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DOE OSTI2022

A Framework for Inverse Prediction Using Functional Response Data

Inverse prediction models have commonly been developed to handle scalar data from physical experiments. However, it is not uncommon for data to be collected in functional form. When data are collected in functional form, it must be aggregated to fit the form of traditional methods, which often results in a loss of information. For expensive experiments, this loss of information can be costly. In this study, we introduce the functional inverse prediction (FIP) framework, a general approach which uses the full information in functional response data to provide inverse predictions with probabilistic prediction uncertainties obtained with the bootstrap. The FIP framework is a general methodology that can be modified by practitioners to accommodate many different applications and types of data. We demonstrate the framework, highlighting points of flexibility, with a simulation example and applications to weather data and to nuclear forensics. Results show how functional models can improve the accuracy and precision of predictions.

42 ENGINEERING↗

DOE OSTI2022

Ab-Initio Investigation of Finite Size Effects in Rutile Titania Nanoparticles with Semilocal and Nonlocal Density Functionals

In this work, we employ hybrid and generalized gradient approximation (GGA) level density functional theory (DFT) calculations to investigate the convergence of surface properties and electronic gap of rutile titania nanoparticles with particle size. The surface energies and electronic gaps are calculated for cuboidal particles with minimum dimension ranging from 3.7 Angstrom (24 atoms) to 10.3 Angstrom (384 atoms) using a highly-parallel real-space DFT code to enable hybrid level DFT calculations of larger nanoparticles than are typically practical. We deconvolute the geometric and electronic finite size effects in surface energy, and evaluate the influence of defects on electronic gap and density of states (DOS). The electronic finite size effects in surface energy vanish when the minimum length scale of the nanoparticles becomes greater than 10 Angstrom. We show that this length scale is consistent with a computationally efficient numerical analysis of the characteristic length scale of electronic interactions. The surface energy of nanoparticles having minimum dimension beyond this characteristic length can be approximated using slab calculations that account for the geometric defects. In contrast, the finite size effects on the electronic gap and DOS is highly dependent on the shape and size of these particles. Furthermore, the DOS for cuboidal particles and more realistic particles constructed using the Wulff algorithm reveal that defect states within the electronic gap play a key role in determining the eigen value distribution of nanoparticles and the electronic gap does not converge to the bulk limit for the particle sizes investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2003

The evolution of transcriptional regulation in eukaryotes

Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.

Review, Academic↗

DOE OSTI2023

Self-consistent implementation of locally scaled self-interaction-correction method

Recently proposed local self-interaction correction (LSIC) method is a one-electron self-interaction-correction (SIC) method that uses an iso-orbital indicator to apply the SIC at each point in space by scaling the exchange–correlation and Coulomb energy densities. The LSIC method is exact for the one-electron densities, also recovers the uniform electron gas limit of the uncorrected density functional approximation, and reduces to the well-known Perdew–Zunger SIC (PZSIC) method as a special case. This article presents the self-consistent implementation of the LSIC method using the ratio of Weizsäcker and Kohn–Sham kinetic energy densities as an iso-orbital indicator. The atomic forces as well as the forces on the Fermi-Löwdin orbitals are also implemented for the LSIC energy functional. Results show that LSIC with the simplest local spin density functional predicts atomization energies of the AE6 dataset better than some of the most widely used generalized-gradient-approximation (GGA) functional and barrier heights of the BH6 database better than some of the most widely used hybrid functionals. The LSIC method [a mean absolute error (MAE) of 0.008 Å] predicts bond lengths of a small set of molecules better than the PZSIC-LSDA (MAE 0.042 Å) and LSDA (0.011 Å). Furthermore, this work shows that accurate results can be obtained from the simplest density functional by removing the self-interaction-errors using an appropriately designed SIC method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Diamond surface functionalization via visible light–driven C–H activation for nanoscale quantum sensing

Nitrogen-vacancy (NV) centers in diamond are a promising platform for nanoscale NMR sensing. Despite significant progress toward using NV centers to detect and localize nuclear spins down to the single spin level, NV-based spectroscopy of individual, intact, arbitrary target molecules remains elusive. Such sensing requires that target molecules are immobilized within nanometers of NV centers with long spin coherence. The inert nature of diamond typically requires harsh functionalization techniques such as thermal annealing or plasma processing, limiting the scope of functional groups that can be attached to the surface. Solution-phase chemical methods can be readily generalized to install diverse functional groups, but they have not been widely explored for single-crystal diamond surfaces. Moreover, realizing shallow NV centers with long spin coherence times requires highly ordered single-crystal surfaces, and solution-phase functionalization has not yet been shown with such demanding conditions. In this work, we report a versatile strategy to directly functionalize C–H bonds on single-crystal diamond surfaces under ambient conditions using visible light, forming C–F, C–Cl, C–S, and C–N bonds at the surface. This method is compatible with NV centers within 10 nm of the surface with spin coherence times comparable to the state of the art. As a proof-of-principle demonstration, we use shallow ensembles of NV centers to detect nuclear spins from surface-bound functional groups. Our approach to surface functionalization opens the door to deploying NV centers as a tool for chemical sensing and single-molecule spectroscopy.

Science & Technology - Other Topics↗

DOE OSTI2021

Unraveling the intrinsic atomic physics behind x-ray absorption line shifts in warm dense silicon plasmas

Here, we present a novel free-energy density functional theory (DFT)-based methodology for optical property calculations of warm dense matter to cover a wide range of thermodynamic conditions and photon energies including the entire x-ray range. It uses Mermin–Kohn–Sham density functional theory with exchange-correlation (XC) thermal effects taken into account via a fully temperature dependent generalized gradient approximation XC functional. The methodology incorporates a combination of the ab initio molecular dynamics (AIMD) snapshotted Kubo–Greenwood optic data with a single-atom in simulation cell calculations to close the photon energy gap between the L and K edges and extend the K-edge tail toward many-keV photon energies. This gap arises in the standard scheme due to a prohibitively large number of bands required for the Kubo–Greenwood calculations with AIMD snapshots. Kubo–Greenwood data on snapshots provide an accurate description of optic properties at low photon frequencies slightly beyond the L-edge and x-ray absorption near edges structure (XANES) spectra, while data from periodic calculations with single atoms cover the tail regions beyond the edges. To demonstrate its applicability to mid-Z materials where the standard DFT-based approach is not computationally feasible, we have applied it to opacity calculations of warm dense silicon plasmas. These first-principles calculations revealed a very interesting phenomon of red-to-blue shift in K–L (1s → 2p) and K-edge absorptions along both isotherm and isochore, which are absent in most continuum-lowering models of traditional plasma physics. This new physics phenomenon can be attributed to the underlying competition between the screening of deeply bound core electrons and the screening of outer-shell electrons caused by warm-dense-plasma conditions. We further demonstrate that the ratio of 1s → 2p to the K-edge x-ray absorptions can be used to characterize warm-dense-plasma conditions. Eventually, based on our absorption calculations, we have established a first-principles opacity table (FPOT) for silicon in a wide range of material densities and temperatures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1980

Broadness, decay, and correlation functions of isotropic homogeneous turbulence

General theoretical relationships consistent with experiments are obtained for isotropic homogeneous incompressible-fluid turbulence governed by the Navier-Stokes flow equation. A key quantity that structures the turbulence is the 'broadness' B of the probability measure over velocity fields. Both the decay law and the longitudinal correlation function for small r appear as simple functions of this quasiconstant parameter B.

Rosen, G.↗

DOE OSTI2020

The Effects of Atmospheric Models on the Estimation of Infrasonic Source Functions at the Source Physics Experiment

We invert infrasound signals for an equivalent seismoacoustic source function using different atmospheric models to produce the necessary Green’s functions. The infrasound signals were produced by a series of underground chemical explosions as part of the Source Physics Experiment (SPE). In a previous study, we inverted the infrasound data using so-called predictive atmospheric models, which were based on historic, regional-scaled, publicly available weather observations interpolated onto a 3D grid. For the work presented here, we invert the same infrasound data, but using atmospheric models based on weather data collected in a time window that includes the approximate time of the explosion experiments, which we term postdictive models. We build two versions of the postdictive models for each SPE event: one that is based solely on the regional scaled observations, and one that is based on both regional scaled observations combined with on-site observations obtained by a weather sonde released at the time of the SPE. We then invert the observed data set three times, once for each atmospheric model type. We find that the estimated seismoacoustic source functions are relatively similar in waveform shape regardless of which atmospheric model that we used to construct the Green’s functions. However, we find that the amplitude of the estimated source functions is systematically dependent on the atmospheric model type: using the predictive atmospheric models to invert the data generally yields estimated source functions that are larger in amplitude than those estimated using the postdictive models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

A Functional Reference Architecture and Assessment Thereof for the National Ignition Facility Industrial Controls Systems

The Industrial Control System (ICS) at the National Ignition Facility (NIF) has an effective, well-established architecture based off a conventional cyclical software paradigm focused on maintainability and the identification of issues. This architecture exhibits scalability in ensuring expansions of the system conform to the existing architecture, modularity enough to allow relatively easy integrations of such expansions and works as a successful tool to introduce control system engineers new to the NIF ICS to the structure of the system at each layer. This architecture, like most software architectures, is object-oriented, lending itself to ease of understanding by control systems engineers and software engineers familiar with an object-oriented perspective. There are occasions, however, where engineers of other disciplines require insight into the functionality and structure of the ICS for the purposes of understanding fundamentally how their own system is or will be governed by the ICS, without the need for the details of operation of the ICS or the object-oriented view. For this reason, a functional architecture of the ICS could be a potent tool for communicating this insight. Even more powerful, a generalization of this proposed functional ICS architecture in the form of a National Ignition Facility and Photon Science (NIF & PS) Industrial Controls Reference Architecture could communicate this insight not just to systems governed by the ICS in the NIF proper, but across entirety of the NIF & PS Principal Associate Directorate (PAD), anywhere an instance of the ICS architecture is present, such as the approximately 40 “small labs” distributed across the directorate. Such a tool will provide an alternative means of understanding the implementation of these control systems, conducive to a larger variety of engineering and scientific disciplines.

42 ENGINEERING↗

NASA NTRS1990

Stability of an oscillated fluid with a uniform density gradient

Instabilities in a fluid with a constant density gradient that is subject to arbitrarily oriented oscillatory accelerations are considered. With the Boussinesq approximation and for the case of an unbounded fluid, transformation to Lagrangian coordinates allows the reduction of the problem to an ordinary differential equation for each three-dimensional wavenumber. The problem has three parameters: the nondimensional amplitude R of the base-state oscillation, the nondimensional level of background steady acceleration, which for some cases can be represented in terms of a local (in time) Richardson number Ri, and the Prandtl number Pr. Some general bounds on stability are derived. For Pr = 1 closed-form solutions are found for impulse (delta function) accelerations and a general asymptotic solution is constructed for large R and general imposed accelerations. The asymptotic solution takes advantage of the fact that at large R wave growth is concentrated at 'zero points'. These are times when the effective vertical wavenumber passes through zero. Kelvin-Helmholtz instabilities are found to dominate at low R, while Rayleigh-Taylor instabilities dominate at high R. At high R, the uniform shear of the Kelvin-Helmholtz case tends to distort and weaken instability waves. With unsteady flows, Ri = 1/4 is no longer an instability limit. Significant instabilities have been found for sinusoidal forcing for Ri up to 0.6.

Jacqmin, David↗

NASA NTRS1972

Response of discrete linear systems to forcing functions with inequality constraints.

An analysis is made of the maximum response of discrete, linear mechanical systems to arbitrary forcing functions which lie within specified bounds. Primary attention is focused on the complete determination of the forcing function which will engender maximum displacement to any particular mass element of a multi-degree-of-freedom system. In general, the desired forcing function is found to be a bang-bang type function, i.e., a function which switches from the maximum to the minimum bound and vice-versa at certain instants of time. Examples of two-degree-of-freedom systems, with and without damping, are presented in detail. Conclusions are drawn concerning the effect of damping on the switching times and the general procedure for finding these times is discussed.

Michalopoulos, C. D.↗

NASA NTRS2001

Complex Correlation Kohn-T Method of Calculating Total and Elastic Cross Sections: Electron-Hydrogen Elastic Scattering - Part 1

We report on the first part of a study of electron-hydrogen scattering, using a method which allows for the ab initio calculation of total and elastic cross sections at higher energies. In its general form the method uses complex 'radial' correlation functions, in a (Kohn) T-matrix formalism. The titled method, abbreviated Complex Correlation Kohn T (CCKT) method, is reviewed, in the context of electron-hydrogen scattering, including the derivation of the equation for the (complex) scattering function, and the extraction of the scattering information from the latter. The calculation reported here is restricted to S-waves in the elastic region, where the correlation functions can be taken, without loss of generality, to be real. Phase shifts are calculated using Hylleraas-type correlation functions with up to 95 terms. Results are rigorous lower bounds; they are in general agreement with those of Schwartz, but they are more accurate and outside his error bounds at a couple of energies,

Bhatia, A. K.↗

NASA NTRS1984

Computer simulation of surface and film processes

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Tiller, W. A.↗

NASA NTRS1986

Automated Design Synthesis

Automated Design Synthesis (ADS) program is general-purpose numerical optimization program containing wide variety of algorithms. Assumed user prepares analysis problem capable of computing objective function and constraints. Program able to accept as part of input design variable quantities. Optimization process carried out by ADS coupled with user's program. ADS used for constrained and unconstrained function minimization. Solution of general problem separated into three basic levels: Strategy, Optimizer, and One-Dimensional Search. Already significant applications in area of structural synthesis (minimum-weight design).

Vanderplaats, G. N.↗

DOE OSTI2022

A General Route to Flame Aerosol Synthesis and In Situ Functionalization of Mesoporous Silica

Mesoporous silica is a versatile material for energy, environmental, and medical applications. In this work, for the first time, we report a flame aerosol synthesis method for a class of mesoporous silica with hollow structure and specific surface area exceeding 1000 m 2 /g -1 . We show its superior performance in water purification, drug carrier, and thermal insulation. Moreover, we propose a general route to produce mesoporous nanoshell supported nanocatalysts by in situ decorating active nanoclusters, including noble metal (Pt/SiO 2 ), transition metal (Ni/SiO 2 ), metal oxide (CrO 3 /SiO 2 ), and alumina support (Co/Al 2 O 3 ). As a prototypical application, we perform dry reforming of methane using Ni/SiO 2 , achieving constant 97% CH 4 and CO 2 conversions for more than 200 hours, dramatically outperforming MCM-41 supported Ni catalyst. This work provides a scalable strategy to produce mesoporous nanoshells and proposes an in situ functionalization mechanism to flexible catalysts design for many reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Comparing GGA, GGA+ U , and meta-GGA functionals for redox-dependent binding at open metal sites in metal–organic frameworks

Metal–organic frameworks (MOFs) with open metal sites have been widely investigated for the selective adsorption of small molecules via redox mechanisms where charge transfer can take place between the binding site and the adsorbate of interest. Quantum-chemical screening methods based on density functional theory have emerged as a promising route to accelerate the discovery of MOFs with enhanced binding affinities toward various adsorbates. However, the success of this approach is linked to the accuracy of the underlying density functional approximations (DFAs). In this work, we compare commonly used generalized gradient approximation (GGA), GGA+U, and meta-GGA exchange-correlation functionals in modeling redox-dependent binding at open metal sites in MOFs using O 2 and N 2 as representative small molecules. We find that the self-interaction error inherent to the widely used Perdew, Burke, and Ernzerhof (PBE) GGA predicts metal sites that are artificially redox-active, as evidenced by their strong binding affinities, short metal–adsorbate bond distances, and large degree of charge transfer. The incorporation of metal-specific, empirical Hubbard U corrections based on the transition metal oxide literature systematically reduces the redox activity of the open metal sites, often improving agreement with experiment. Additionally, the binding behavior shifts from strong chemisorption to weaker physisorption as a function of U. The M06-L meta-GGA typically predicts binding energies between those of PBE-D3(BJ) and PBE-D3(BJ)+U when using empirically derived U values from the transition metal oxide literature. Despite the strong sensitivity of the binding affinities toward a given DFA, the GGA, GGA+U, and meta-GGA approaches often yield the same qualitative trends and structure–property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

A General Route to Flame Aerosol Synthesis and In Situ Functionalization of Mesoporous Silica

Abstract Mesoporous silica is a versatile material for energy, environmental, and medical applications. Here, for the first time, we report a flame aerosol synthesis method for a class of mesoporous silica with hollow structure and specific surface area exceeding 1000 m 2 g −1 . We show its superior performance in water purification, as a drug carrier, and in thermal insulation. Moreover, we propose a general route to produce mesoporous nanoshell‐supported nanocatalysts by in situ decoration with active nanoclusters, including noble metal (Pt/SiO 2 ), transition metal (Ni/SiO 2 ), metal oxide (CrO 3 /SiO 2 ), and alumina support (Co/Al 2 O 3 ). As a prototypical application, we perform dry reforming of methane using Ni/SiO 2 , achieving constant 97 % CH 4 and CO 2 conversions for more than 200 hours, dramatically outperforming an MCM‐41 supported Ni catalyst. This work provides a scalable strategy to produce mesoporous nanoshells and proposes an in situ functionalization mechanism to design and produce flexible catalysts for many reactions.

Liu, Shuo↗

NASA NTRS2005

Effects of 17-day spaceflight on knee extensor muscle function and size

It is generally held that space travelers experience muscle dysfunction and atrophy during exposure to microgravity. However, observations are scarce and reports somewhat inconsistent with regard to the time course, specificity and magnitude of such changes. Hence, we examined four male astronauts (group mean approximately 43 years, 86 kg and 183 cm) before and after a 17-day spaceflight (Space Transport System-78). Knee extensor muscle function was measured during maximal bilateral voluntary isometric and iso-inertial concentric, and eccentric actions. Cross-sectional area (CSA) of the knee extensor and flexor, and gluteal muscle groups was assessed by means of magnetic resonance imaging. The decrease in strength (P<0.05) across different muscle actions after spaceflight amounted to 10%. Eight ambulatory men, examined on two occasions 20 days apart, showed unchanged (P>0.05) muscle strength. CSA of the knee extensor and gluteal muscles, each decreased (P<0.05) by 8%. Knee flexor muscle CSA showed no significant (P>0.05) change. The magnitude of these changes concord with earlier results from ground-based studies of similar duration. The results of this study, however, do contrast with the findings of no decrease in maximal voluntary ankle plantar flexor force previously reported in the same crew.

NASA Discipline Musculoskeletal↗