions at varying time durations. Preliminary results reveal an initial increase in permeability, while subsequent exposures show a decrease, indicating potential microstructural changes.

08 HYDROGEN↗
DOE OSTI2023

First Use of a Longitudinally Polarized Target with CLAS12

Run Group C comprises eight experiments utilizing the CLAS12 detector system in Hall B at Jefferson Lab to study the multidimensional partonic structure of nucleons. The experiments scatter electrons from polarized protons and neutrons in samples of solid NH$_3$ and ND$_3$, dynamically polarized at a temperature of 1 K in a 5 T magnetic field. After a brief description of the target system, the current status of the target and preliminary results of its performance in the experiment are presented.

Keith, Christopher↗
DOE OSTI2017

Activity and Kinematics of White Dwarf-M Dwarf Binaries from the SUPERBLINK Proper Motion Survey

We present an activity and kinematic analysis of high proper motion white dwarf-M dwarf binaries (WD+dMs) found in the SUPERBLINK survey, 178 of which are new identifications. To identify WD+dMs, we developed a UV–optical–IR color criterion and conducted a spectroscopic survey to confirm each candidate binary. For the newly identified systems, we fit the two components using model white dwarf spectra and M dwarf template spectra to determine physical parameters. We use H α chromospheric emission to examine the magnetic activity of the M dwarf in each system, and investigate how its activity is affected by the presence of a white dwarf companion. We find that the fraction of WD+dM binaries with active M dwarfs is significantly higher than their single M dwarf counterparts at early and mid-spectral types. We corroborate previous studies that find high activity fractions at both close and intermediate separations. At more distant separations, the binary fraction appears to approach the activity fraction for single M dwarfs. Using derived radial velocities and the proper motions, we calculate 3D space velocities for the WD+dMs in SUPERBLINK. For the entire SUPERBLINK WD+dMs, we find a large vertical velocity dispersion, indicating a dynamically hotter population compared to high proper motion samples of single M dwarfs. We compare the kinematics for systems with active M dwarfs and those with inactive M dwarfs, and find signatures of asymmetric drift in the inactive sample, indicating that they are drawn from an older population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Extending the Calibration of C iv-based Single-epoch Black Hole Mass Estimators for Active Galactic Nuclei

We provide an updated calibration of C iv λ1549 broad emission line–based single-epoch (SE) black hole (BH) mass estimators for active galactic nuclei (AGNs) using new data for six reverberation-mapped AGNs at redshift z=0.005--0.028 with BH masses (bolometric luminosities) in the range 10{sup 6.5}--10{sup 7.5} M{sub ⊙} (10{sup 41.7}--10{sup 43.8} erg s{sup −1}). New rest-frame UV-to-optical spectra covering 1150–5700 Å for the six AGNs were obtained with the Hubble Space Telescope (HST). Multicomponent spectral decompositions of the HST spectra were used to measure SE emission-line widths for the C iv, Mg ii, and Hβ lines, as well as continuum luminosities in the spectral region around each line. We combine the new data with similar measurements for a previous archival sample of 25 AGNs to derive the most consistent and accurate calibrations of the C iv-based SE BH mass estimators against the Hβ reverberation-based masses, using three different measures of broad-line width: full width at half maximum (FWHM), line dispersion (σ{sub line}), and mean absolute deviation (MAD). The newly expanded sample at redshift z=0.005--0.234 covers a dynamic range in BH mass (bolometric luminosity) of logM{sub BH}/M{sub ⊙}=6.5--9.1 (logL{sub bol}/ erg s{sup −1} = 41.7--46.9), and we derive the new C iv-based mass estimators using a Bayesian linear regression analysis over this range. We generally recommend the use of σ{sub line} or MAD rather than FWHM to obtain a less biased velocity measurement of the C iv emission line, because its narrow-line component contribution is difficult to decompose from the broad-line profile.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Optical Photometric Indicators of Galaxy Cluster Relaxation

Abstract The most dynamically relaxed clusters of galaxies play a special role in cosmological studies as well as astrophysical studies of the intracluster medium (ICM) and active galactic nucleus feedback. While high-spatial-resolution imaging of the morphology of the ICM has long been the gold standard for establishing a cluster’s dynamical state, such data are not available from current or planned surveys, and thus require separate, pointed follow-up observations. With optical and/or near-IR photometric imaging, and red-sequence cluster finding results from those data, expected to be ubiquitously available for clusters discovered in upcoming optical and millimeter-wavelength surveys, it is worth asking how effectively photometric data alone can identify relaxed cluster candidates, before investing in, e.g., high-resolution X-ray observations. Here we assess the ability of several simple photometric measurements, based on the redMaPPer cluster finder run on Sloan Digital Sky Survey data, to reproduce X-ray classifications of dynamical state for an X-ray selected sample of massive clusters. We find that two simple metrics contrasting the bright central galaxy (BCG) to other cluster members can identify a complete sample of relaxed clusters with a purity of ∼40% in our data set. Including minimal ICM information in the form of a center position increases the purity to ∼60%. However, all three metrics depend critically on correctly identifying the BCG, which is presently a challenge for optical red-sequence cluster finders.

79 ASTRONOMY AND ASTROPHYSICS↗