Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “INTERACTION RANGE”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

An Electrostatic Funnel in the GABA-Binding Pathway

The γ-aminobutyric acid type A receptor (GABA A -R) is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABA A -R is well characterized, and many of the binding site residues have been identified. However, most of these residues are obscured behind the C-loop that acts as a cover to the binding site. Thus, the mechanism by which the GABA molecule recognizes the binding site, and the pathway it takes to enter the binding site are both unclear. Through the completion and detailed analysis of 100 short, unbiased, independent molecular dynamics simulations, we have investigated this phenomenon of GABA entering the binding site. In each system, GABA was placed quasi-randomly near the binding site of a GABA A -R homology model, and atomistic simulations were carried out to observe the behavior of the GABA molecules. GABA fully entered the binding site in 19 of the 100 simulations. The pathway taken by these molecules was consistent and non-random; the GABA molecules approach the binding site from below, before passing up behind the C-loop and into the binding site. This binding pathway is driven by long-range electrostatic interactions, whereby the electrostatic field acts as a ‘funnel’ that sweeps the GABA molecules towards the binding site, at which point more specific atomic interactions take over. These findings define a nuanced mechanism whereby the GABA A -R uses the general zwitterionic features of the GABA molecule to identify a potential ligand some 2 nm away from the binding site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Atomic-precision advanced manufacturing for Si quantum computing

Abstract A materials synthesis method that we call atomic-precision advanced manufacturing (APAM), which is the only known route to tailor silicon nanoelectronics with full 3D atomic precision, is making an impact as a powerful prototyping tool for quantum computing. Quantum computing schemes using atomic ( 31 P) spin qubits are compelling for future scale-up owing to long dephasing times, one- and two-qubit gates nearing high-fidelity thresholds for fault-tolerant quantum error correction, and emerging routes to manufacturing via proven Si foundry techniques. Multiqubit devices are challenging to fabricate by conventional means owing to tight interqubit pitches forced by short-range spin interactions, and APAM offers the required (Å-scale) precision to systematically investigate solutions. However, applying APAM to fabricate circuitry with increasing numbers of qubits will require significant technique development. Here, we provide a tutorial on APAM techniques and materials and highlight its impacts in quantum computing research. Finally, we describe challenges on the path to multiqubit architectures and opportunities for APAM technique development. Graphic Abstract

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cabana: A Performance Portable Library for Particle-Based Simulations

Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Subsystem Rényi entropy of thermal ensembles for SYK-like models

The Sachdev-Ye-Kitaev model is an N N -modes fermionic model with infinite range random interactions. In this work, we study the thermal Rényi entropy for a subsystem of the SYK model using the path-integral formalism in the large- N N limit. The results are consistent with exact diagonalization and can be well approximated by thermal entropy with an effective temperature when subsystem size M\leq N/2 M ≤ N / 2 . We also consider generalizations of the SYK model with quadratic random hopping term or U(1) U ( 1 ) charge conservation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubble evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink strength of interstitial loop for interstitials. In part II, we present a generic phase field model and discuss the thermodynamic and kinetic properties in phase-field models including the reaction kinetics of radiation defects and local free energy of irradiated materials. In particular, a two-sublattice thermodynamic model is suggested to describe the local free energy of alloys with irradiated defects. Fe-Cr alloy is taken as an example to explain the required thermodynamic and kinetic properties for quantitative phase-field modeling. Finally the great challenges in phase-field modeling will be discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2014

LAMMPS strong scaling performance optimization on Blue Gene/Q

LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.

Coffman, Paul↗
DOE OSTI2015

Advancing the Theory of Nuclear Reactions with Rare Isotopes. From the Laboratory to the Cosmos

The mission of the Topical Collaboration on the Theory of Reactions for Unstable iSotopes (TORUS) was to develop new methods to advance nuclear reaction theory for unstable isotopes—particularly the (d,p) reaction in which a deuteron, composed of a proton and a neutron, transfers its neutron to an unstable nucleus. After benchmarking the state-of-the-art theories, the TORUS collaboration found that there were no exact methods to study (d,p) reactions involving heavy targets; the difficulty arising from the long-range nature of the well known, yet subtle, Coulomb force. To overcome this challenge, the TORUS collaboration developed a new theory where the complexity of treating the long-range Coulomb interaction is shifted to the calculation of so-called form-factors. An efficient implementation for the computation of these form factors was a major achievement of the TORUS collaboration. All the new machinery developed are essential ingredients to analyse (d,p) reactions involving heavy nuclei relevant for astrophysics, energy production, and stockpile stewardship.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Neutrino-Nucleus Interactions and the Short-Range Structure of Nuclei

Improvements in theoretical modeling of Short Range structures and phenomena, and comparisons with data, will require sustained collaboration between nuclear theorists and neutrino experimentalists. The extensive history of studying this area of nuclear physics in electron- and hadron-scattering experiments, coupled with the transformative capabilities of LArTPCs to identify neutrinos, will provide a ripe opportunity for new discoveries that will further our understanding of the nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Stochastic modeling of catalytic processes in nanoporous materials: Beyond mean-field approach

Transport and reaction in zeolites and other porous materials, such as mesoporous silica particles, has been a focus of interest in recent years. This is in part due to the possibility of anomalous transport effects (e.g. single-file diffusion) and its impact in the reaction yield in catalytic processes. Computational simulations are often used to study these complex nonequilibrium systems. Computer simulations using Molecular Dynamics (MD) techniques are prohibitive, so instead coarse grained one-dimensional models with the aid of Kinetic Monte Carlo (KMC) simulations are used. Both techniques can be computationally expensive, both time and resource wise. These coarse-grained systems can be exactly described by a set of coupled stochastic master equations, that describe the reaction-diffusion kinetics of the system. The equations can be written exactly, however, coupling between the equations and terms within the equations make it impossible to solve them exactly; approximations must be made. One of the most common methods to obtain approximate solutions is to use Mean Field (MF) theory. MF treatments yield reasonable results at high ratios of reaction rate k to hop rate h of the particles, but fail completely at low k=h due to the over-estimation of fluxes of particles within the pore. We develop a method to estimate fluxes and intrapore diffusivity in simple one- dimensional reaction-diffusion models at high and low k=h, where the pores are coupled to an equilibrated three-dimensional fluid. We thus successfully describe analytically these simple reaction-diffusion one-dimensional systems. Extensions to models considering behavior with long range steric interactions and wider pores require determination of multiple boundary conditions. We give a prescription to estimate the required parameters for these simulations. For one dimensional systems, if single-file diffusion is relaxed, additional parameters to describe particle exchange have to be introduced. We use Langevin Molecular Dynamics (MD) simulations to assess these parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Pi+ Cross Section on Argon for the LArIAT Experiment

LArIAT (Liquid Argon in a Testbeam) was a LArTPC experiment exposed to a charged-particle beam at the test-beam facility at Fermi National Accelerator Laboratory. This analysis measures the $\pi^+$-Ar cross section over an interacting energy range of 50-1100 MeV, accounting for background species and reconstruction effects. This is the first such measurement of this process. The result can be useful in tuning simulations for future liquid argon experiments such as DUNE and SBN.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Sliding Dynamics for Bubble Phases on Periodic Modulated Substrates

We analyze a bubble-forming system composed of particles with competing long-range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a function of substrate strength and drive amplitude. When the substrate is weak, a pinned bubble phase appears that depins elastically into a sliding bubble lattice. For stronger substrates, we find anisotropic bubbles, disordered bubbles, and stripe phases. Plastic depinning occurs via the hopping of individual particles from one bubble to the next in a pinned bubble lattice, and as the drive increases, there is a transition to a state where all of the bubbles are moving but are continuously shedding and absorbing individual particles. This is followed at high drives by a moving bubble lattice in which the particles can no longer escape their individual bubbles. The transition between the plastic and elastic sliding phases can be detected via signatures in the velocity-force curves, differential conductivity, and noise. When the bubbles shrink due to an increase in the attractive interaction term, they fit better inside the pinning troughs and become more strongly pinned, leading to a reentrant pinning phase. For weaker attractive terms, the size of the bubbles becomes greater than the width of the pinning troughs and the depinning becomes elastic with a reduced depinning threshold.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Datasets for Custom-trained Machine-learning Interatomic Potentials: Nitric Acid Aqueous Solution

This dataset was generated using an iterative active learning strategy with the ArcaNN software package (https://github.com/arcann-chem/arcann_training) to train machine-learning interatomic potentials (MLIPs) for aqueous nitric acid. Each active-learning cycle consisted of three stages: (1) training, (2) exploration, and (3) labeling. The initial training set comprised approximately 800 randomly selected configurations from a previous study by Lewis et al. (https://doi.org/10.1021/jp205510q), which investigated nitric acid solutions at 2, 3, 4, and 5 mol/L. For all configurations, single-point calculations of atomic forces and total energies were performed at the quantum density functional theory BLYP-D2 and PBE-D3 levels of theory using the CP2K Quickstep module. Valence electrons were treated explicitly, while core electrons on all atoms were represented by norm-conserving Goedecker–Teter–Hutter (GTH) pseudopotentials. Long-range dispersion interactions were accounted for using Grimme dispersion corrections. Wave functions were expanded in a mixed Gaussian-and-plane-wave scheme using TZV2P-MOLOPT basis sets for all elements and an 800 Ry auxiliary plane-wave cutoff for the electron density. Self-consistent field convergence was accelerated using orbital transformation and Direct Inversion in the Iterative Subspace, with a convergence threshold of 10^{-6}. All single-point calculations were carried out in periodic orthorhombic cells whose dimensions match those of the molecular configurations sampled from earlier trajectories. The CELL_REF keyword in CP2K was used to define a fixed reference cell, ensuring consistency in the reference data used for MLIP training, particularly when cell fluctuations are present in NpT simulations. The resulting high-fidelity energies and forces constitute the ground-truth labels used to train the MLIPs contained in this dataset.

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗
DOE OSTI2015

Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins

Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. As a result, ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Theoretical Determination of Size Effects in Zeolite-Catalyzed Alcohol Dehydration

In the upgrading of biomass pyrolysis vapors to hydrocarbons, dehydration accomplishes a primary objective of removing oxygen, and acidic zeolites represent promising catalysts for the dehydration reaction. Here, we utilized density functional theory calculations to estimate adsorption energetics and intrinsic kinetics of alcohol dehydration over H-ZSM-5, H-BEA, and H-AEL zeolites. The ONIOM (our Own N-layered Integrated molecular Orbital and molecular Mechanics) calculations of adsorption energies were observed to be inconsistent when benchmarked against QM (Quantum Mechanical)/Hartree–Fock and periodic boundary condition calculations. However, reaction coordinate calculations of adsorbed species and transition states were consistent across all levels considered. Comparison of ethanol, isopropanol (IPA), and tert-amyl alcohol (TAA) over these three zeolites allowed for a detailed examination of how confinement impacts on reaction mechanisms and kinetics. The TAA, seen to proceed via a carbocationic mechanism, was found to have the lowest activation barrier, followed by IPA and then ethanol, both of which dehydrate via a concerted mechanism. Barriers in H-BEA were consistently found to be lower than in H-ZSM-5 and H-AEL, attributed to late transition states and either elevated strain or inaccurately estimating long-range electrostatic interactions in H-AEL, respectively. Molecular dynamics simulations revealed that the diffusivity of these three alcohols in H-ZSM-5 were significantly overestimated by Knudsen diffusion, which will complicate experimental efforts to develop a kinetic model for catalytic fast pyrolysis.

09 BIOMASS FUELS↗
DOE OSTI2017

A nearly naked supermassive black hole

During a systematic search for supermassive black holes (SMBHs) not in galactic nuclei, we identified the compact, symmetric radio source B3 1715+425 with an emission-line galaxy offset ≈8.5 kpc from the nucleus of the brightest cluster galaxy (BCG) in the redshift z = 0.1754 cluster ZwCl 8193. B3 1715+425 is too bright (brightness temperature T{sub b}∼3×10{sup 10} K at observing frequency ν=7.6 GHz) and too luminous (1.4 GHz luminosity L{sub 1.4GHz}∼10{sup 25} W Hz{sup −1}) to be powered by anything but an SMBH, but its host galaxy is much smaller (∼0.9 kpc×0.6 kpc full width between half-maximum points) and optically fainter (R-band absolute magnitude M{sub r}≈−18.2) than any other radio galaxy. Its high radial velocity v{sub r}≈1860 km s{sup −1} relative to the BCG, continuous ionized wake extending back to the BCG nucleus, and surrounding debris indicate that the radio galaxy was tidally shredded passing through the BCG core, leaving a nearly naked SMBH fleeing from the BCG with space velocity v≳2000 km s{sup −1}. The radio galaxy has mass M≲6×10{sup 9} M{sub ⊙} and infrared luminosity L{sub IR}∼3×10{sup 11} L{sub ⊙} close to its dust Eddington limit, so it is vulnerable to further mass loss from radiative feedback.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1966

Numerical Studies of the Non-linear Vlasov Equation

The subject of this dissertation is the numerical integration of the initial-value problem for the non-linear Vlasov equation. The Vlasov equation is used to describe the dynamics of a "collisionless", one-dimensional, classical electron gas confined between two perfectly reflecting boundaries. Only the long-range Coulomb interactions of the electrons are considered; effects associated with the discrete structure are neglected. The numerical results obtained for non-linear Landau damping compare well with similar results obtained by Knorr. A general statement of the results on stable initial conditions is: As the degree of non-linearity of the initial conditions is increased, the deviation from linear Landau damping appears sooner and is more severe. In some cases damping was observed to cease. Curves showing the time dependence of the damping decrement are derived and compared with predictions of non-linear theories. New results obtained in this study include the observation that for strongly non-linear cases, the damping of the electric field causes an initially Maxwellian fo (v, O) to develop a peak in the neighborhood of the phase velocity; strong growth of the second harmonic is seen after fo (v, t) develops such a peak. Also new in this study is the interpretation of the development of a certain class of strongly unstable initial conditions as approaching an inhomogeneous equilibrium.

NUMERICAL INTEGRATION↗
NASA NTRS1975

Interactive handling of TV and range data for remotely controlled systems

The sensory subsystem of the JPL robotics project is described. The first sensory instrument is a pair of TV cameras, which provides a stereo view of the area of interest. The second is a laser range finder, which can be aimed in a requested direction and measure distance to a surface point that reflects the beam back. Both instruments are controlled by and are interfaced to computer. The calibration process and basic applications to obtain measurements of the external environment are described.

Yakimovsky, Y.↗