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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 1,675 records · Page 93
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

GenASiS Basics: Object-oriented utilitarian functionality for large-scale physics simulations

Aside from numerical algorithms and problem setup, large-scale physics simulations on distributed-memory supercomputers require more basic utilitarian functionality, such as physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. Here we describe and make available Fortran 2003 classes furnishing extensible object-oriented implementations of this sort of rudimentary functionality, along with individual `unit test' programs and larger example problems demonstrating their use. Lastly, these classes compose the Basics division of our developing astrophysics simulation code GenASiS (General Astrophysical Simulation System), but their fundamental nature makes them useful for physics simulations in many fields.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Revising the Role of Cortical Cytoskeleton during Secretion: Actin and Myosin XI Function in Vesicle Tethering

In plants, secretion of cell wall components and membrane proteins plays a fundamental role in growth and development as well as survival in diverse environments. Exocytosis, as the last step of the secretory trafficking pathway, is a highly ordered and precisely controlled process involving tethering, docking, and fusion of vesicles at the plasma membrane (PM) for cargo delivery. Although the exocytic process and machinery are well characterized in yeast and animal models, the molecular players and specific molecular events that underpin late stages of exocytosis in plant cells remain largely unknown. Here, by using the delivery of functional, fluorescent-tagged cellulose synthase (CESA) complexes (CSCs) to the PM as a model system for secretion, as well as single-particle tracking in living cells, we describe a quantitative approach for measuring the frequency of vesicle tethering events. Genetic and pharmacological inhibition of cytoskeletal function, reveal that the initial vesicle tethering step of exocytosis is dependent on actin and myosin XI. In contrast, treatments with the microtubule inhibitor, oryzalin, did not significantly affect vesicle tethering or fusion during CSC exocytosis but caused a minor increase in transient or aborted tethering events. With data from this new quantitative approach and improved spatiotemporal resolution of single particle events during secretion, we generate a revised model for the role of the cortical cytoskeleton in CSC trafficking.

Zhang, Weiwei↗
DOE OSTI2016

UQ Toolkit v. 3.0

The Uncertainty Quantification (UQ) Toolkit is a software library for the characterization and propagation of uncertainties in computational models. This library provides Bayesian inference tools to infer uncertain model parameters, Bayesian compressive sensing methods for discovering sparse representations of high-dimensional input-output response surfaces, methods for constructing Karhunen-Loève representations of stochastic processes, and global sensitivity analysis tools used to compute Sobol indices in order to characterize the importance of uncertain inputs or the interactions between them. The basis for many of these methods relies on representing random variables with Polynomial Chaos expansions (PCEs). This library implements several spectral basis function types (e.g. Hermite basis functions in terms of Gaussian random variables or Legendre basis functions in terms of uniform random variables) that can be used to represent random variables with PCEs. For the propagation of uncertainty, tools are provided to propagate PCEs that describe the input uncertainty through the computational model using either intrusive methods (Galerkin projection of equations onto basis functions) or non-intrusive methods (perform deterministic operation at sampled values of the random values and project the obtained results onto basis functions).

Sargsyan, Khachik↗
DOE OSTI2018

Stability of Solutions of Initial Boundary-Balue Problems of Aerohydroelasticity

In designing structures and devices interacting with the flow of gas or liquid, it is necessary to solve the problems associated with the investigation of the stability required for their functioning and operational reliability. The definition of stability of an elastic body taken in the article corresponds to Lyapunov’s concept of stability of a dynamical system. On the base of the proposed nonlinear mathematical model the dynamic stability of the elastic aileron of the wing taking into account the incident subsonic flow of gas or liquid (in an ideal model of an incompressible environment) is investigated. Also a nonlinear mathematical model of the device relating to the vibration technique, which is intended for intensification of technological processes, for example, the process of mixing, is considered. The action of these devices is based on the oscillations of elastic elements during the gas or liquid flow. The dynamic stability of the elastic element located on one wall of the flow channel with the subsonic flow of gas or liquid (in an ideal model of a compressible environment) is investigated. Both models are described by a coupled nonlinear system of differential equations for the unknown functions — the potential of the gas velocity and deformation of the elastic element. On the basis of the construction of functionals, we obtain the sufficient conditions of the stability, the imposed restrictions on the free-stream velocity of the gas, the flexural stiffness of the elastic element, and other parameters of the mechanical system. The examples of construction of the stability regions for particular parameters of the mechanical system are presented.

42 ENGINEERING↗
DOE OSTI2020

Uncovering interpretable relationships in high-dimensional scientific data through function preserving projections

Abstract In many fields of science and engineering, we frequently encounter experiments or simulations datasets that describe the behavior of complex systems and uncovering human interpretable patterns between their inputs and outputs via exploratory data analysis is essential for building intuition and facilitating discovery. Often, we resort to 2D embeddings for examining these high-dimensional relationships (e.g. dimensionality reduction). However, most existing embedding methods treat the dimensions as coordinates for samples in a high-dimensional space, which fail to capture the potential functional relationships, and the few methods that do take function into consideration either only focus on linear patterns or produce non-linear embeddings that are hard to interpret. To address these challenges, we proposed function preserving projections (FPP), which construct 2D linear embeddings optimized to reveal interpretable yet potentially non-linear patterns between the domain and the range of a high-dimensional function. The intuition here is that humans are good at understanding potentially non-linear patterns in 2D but unable to interpret non-linear mapping from high-dimensional space to 2D. Therefore, we should restrict the projection to linear but not the pattern we are seeking. Using FPP on real-world datasets, one can obtain fundamentally new insights about high-dimensional relationships in extremely large datasets that could not be processed with existing dimension reduction methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Hole–hole Tamm–Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation

The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole–hole Tamm–Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole–hole counterpart to the more established particle–particle TDA (pp-TDA) method, both of which are derived from the particle–particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. Furthermore, the treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. Additionally, we show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states—particularly those with both low-lying ππ* and nπ* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.

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

Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag{sub 2}/graphene

A combined density functional (DFT) and incremental post-Hartree-Fock (post-HF) approach, proven earlier to calculate He-surface potential energy surfaces [de Lara-Castells et al., J. Chem. Phys. 141, 151102 (2014)], is applied to describe the van der Waals dominated Ag{sub 2}/graphene interaction. It extends the dispersionless density functional theory developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] by including periodic boundary conditions while the dispersion is parametrized via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. Starting with the elementary cluster unit of the target surface (benzene), continuing through the realistic cluster model (coronene), and ending with the periodic model of the extended system, modern ab initio methodologies for intermolecular interactions as well as state-of-the-art van der Waals-corrected density functional-based approaches are put together both to assess the accuracy of the composite scheme and to better characterize the Ag{sub 2}/graphene interaction. The present work illustrates how the combination of DFT and post-HF perspectives may be efficient to design simple and reliable ab initio-based schemes in extended systems for surface science applications.

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

Projector-Free Capped-Fragment Scheme within Density Functional Embedding Theory for Covalent and Ionic Compounds

Quantum-mechanics-(QM)-based simulations now routinely aid in understanding and even discovering new chemistries involving molecules and materials exhibiting desired functionalities. Ab initio correlated wavefunction (CW) theories systematically improve QM methods, with many exhibiting high accuracy. However, execution of CW methods requires expensive computations that typically scale poorly with system size. Divide-and-conquer approaches partition large systems into smaller fragments; a lower level of theory treats fragment interactions while a preferred higher level of theory describes the important fragment. These methods offer ways to incorporate CWs into chemical simulations of large systems, e.g., biomolecules, surfaces, large inorganic clusters, bulk crystals, etc. Here we propose a partitioning protocol that utilizes capping atoms to saturate severed covalent bonds at fragment interfaces and density functional embedding theory (DFET) to describe fragment interactions. The capping groups in each fragment provide an ad-hoc potential that approximates the effects of the environment. An embedding potential optimized via DFET then serves as an augmentation of the capping group to simulate the effects of the environment. We concurrently use an auxiliary fragment (a separate system comprised of only the combined capping groups) to account for, and thereby correct, the electron density contributions of all the capping groups added to all of the fragments. This method depends only on the capped-subsystem and auxiliary-fragment electron densities, forgoing, as with the original DFET developed for metallic systems, orbital-based projector approaches that determine a nonlocal action of the embedding potential onto the fragment electrons. By using an auxiliary fragment, the method maintains a purely electron-density-dependent embedding potential, substantially lessening the cost and leading to simpler implementation. In this work, we demonstrate the utility of our capped-DFET and ensuing capped embedded CW method in two contrasting systems, namely, an organic molecule and an ionic metal oxide cluster.

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

Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)

Zeolites, an important class of 3-dimensional nanoporous materials, have been widely explored for a variety of applications including gas storage, separations, and catalysis. As the properties of these aluminosilicate materials depend on a number of factors (e.g., framework topology, Si/Al ratio, extra-framework cations etc.), detailed experiments (e.g., catalytic properties, adsorption capacities etc.) are often limited to only a handful of materials. Computational methods have played an important role in (1) providing molecular level insights to rationalize experimental observations, and (2) screening large libraries of zeolites to identify promising candidates for experimental synthesis and validation. Different levels of theory and computational chemistry codes are necessary to describe the range of relevant phenomena such as adsorption (e.g., grand canonical Monte Carlo), diffusion (e.g., molecular dynamics), and chemical reactions (e.g., density functional theory). Manipulation of atomic structures, handling of input files, and developing robust workflows becomes quite cumbersome. To mitigate these challenges, we describe the development of the Multiscale Atomic Zeolite Simulation Environment (MAZE) – a Python package that simplifies zeolite-specific calculation workflows by providing a user-friendly interface for systematically manipulating zeolite structures

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Diffusion of Sn donors in β-Ga 2 O 3

Diffusion of the n-type dopant Sn in β-Ga 2 O 3 is studied using secondary-ion mass spectrometry combined with hybrid functional calculations. The diffusion of Sn from a Sn-doped bulk substrate with surface orientation (001) into an epitaxial layer is observed after heat treatments in the temperature range of 1050–1250 °C. Calculated formation energies of Sn-related and intrinsic defects show that the migration of Sn is mediated by Ga vacancies ( V Ga ) through the formation and dissociation of intermittent mobile V Ga Sn Ga complexes. The evolution of the Sn concentration vs depth profiles after heat treatments can be well described by a reaction–diffusion model. Using model parameters guided by the hybrid functional calculations, we extract a V Ga Sn Ga complex migration barrier of 3.0 ± 0.4 eV with a diffusion coefficient of 2 × 10 –1 cm 2 /s. The extracted migration barrier is consistent with our theoretical predictions using the nudged elastic band method, which shows migration barriers of 3.42, 3.15, and 3.37 eV for the [100], [010], and [001] directions, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Currents and Green's functions of impurities out of equilibrium: Results from inchworm quantum Monte Carlo

Here, we generalize the recently developed inchworm quantum Monte Carlo method to the full Keldysh contour with forward, backward, and equilibrium branches to describe the dynamics of strongly correlated impurity problems with time-dependent parameters. We introduce a method to compute Green's functions, spectral functions, and currents for inchworm Monte Carlo and show how systematic error assessments in real time can be obtained. We then illustrate the capabilities of the algorithm with a study of the behavior of quantum impurities after an instantaneous voltage quench from a thermal equilibrium state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Taming the fixed-node error in diffusion Monte Carlo via range separation

By combining density-functional theory (DFT) and wave function theory via the range separation (RS) of the interelectronic Coulomb operator, we obtain accurate fixed-node diffusion Monte Carlo (FN-DMC) energies with compact multi-determinant trial wave functions. In particular, we combine here short-range exchange-correlation functionals with a flavor of selected configuration interaction known as configuration interaction using a perturbative selection made iteratively (CIPSI), a scheme that we label RS-DFT-CIPSI. One of the take-home messages of the present study is that RS-DFT-CIPSI trial wave functions yield lower fixed-node energies with more compact multi-determinant expansions than CIPSI, especially for small basis sets. Indeed, as the CIPSI component of RS-DFT-CIPSI is relieved from describing the short-range part of the correlation hole around the electron-electron coalescence points, the number of determinants in the trial wave function required to reach a given accuracy is significantly reduced as compared to a conventional CIPSI calculation. Importantly, by performing various numerical experiments, we evidence that the RS-DFT scheme essentially plays the role of a simple Jastrow factor by mimicking short-range correlation effects, hence avoiding the burden of performing a stochastic optimization. Considering the 55 atomization energies of the Gaussian-1 benchmark set of molecules, we show that using a fixed value of mu = 0.5 bohr(-1) provides effective error cancellations as well as compact trial wave functions, making the present method a good candidate for the accurate description of large chemical systems.

Scemama, Anthony↗
DOE OSTI2015

Quantifying charge resonance and multiexciton character in coupled chromophores by charge and spin cumulant analysis

We extend excited-state structural analysis to quantify the charge-resonance and multi-exciton character in wave functions of weakly interacting chromophores such as molecular dimers. The approach employs charge and spin cumulants which describe inter-fragment electronic correlations in molecular complexes. We introduce indexes corresponding to the weights of local, charge resonance, and biexciton (with different spin structure) configurations that can be computed for general wave functions thus allowing one to quantify the character of doubly excited states. The utility of the approach is illustrated by applications to several small dimers, e.g., He-H{sub 2}, (H{sub 2}){sub 2}, and (C{sub 2}H{sub 4}){sub 2}, using full and restricted configuration interaction schemes. In addition, we present calculations for several systems relevant to singlet fission, such as tetracene, 1,6-diphenyl-1,3,5-hexatriene, and 1,3-diphenylisobenzofuran dimers.

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

Overhaul and installation of the ICARUS-T600 liquid argon TPC electronics for the FNAL Short Baseline Neutrino program

The ICARUS T600 liquid argon (LAr) time projection chamber (TPC) underwent a major overhaul at CERN in 2016–2017 to prepare for the operation at FNAL in the Short Baseline Neutrino (SBN) program. This included a major upgrade of the photo-multiplier system and of the TPC wire read-out electronics. The full TPC wire read-out electronics together with the new wire biasing and interconnection scheme are described. The design of a new signal feed-through flange is also a fundamental piece of this overhaul whose major feature is the integration of all electronics components onto the signal flange. Initial functionality tests of the full TPC electronics chain installed in the T600 detector at FNAL are also described.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Modeling Pb(II) Adsorption on Mineral Surfaces: Bridging Density Functional Theory and Experiment with Thermodynamic Insights

Despite decades of work on aqueous lead (Pb) adsorption on a-Fe2O3 (hematite) and a-Al2O3 (alumina), gaps between measurements and modeling obscure molecular-level understanding. Achieving well-matched geometries between theory and experimental for mineral-water interfaces is a hurdle, as surface functional group type and distribution must be accounted for in determining mechanisms. Additionally, computational methods that can describe the substrate are often not appropriate to capture aqueous effects. Progress requires focusing on well-studied and relevant systems, such as key facets (001),(012), and (110) of hematite and alumina, and ubiquitous contaminants such as aqueous Pb. In the past, bulk-parametrized bond-valence principles were used to rationalize Pb(II) adsorption trends. These approaches can break down at surfaces, where flexible bonding environments and adsorption-induced surface relaxations play a critical role. Here, we adapt and apply a density functional theory (DFT) and thermodynamics framework, integrating DFT-calculated energies with experimental data and electrochemical principles, to predict Pb(II) adsorption. Our model results capture trends across the full set of surfaces and predict that inner-sphere Pb(II) sorption on (001) alumina varies from unfavorable to weakly favorable across a range of pH conditions. This aligns with experiment insights that Pb(II) interacts at that surface through outer-sphere interactions. Extending to Fe(II) adsorption, we demonstrate a coverage-dependent site preference, potentially explaining disorder in overlayers grown by the oxidative adsorption of Fe(II) on hematite (001).

lead contamination↗
DOE OSTI2016

A mechanistic model for depth-dependent hardness of ion irradiated metals

A mechanistic model was developed for modeling the depth-dependent hardness in ion irradiated metallic materials. The model is capable of capturing the indentation size effect, ion irradiation induced damage gradient effect, and effect of unirradiated region acting as a soft substrate. A procedure was developed and described in detail to parametrize the model based on experimentally obtained hardness vs. indentation depth curves. Very good agreement was observed between our model predictions and experimental data of several different stainless steels subjected to various ion irradiation conditions. Additionally, two hardening mechanisms are revealed in the new model. One is the well-known indentation size effect arising from the creation of geometrically necessary dislocations as the indenter pierces into the materials. The other is the irradiation hardening due to the presence of irradiation-induced defects. As a function of indentation depth h, the hardening due to indentation size effect is described by $\bar{h}^*/h$, while the hardening due to irradiation first follows a power law form $ph^n$, then changes to Z/h - Q/h 3 , where $\bar{h}^*$, P, n, Z and Q > 0 are constants. This transition occurs at the indentation depth when the plastic zone reaches the end of the irradiated layer.

36 MATERIALS SCIENCE↗