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All sources NASA NTRS DOE OSTI

DOE OSTI2014

The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1981

Theory of inhomogeneous fluids

A theory of nonuniform liquids is presented which is based on the Yvon-Born-Green equation for the one-particle density and the Ornstein-Zernike equation of an inhomogeneous system. The necessary closure is effected by exploiting the solution of a modified hypernetted-chain equation and making a local approximation on the (highly universal) bridge function. The theory is successfully applied to model problems that have also been studied by direct-simulation methods. A brief generalization to quantum liquids is also given.

Nieminen, R. M.↗

NASA NTRS1998

Minimum High Fire Temperatures Detected in AVIRIS Spectral Measurements from Brazil in 1995

In August and September of 1995 the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) was deployed to Brazil as part of the NASA Smoke Cloud Aerosol and Radiation experiment in Brazil (SCAR-B). AVIRIS measures spectra from 400 to 2500 nm at 10-nm intervals. These spectra are acquired as images with dimensions of 11 by up to 800 km with 20-m spatial resolution. Spectral images measured by AVIRIS are spectrally, radiometrically, and spatially calibrated. During the SCAR-B deployment, AVIRIS measured more than 300 million spectra of regions of Brazil. A portion of these spectra were acquired over areas of actively burning fires. Actively burning fires emit radiance in the AVIRIS spectral range as a function of temperature. This emitted radiance is expressed from the 2500-nm end of the AVIRIS spectrum to shorter wavelengths as a function of intensity and modeled by the Planck function. The objective of this research and analysis was to use spectroscopic methods to determine the minimum high temperature of the most intense fires measured in the SCAR-B AVIRIS data set. Spectra measured by AVIRIS with hot sources have been previously examined for volcanic lava.

Green, Robert O.↗

DOE OSTI2016

Non-Markovian dynamics of a superconducting qubit in an open multimode resonator

In this work, we study the dynamics of a transmon qubit that is capacitively coupled to an open multimode superconducting resonator. Our effective equations are derived by eliminating resonator degrees of freedom while encoding their effect in the Green's function of the electromagnetic background. We account for the dissipation of the resonator exactly by employing a spectral representation for the Green's function in terms of a set of non-Hermitian modes and show that it is possible to derive effective Heisenberg-Langevin equations without resorting to the rotating-wave, two-level, Born, or Markov approximations. A well-behaved time-domain perturbation theory is derived to systematically account for the nonlinearity of the transmon. We apply this method to the problem of spontaneous emission, capturing accurately the non-Markovian features of the qubit dynamics, valid for any qubit-resonator coupling strength.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Image Analysis for Rapid Assessment and Quality-Based Sorting of Corn Stover

Imaging in the visible spectrum is a low-cost tool that can be readily deployed for in-field or over-belt monitoring of biomass quality for bio-refining operations. Rapid image analysis coupled with innovative preprocessing may reduce the impacts of feedstock variability through identification of contaminants or other material attributes to guide selective sorting and quality management. Image analysis was employed to evaluate the quality of corn stover in red-green-blue (RGB) chromatic space. This study used controlled, bench-scale imaging as a proof-of-concept for rapid quality assessment of corn stover based on variations in material attributes, including chemical and physical attributes, that relate to biological degradation and soil contamination. Additionally, logistic regression-based classification algorithms were used to develop a method for biomass screening as a function of biological degradation or soil contamination. This study demonstrated the use of image analysis to extract features from RGB color space to investigate variations in critical material attributes from chemical composition of corn stover. Fourier transform infrared (FT-IR) suggested a correlation between red band intensity and biological degradation, while detailed surface texture analysis was found to distinguish among variations in ash. These insights offer promise for development of a rapid screening tool that could be deployed by farmers for in-field assessment of biomass quality or biorefinery operators for in-line sorting and process optimization.

09 BIOMASS FUELS↗

NASA NTRS2015

Pioneering a Biobased UAS

With the exponential growth of interest in unmanned aerial vehicles (UAVs) and their vast array of applications in both space exploration and terrestrial uses such as the delivery of medicine and monitoring the environment, the 2014 Stanford-Brown-Spelman iGEM team is pioneering the development of a fully biological UAV for scientific and humanitarian missions. The prospect of a biologically-produced UAV presents numerous advantages over the current manufacturing paradigm. First, a foundational architecture built by cells allows for construction or repair in locations where it would be difficult to bring traditional tools of production. Second, a major limitation of current research with UAVs is the size and high power consumption of analytical instruments, which require bulky electrical components and large fuselages to support their weight. By moving these functions into cells with biosensing capabilities - for example, a series of cells engineered to report GFP, green fluorescent protein, when conditions exceed a certain threshold concentration of a compound of interest, enabling their detection post-flight - these problems of scale can be avoided. To this end, we are working to engineer cells to synthesize cellulose acetate as a novel bioplastic, characterize biological methods of waterproofing the material, and program this material's systemic biodegradation. In addition, we aim to use an "amberless" system to prevent horizontal gene transfer from live cells on the material to microorganisms in the flight environment. So far, we have: successfully transformed Gluconacetobacter hansenii, a cellulose-producing bacterium, with a series of promoters to test transformation efficiency before adding the acetylation genes; isolated protein bands present in the wasp nest material; transformed the cellulose-degrading genes into Escherichia coli; and we have confirmed that the amberless construct prevents protein expression in wild-type cells. In addition, as part of our human outreach project, we have been in touch with leaders in the fields of UAVs, synthetic biology, and earth sciences, and it is clear that biodegradable UAVs could have a significant impact on the industry.

Escherichia↗

NASA NTRS2014

Towards a Biosynthetic UAV

We are currently working on a series of projects towards the construction of a fully biological unmanned aerial vehicle (UAV) for use in scientific and humanitarian missions. The prospect of a biologically-produced UAV presents numerous advantages over the current manufacturing paradigm. First, a foundational architecture built by cells allows for construction or repair in locations where it would be difficult to bring traditional tools of production. Second, a major limitation of current research with UAVs is the size and high power consumption of analytical instruments, which require bulky electrical components and large fuselages to support their weight. By moving these functions into cells with biosensing capabilities - for example, a series of cells engineered to report GFP, green fluorescent protein, when conditions exceed a certain threshold concentration of a compound of interest, enabling their detection post-flight - these problems of scale can be avoided. To this end, we are working to engineer cells to synthesize cellulose acetate as a novel bioplastic, characterize biological methods of waterproofing the material, and program this material's systemic biodegradation. In addition, we aim to use an "amberless" system to prevent horizontal gene transfer from live cells on the material to microorganisms in the flight environment.

Biological↗

NASA NTRS2015

Pioneering a Biobased UAS

With the exponential growth of interest in unmanned aerial vehicles (UAVs) and their vast array of applications in both space exploration and terrestrial uses such as the delivery of medicine and monitoring the environment, the 2014 Stanford-Brown-Spelman iGEM team is pioneering the development of a fully biological UAV for scientific and humanitarian missions. The prospect of a biologically-produced UAV presents numerous advantages over the current manufacturing paradigm. First, a foundational architecture built by cells allows for construction or repair in locations where it would be difficult to bring traditional tools of production. Second, a major limitation of current research with UAVs is the size and high power consumption of analytical instruments, which require bulky electrical components and large fuselages to support their weight. By moving these functions into cells with biosensing capabilities – for example, a series of cells engineered to report GFP, green fluorescent protein, when conditions exceed a certain threshold concentration of a compound of interest, enabling their detection post-flight – these problems of scale can be avoided. To this end, we are working to engineer cells to synthesize cellulose acetate as a novel bioplastic, characterize biological methods of waterproofing the material, and program this material’s systemic biodegradation. In addition, we aim to use an “amberless” system to prevent horizontal gene transfer from live cells on the material to microorganisms in the flight environment. So far, we have: successfully transformed Gluconacetobacter hansenii, a cellulose-producing bacterium, with a series of promoters to test transformation efficiency before adding the acetylation genes; isolated protein bands present in the wasp nest material; transformed the cellulose-degrading genes into Escherichia coli; and we have confirmed that the amberless construct prevents protein expression in wild-type cells. In addition, as part of our human outreach project, we have been in touch with leaders in the fields of UAVs, synthetic biology, and earth sciences, and it is clear that biodegradable UAVs could have a significant impact on the industry.

Escherichia↗

DOE OSTI2018

Wide ranging equation of state with Tartarus: A hybrid Green’s function/orbital based average atom code

Average atom models are widely used to make equation of state tables and for calculating other properties of materials over a wide range of conditions, from zero temperature isolated atom to fully ionized free electron gases. The numerical challenge of making these density functional theory based models work for any temperature, density or nuclear species is formidable. Here we present in detail a hybrid Green’s function/orbital based approach that has proved to be stable and accurate for wide ranging conditions. Algorithmic strategies are discussed. In particular the decomposition of the electron density into numerically advantageous parts is presented and a robust and rapid self consistent field method based on a quasi-Newton algorithm is given. Example application to the equation of state of lutetium (Z = 71) is explored in detail, including the effect of relativity, finite temperature exchange and correlation, and a comparison to a less approximate method. Furthermore, the hybrid scheme is found to be numerically stable and accurate for lutetium over at least 6 orders of magnitude in density and 5 orders of magnitude in temperature.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2013

Virtual and super - virtual refraction method: Application to synthetic data and 2012 of Karangsambung survey data

Seismic refraction survey is one of geophysical method useful for imaging earth interior, definitely for imaging near surface. One of the common problems in seismic refraction survey is weak amplitude due to attenuations at far offset. This phenomenon will make it difficult to pick first refraction arrival, hence make it challenging to produce the near surface image. Seismic interferometry is a new technique to manipulate seismic trace for obtaining Green's function from a pair of receiver. One of its uses is for improving first refraction arrival quality at far offset. This research shows that we could estimate physical properties such as seismic velocity and thickness from virtual refraction processing. Also, virtual refraction could enhance the far offset signal amplitude since there is stacking procedure involved in it. Our results show super - virtual refraction processing produces seismic image which has higher signal-to-noise ratio than its raw seismic image. In the end, the numbers of reliable first arrival picks are also increased.

58 GEOSCIENCES↗

NASA NTRS1986

Theoretical models of single-element LTSA antenna elements

The spectral domain computations for slotline guide wavelength and characteristic impedance provide the basic parameters that are need to calculate the radiation pattern of an Linearly Tapered Slot Antenna (LTSA) by using the half-plane Green's function and a stepped approximation to the LTSA structure. However, the spectral domain computations are somewhat time consuming and not suitable for computer aided design application. Therefore, the results of several computation were fitted by formulas that are readily evaluated on a calculator or computer. Antenna measurements were continued, and an attempt was made to predict the truncation effect by three different methods.

Source record↗

DOE OSTI2022

Pore space partition of metal-organic frameworks for gas storage and separation

Pore space partition (PSP) concept is a synthetic design concept and can also serve as a structure analysis method useful for next-step synthetic planning and execution. PSP provides an integrated chemistry-topology-focused tool to design new materials platforms. While PSP is no less effective for making large-pore materials, the growing importance of small-molecule gas storage and separation for green-energy applications provides impetus for developing small-pore materials for which the PSP strategy is uniquely suited. Currently, the best embodiment of the PSP concept is the partitioned-acs (pacs) platform in which both fine or coarse adjustments to the building blocks have sparked a transformation of a prototype framework into a huge and continuously expanding family of chemically robust materials with controllable pore metrics and functionalities suitable for tailored applications. The pacs compositional diversity results from the platform’s intrinsic multi-module nature, geometric flexibility and tolerance towards individual module variations, and mutual structure-directing effects among various modules, all of which combine to enable the molecular-level uniform co-assemblies of chemical components rarely seen together elsewhere. Here, in this contribution, we present an overview of different pore space engineering methods and how different MOF materials have contributed to important advances in chemical stability, industrial gas storage and gas separation. In particular, we will focus on synthetic assembly of the pacs system, highlighting the differences of pacs materials from other MOF platforms and advantages of pacs materials in enhancing various MOF properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Kinetics and mechanisms of polycondensation reactions between aryl halides and bisphenol A

Aryl chlorides (ArCl) or aryl fluorides (ArF) were used in polycondensation reactions to form poly(arylene ether sulfone)s (PAES). Interestingly, the kinetics of the ArF reaction fit a third-order rate law, which is attributed to the activation of the carbon–fluorine bond by two potassium cations (at least one bound to phenolate), which form a three-body complex. Here, the ArCl monomer follows a second-order rate law, where a two-body complex forms at the initial state of the aromatic nucleophilic substitution (S N Ar) pathway. These metal cation-activated complexes act as intermediates during the attack by the nucleophile. This finding was reproduced with either the potassium or the sodium counterion (introduced via potassium carbonate or sodium carbonate). Through a combination of experimental analysis of reaction kinetics and computational calculations with density functional theory (DFT) methods, the present work extends the fundamental understanding of polycondensation mechanisms for two aryl halides and highlights the importance of the CX–metal interaction(s) in the S N Ar reaction, which is translational to other ion-activated substitution reactions.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Ab initio phonon point defect scattering and thermal transport in graphene

Here, we study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitude smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (~ω 0 ) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. In conclusion, this work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.

36 MATERIALS SCIENCE↗

DOE OSTI2018

The Effects of Stochastic Velocity Variations on Estimating Time Dependent Seismic Moment Tensors: Applications to the Blue Mountain Well Perforation Data

Resolving the time dependent terms in the seismic moment tensor provides important information that can be used to interpret the source process of an explosion, including the separation of isotropic explosion terms from shear forces and potentially isolated force couples. In this report, we detail our method of inverting three component seismic data for the seismic moment tensor. We review possible seismic source models from the simplest isotropic explosion type source to those incorporating the six independent moment tensor terms. The inversion we describe is formulated in the frequency domain, and results in estimates of time dependent moment tensor components. The inversion relies on an accurate estimate of the Green's functions of the Earth. However, given the complexity of the Earth, we explore the effects of inaccuracies in the presumed Earth model used to estimate the Green's functions needed for the inversion. Specifically, we explore the effects of stochastic variations in the Earth models on the inversion results. These tests are synthetic throughout, and show that adding stochastic density/velocity heterogeneity in the presumed Earth model results in reduced amplitude seismic moment tensor estimates, as well as degrading the data misfit. We suggest two mitigation strategies. First, produce a suite of Green's functions using different realizations of the stochastic field within the Earth Model. Secondly, perform the in- version in the power spectral domain, eliminating all phase information. Finally, we analyze actual seismic data collected in winter 2017/2018. The seismic data was collected at in active geothermal well site outside of Winnimucca, NV, and was produced during well stimulation operations. In general, the inversion results were poor, with a high degree of data misfit. We hypothesize that the poor results are a function of a poorly constrained Earth model as well as noisy, high-frequency data being used in the inversion.

58 GEOSCIENCES↗

NASA NTRS1984

SASS wind ambiguity removal by direct minimization. II - Use of smoothness and dynamical constraints

A variational analysis method (VAM) is used to remove the ambiguity of the Seasat-A Satellite Scatterometer (SASS) winds. The VAM yields the best fit to the data by minimizing an objective function S which is a measure of the lack of fit. The SASS data are described and the function S and the analysis procedure are defined. Analyses of a single ship report which are analogous to Green's functions are presented. The analysis procedure is tuned and its sensitivity is described using the QE II storm. The procedure is then applied to a case study of September 6, 1978, south of Japan.

Hoffman, R. N.↗

DOE OSTI2019

Absolutely Localized Projection-Based Embedding for Excited States

We present a quantum embedding method that allows for calculation of local excited states embedded in a Kohn–Sham density functional theory (DFT) environment. Projection-based quantum embedding methodologies provide a rigorous framework for performing DFT-in-DFT and wave function in DFT (WF-in-DFT) calculations. The use of absolute localization, where the density of each subsystem is expanded in only the basis functions associated with the atoms of that subsystem, provide improved computationally efficiency for WF-in-DFT calculations by reducing the number of orbitals in the WF calculation. In this work, we extend absolutely localized projection-based quantum embedding to study localized excited states using EOM-CCSD-in-DFT and TDDFT-in-DFT. The embedding results are highly accurate compared to the corresponding canonical EOM-CCSD and TDDFT results on the full system, with TDDFT-in-DFT frequently more accurate than canonical TDDFT. The absolute localization method is shown to eliminate the spurious low-lying excitation energies for charge-transfer states and prevent overdelocalization of excited states. Additionally, we attempt to recover the environment response caused by the electronic excitations in the high-level subsystem using different schemes and compare their accuracy. Finally, we apply this method to the calculation of the excited-state energy of green fluorescent protein and show that we systematically converge to the full system results. Here we demonstrate how this method can be useful in understanding excited states, specifically which chemical moieties polarize to the excitation. Furthermore, this work shows absolutely localized projection-based quantum embedding can treat local electronic excitations accurately and make computationally expensive WF methods applicable to systems beyond current computational limits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

ON GALACTIC DENSITY MODELING IN THE PRESENCE OF DUST EXTINCTION

Inferences about the spatial density or phase-space structure of stellar populations in the Milky Way require a precise determination of the effective survey volume. The volume observed by surveys such as Gaia or near-infrared spectroscopic surveys, which have good coverage of the Galactic midplane region, is highly complex because of the abundant small-scale structure in the three-dimensional interstellar dust extinction. We introduce a novel framework for analyzing the importance of small-scale structure in the extinction. This formalism demonstrates that the spatially complex effect of extinction on the selection function of a pencil-beam or contiguous sky survey is equivalent to a low-pass filtering of the extinction-affected selection function with the smooth density field. We find that the angular resolution of current 3D extinction maps is sufficient for analyzing Gaia sub-samples of millions of stars. However, the current distance resolution is inadequate and needs to be improved by an order of magnitude, especially in the inner Galaxy. We also present a practical and efficient method for properly taking the effect of extinction into account in analyses of Galactic structure through an effective selection function. We illustrate its use with the selection function of red-clump stars in APOGEE using and comparing a variety of current 3D extinction maps.

79 ASTRONOMY AND ASTROPHYSICS↗