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Results for “explicit correlation”

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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

The allosteric switching mechanism in bacteriophage MS2

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Foam Degradation Model during Thermal Hypothetical Accident Conditions

Current practice in Safety Analysis Report for Packaging (SARP) thermal analysis for hypothetical accident conditions (HAC) of packages is to not explicitly model the consequence to the foam impact limiting material, but instead to make conservative estimates of those consequences and begin calculations from that point. This approach is typically used for the foam regression distance, which is the thickness of the degraded foam layer after the 30-minute fire event. Estimates for regression distance can come directly from package burn test results or from correlations based on one-dimensional testing by the foam manufacturer. In either case, this is a subjective process, and although it can be used to produce a conservative result, it is a significant approximation in the analysis. This paper describes testing and refinement of a simplified foam regression model. Comparisons are made against available data from laboratory experiments. Model refinements were tested until satisfactory agreement was achieved. The final modeling approach was then compared with post-test inspection results from HAC burn test data. A new model with an effective thermal conductivity based on foam to char density variation was shown successful in representing laboratory-scale foam thermal degradation experiments and full-scale burn tests of a current package. This model offers a technically defensible and predictive approach for modeling thermal degradation of rigid polyurethane insulation in transport packages.

36 MATERIALS SCIENCE↗
NASA NTRS1998

Ab Initio Calculations of Water Line Strengths

We report on the determination of a high quality ab initiu potential energy surface (PES) and dipole moment function for water. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base with J less than 6 for H2O. The changes in the PES are small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Using this adjusted PES, we can match 30,092 of the 30,117 transitions in the HITRAN 96 data base for H2O with theoretical lines. The 10,25,50,75, and 90 percentiles of the difference between the calculated and tabulated line positions are -0.11, -0.04, -0.01, 0.02, and 0.07 l/cm. Non-adiabatic effects are not explicitly included. About 3% of the tabulated line positions appear to be incorrect. Similar agreement using this adjusted PES is obtained for the oxygen 17 and oxygen 18 isotopes. For HDO, the agreement is not as good, with root-mean-square error of 0.25 l/cm for lines with J less than 6. This error is reduced to 0.02 l/cm by including a small asymmetric correction to the PES, which is parameterized by simultaneously fitting to HDO md D2O data. Scaling this correction by mass factors yields good results for T2O and HTO. The intensities summed over vibrational bands are usually in good agreement between the calculations and the tabulated results, but individual lines strengths can differ greatly. A high temperature list consisting of 307,721,352 lines is generated for H2O using our PES and dipole moment function.

Schwenke, David W.↗
DOE OSTI2018

Simulating Electron Dynamics of Complex Molecules with Time-Dependent Complete Active Space Configuration Interaction

In this paper, time-dependent electronic structure methods are growing in popularity as tools for modeling ultrafast and/or nonlinear processes, for computing spectra, and as the electronic structure component of mean-field molecular dynamics simulations. Time-dependent configuration interaction (TD-CI) offers several advantages over the widely used real-time time-dependent density functional theory: namely, that it correctly models Rabi oscillations; it offers a spin-pure description of open-shell systems; and a hierarchy of TD-CI methods can be defined that systematically approach the exact solution of the time-dependent Schrodinger equation (TDSE). In this work, we present a novel TD-CI approach that extends TD-CI to large complete active-space configuration expansions. Such extension is enabled by use of a direct configuration interaction approach that eliminates the need to explicitly build, store, or diagonalize the Hamiltonian matrix. Graphics processing unit (GPU) acceleration enables fast solution of the TDSE even for large active spaces—up to 12 electrons in 12 orbitals (853776 determinants) in this work. A symplectic split operator propagator yields long-time norm conservation. We demonstrate the applicability of our approach by computing the response of a large molecule with a strongly correlated ground state, decacene (C 42 H 24 ), to various pulses (δ-function, transform limited, chirped). Our simulations predict that chirped pulses can be used to induce dipole-forbidden transitions. Simulations of decacene using the 6-31G(d) basis set and a 12 electrons/12 orbitals active space took 20.1 h to propagate for 100 fs with a 1 attosecond time step on a single NVIDIA K40 GPU. Convergence with respect to time step is found to depend on the property being computed and the chosen active space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Communication: Self-interaction correction with unitary invariance in density functional theory

Standard spin-density functionals for the exchange-correlation energy of a many-electron ground state make serious self-interaction errors which can be corrected by the Perdew-Zunger self-interaction correction (SIC). We propose a size-extensive construction of SIC orbitals which, unlike earlier constructions, makes SIC computationally efficient, and a true spin-density functional. The SIC orbitals are constructed from a unitary transformation that is explicitly dependent on the non-interacting one-particle density matrix. When this SIC is applied to the local spin-density approximation, improvements are found for the atomization energies of molecules.

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

Energy band alignment and electronic states of amorphous carbon surfaces in vacuo and in aqueous environment

In this paper, we obtain the energy band positions of amorphous carbon (a–C) surfaces in vacuum and in aqueous environment. The calculations are performed using a combination of (i) classical molecular dynamics (MD), (ii) Kohn-Sham density functional theory with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional, and (iii) the screened-exchange hybrid functional of Heyd, Scuseria, and Ernzerhof (HSE). PBE allows an accurate generation of a-C and the evaluation of the local electrostatic potential in the a-C/water system, HSE yields an improved description of energetic positions which is critical in this case, and classical MD enables a computationally affordable description of water. Our explicit calculation shows that, both in vacuo and in aqueous environment, the a-C electronic states available in the region comprised between the H{sub 2}/H{sub 2}O and O{sub 2}/H{sub 2}O levels of water correspond to both occupied and unoccupied states within the a-C pseudogap region. These are localized states associated to sp{sup 2} sites in a-C. The band realignment induces a shift of approximately 300 meV of the a-C energy band positions with respect to the redox levels of water.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Lambda-scheme spectroscopy in the cat-state field

We investigate the spectroscopical scheme of a three-level system in a Λ-configuration utilizing resonant optical field being a superposition of two Glauber coherent states. The source of the field is explicitly included into the theoretical model. In the limit of strong non-classical field we propose an ansatz for solution of the master equation and calculate the steady-state density matrix. The work of both classical and nonclassical field in the steady-state regime was calculated. It was found that the presence of non-classical field creates strong atom-field correlations that results in absence of dark resonances.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BP SS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BP SS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BP SS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BP SS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R 0 ) and fluorophore orientation factor (κ 2 ) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1977

The origin of stellar winds - Subatmospheric nonthermal storage modes versus radiation pressure

Most current models of matter-flux in hot stars place its origin in radiation pressure, and then model the flow explicitly to produce no chromosphere-corona. Our model of the stellar atmosphere as a transition zone between stellar interior and interstellar medium places the origin of matter-flux, chromosphere-corona, and spectral 'emission classes' in subatmospheric nonthermal kinetic energy storage, equally for all stars, hot or cold. Current observations of both hot and cold stars suggest chromospheres to be a universal phenomenon, correlated with matter-fluxes, and enhanced in 'emission-class' stars. To clarify the difference between the two kinds of models above, we reformulate the wind-tunnel analogy to stellar winds, suggesting that stars satisfy an 'imperfect,' rather than 'perfect,' such model; i.e., transonic shocks occur before the throat, corresponding to an imposed outward velocity in the storage section, or subatmosphere. We then investigate the stability of an arbitrary stellar atmosphere, hot or cold, to suggest a cause for such an outward subatmospheric velocity.

Cannon, C. J.↗
NASA NTRS1984

A hydromagnetic model of corotating conductive solar wind streams

Under the assumption of quasi-azimuthal symmetry the governing equations of a steady hydromagnetic flow in a thermally conductive flux tube possess six invariants. Four of them represent constancy of mass efflux, energy efflux, angular momentum efflux and magnetic flux. Based on the entropy equation we obtain useful approximation in explicit expressions for the two remaining invariants. One of them provides the constraint which determines the compatible heat flux to ensure a vanishing pressure at infinity. Thus, the admissible solution that represents a corotating solar wind stream in terms of specified interplanetary condition can be calculated by an algebraic method, without the necessity of numerical integration. A two-point relationship is then derived, which correlates the solar wind properties at two separated interplanetary sites measured at two properly separated instants. This relationship may be applied to observational data from spacecraft and earth-bound satellites to discern the corotation feature in the solar wind.

Yeh, T.↗
DOE OSTI2025

Revisiting single inclusive jet production: timelike factorization and reciprocity

Factorization theorems for single inclusive jet production play a crucial role in the study of jets and their substructure. In the case of small radius jets, the dynamics of the jet clustering can be factorized from both the hard production dynamics, and the dynamics of the low scale jet substructure measurement, and is described by a matching coefficient that can be computed in perturbative Quantum Chromodynamics (QCD). A proposed factorization formula describing this process has been previously presented in the literature, and is referred to as the semi-inclusive, or fragmenting jets formalism. By performing an explicit two-loop calculation, we show the inconsistency of this factorization formula, in agreement with another recent result in the literature. Building on recent progress in the factorization of single logarithmic observables, and the understanding of reciprocity, we then derive a new all-order factorization theorem for inclusive jet production. The use of a jet algorithm, being only a modification of the infrared structure of the measurement, modifies the structure of convolutions in the factorization theorem, as compared to inclusive fragmentation, but maintains the universality of the inclusive hard function and its associated Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution, which are ultraviolet properties. However, the non-trivial structure of convolutions in the factorization theorem implies that the jet functions exhibit a modified evolution. We perform an explicit two-loop calculation of the jet function in both N = 4 super Yang-Mills (SYM), and for all color channels in QCD, finding exact agreement with the structure derived from our renormalization group equations. In addition, we derive several new results, including an extension of our factorization formula to jet substructure observables, a jet algorithm definition of a generating function for the energy correlators, and new results for exclusive jet functions. Our results are a key ingredient for achieving precision jet substructure at colliders.

Effective Field Theories↗
DOE OSTI2021

Early season prediction of within-field crop yield variability by assimilating CubeSat data into a crop model

Accurate early season predictions of crop yield at the within-field scale can be used to address a range of crop production, management, and precision agricultural challenges. While the remote sensing of within-field insights has been a research goal for many years, it is only recently that observations with the required spatio-temporal resolutions, together with efficient assimilation methods to integrate these into modeling frameworks, have become available to advance yield prediction efforts. Here we explore a yield prediction approach that combines daily high-resolution CubeSat imagery with the APSIM crop model. The approach employs APSIM to train a linear regression that relates simulated yield to simulated leaf area index (LAI). That relationship is then used to identify the optimal regression date at which the LAI provides the best prediction of yield: in this case, approximately 14 weeks prior to harvest. Instead of applying the regression on satellite imagery that is coincident, or closest to, the regression date, our method implements a particle filter that integrates CubeSat-based LAI into APSIM to provide end-of-season high-resolution (3 m) yield maps weeks before the optimal regression date. The approach is demonstrated on a rainfed maize field located in Nebraska, USA, where suitable collections of both imagery and in-situ data were available for assessment. The procedure does not require in-field data to calibrate the regression model, with results showing that even with a single assimilation step, it is possible to provide yield estimates with good accuracy up to 21 days before the optimal regression date. Yield spatial variability was reproduced reasonably well, with a strong correlation to independently collected measurements (R 2 = 0.73 and rRMSE = 12%). When the field averaged yield was compared, our approach reduced yield prediction error from 1 Mg/ha (control case based on a calibrated APSIM model), to 0.5 Mg/ha (using satellite imagery alone), and then to 0.2 Mg/ha (results with assimilation up to three weeks prior to the optimal regression date). Such a capacity to provide spatially explicit yield predictions early in the season has considerable potential to enhance digital agricultural goals and improve end-of-season yield predictions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1995

A phenomenological treatment of rotating turbulence

The strong similarity between the magnetohydrodynamic (MHD) turbulence and initially isotropic turbulence subject to rotation is noted. We then apply the MHD phenomenologies of Kraichnan and Matthaeus & Zhou to rotating turbulence. When the turbulence is subject to a strong rotation, the energy spectrum is found to scale as E(k) = C(sub Omega)(Omega(sub epsilon))(sup 1/2)k(sup -2), where Omega is the rotation rate, k is the wavenumber, and epsilon is the dissipation rate. This spectral form is consistent with a recent letter by Zeman. However, here the constant C(sub Omega) is found to be related to the Kolmogorov constant and is estimated in the range 1.22 - 1.87 for the typical values of the latter constant. A 'rule' that relates spectral transfer times to the eddy turnover time and the time scale for decay of the triple correlations is deduced. A hypothesis for the triple correlation decay rate leads to the spectral law which varies between the '-5/3' (without rotation) and '-2' laws (with strong rotation). For intermediate rotation rates, the spectrum varies according to the value of a dimensionless parameter that measures the strength of the rotation wavenumber k(sub Omega) = (Omega(sup 3)/epsiolon)(sup 1/2) relative to the wavenumber k. An eddy viscosity is derived with an explicit dependence on the rotation rate.

Zhou, YE↗
NASA NTRS1998

Critical Slowing Down in Time-to-Extinction: An Example of Critical Phenomena in Ecology

We study a model for two competing species that explicitly accounts for effects due to discreteness, stochasticity and spatial extension of populations. The two species are equally preferred by the environment and do better when surrounded by others of the same species. We observe that the final outcome depends on the initial densities (uniformly distributed in space) of the two species. The observed phase transition is a continuous one and key macroscopic quantities like the correlation length of clusters and the time-to-extinction diverge at a critical point. Away from the critical point, the dynamics can be described by a mean-field approximation. Close to the critical point, however, there is a crossover to power-law behavior because of the gross mismatch between the largest and smallest scales in the system. We have developed a theory based on surface effects, which is in good agreement with the observed behavior. The course-grained reaction-diffusion system obtained from the mean-field dynamics agrees well with the particle system.

Gandhi, Amar↗
NASA NTRS2007

Fire in the Brazilian Amazon: A Spatially Explicit Model for Policy Impact Analysis

This article implements a spatially explicit model to estimate the probability of forest and agricultural fires in the Brazilian Amazon. We innovate by using variables that reflect farmgate prices of beef and soy, and also provide a conceptual model of managed and unmanaged fires in order to simulate the impact of road paving, cattle exports, and conservation area designation on the occurrence of fire. Our analysis shows that fire is positively correlated with the price of beef and soy, and that the creation of new conservation units may offset the negative environmental impacts caused by the increasing number of fire events associated with early stages of frontier development.

Arima, Eugenio Y.↗
DOE OSTI2022

Calculating Radiation Damage (DPA) from Transmutation Products

This is a poster for an INL poster session. Accurate models for radiation damage are crucial for predicting material performance in radiation environments. The uncertainty of state-of-the-art radiation damage models is large, contributing to excessive safety margins. A major source of this uncertainty is neglecting the effect that transmutation products have on radiation damage. Transmutation products are new nuclides formed by neutron activation during irradiation; they can contribute to radiation damage by additional neutron capture or decay events. Ignoring the contribution of transmutation products leads to a significant underprediction of the radiation damage (e.g., >10% error in 316 stainless steel). This underprediction is accounted for in part by adding larger safety margins to designs. Currently, the state of the art explicitly accounts for only a single transmutation product, namely nickel-59, during the radiation damage calculation. All other transmutation products are assumed to not contribute to the radiation damage, because there is currently no established method to systematically track all or a selection of radiation damage contributions of transmutation products during activation. In the case of nickel-59, the current method is to apply a precalculated correlation that cannot be used for any other nuclide and is largely dependent on all nuclear engineers being experts in this niche topic. This project proposed to methodically find other transmutation products that cause significant radiation damage, and then to develop a general framework for systematically tracking the radiation damage from these nuclides. This was accomplished by combining the radiation damage calculation into the transmutation calculation already performed for irradiated structural materials. The key idea of our framework is to introduce radiation-damage "pseudo-nuclides" to the list of nuclides used in the transmutation analysis. This allows radiation damage to be tracked alongside the creation and destruction of transmutation products. The main deliverable of this project is a general framework for computing radiation damage while the damaged material undergoes transmutation; this capability allows a significantly more accurate estimation of radiation damage, and in turn reduce required safety margins thereby reducing the cost to construct reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

Path-space variational inference for non-equilibrium coarse-grained systems

In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Processing of X-ray snapshots from crystals in random orientations

A new method for the treatment of partial reflections from X-ray snapshots is implemented in the program package nXDS, which yields intensity data of almost the same quality as those obtained by the classical rotation method. A functional expression is introduced that relates scattered X-ray intensities from a still or a rotation snapshot to the corresponding structure-factor amplitudes. The new approach was implemented in the program nXDS for processing monochromatic diffraction images recorded by a multi-segment detector where each exposure could come from a different crystal. For images containing indexable spots, the intensities of the expected reflections and their variances are obtained by profile fitting after mapping the contributing pixel contents to the Ewald sphere. The varying intensity decline owing to the angular distance of the reflection from the surface of the Ewald sphere is estimated using a Gaussian rocking curve. This decline is dubbed ‘Ewald offset correction’, which is well defined even for still images. Together with an image-scaling factor and other corrections, an explicit expression is defined that predicts each recorded intensity from its corresponding structure-factor amplitude. All diffraction parameters, scaling and correction factors are improved by post-refinement. The ambiguous case of a lower point group than the lattice symmetry is resolved by a method reminiscent of the technique of ‘selective breeding’. It selects the indexing alternative for each image that yields, on average, the highest correlation with intensities from all other images. Processing a test set of rotation images by XDS and treating the same images by nXDS as snapshots of crystals in random orientations yields data of comparable quality, clearly indicating an anomalous signal from Se atoms.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗