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DOE OSTI2021

Multimode two-dimensional vibronic spectroscopy. II. Simulating and extracting vibronic coupling parameters from polarization-selective spectra

We report experimental demonstrations of polarization-selection two-dimensional Vibrational-Electronic (2D VE) and 2D Electronic-Vibrational (2D EV) spectroscopies aim to map the magnitudes and spatial orientations of coupled electronic and vibrational coordinates in complex systems. The realization of that goal depends on our ability to connect spectroscopic observables with molecular structural parameters. In this paper, we use a model Hamiltonian consisting of two anharmonically coupled vibrational modes in electronic ground and excited states with linear and bilinear vibronic coupling terms to simulate polarization-selective 2D EV and 2D VE spectra. We discuss the relationships between the linear vibronic coupling and two-dimensional Huang–Rhys parameters and between the bilinear vibronic coupling term and Duschinsky mixing. We develop a description of the vibronic transition dipoles and explore how the Hamiltonian parameters and non-Condon effects impact their amplitudes and orientations. Using simulated polarization-selective 2D EV and 2D VE spectra, we show how 2D peak positions, amplitudes, and anisotropy can be used to measure parameters of the vibronic Hamiltonian and non-Condon effects. This paper, along with the first in the series, provides the reader with a detailed description of reading, simulating, and analyzing multimode, polarization-selective 2D EV and 2D VE spectra with an emphasis on extracting vibronic coupling parameters from complex spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Global optimization of omnidirectional wavelength selective emitters/absorbers based on dielectric-filled anti-reflection coated two-dimensional metallic photonic crystals

Explore the source record for details and available documents.

charge transport↗

DOE OSTI2018

Evolutionary selection growth of two-dimensional materials on polycrystalline substrates

There is a demand for the manufacture of two-dimensional (2D) materials with high-quality single crystals of large size. Usually, epitaxial growth is considered the method of choice in preparing single-crystalline thin films, but it requires single-crystal substrates for deposition. Here in this paper we present a different approach and report the synthesis of single-crystal-like monolayer graphene films on polycrystalline substrates. The technological realization of the proposed method resembles the Czochralski process and is based on the evolutionary selection approach, which is now realized in 2D geometry. The method relies on ‘self-selection’ of the fastest-growing domain orientation, which eventually overwhelms the slower-growing domains and yields a single-crystal continuous 2D film. Here we have used it to synthesize foot-long graphene films at rates up to 2.5 cm h -1 that possess the quality of a single crystal. We anticipate that the proposed approach could be readily adopted for the synthesis of other 2D materials and heterostructures.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Gaussian processes with built-in dimensionality reduction: Applications to high-dimensional uncertainty propagation

Uncertainty quantification (UQ) tasks, such as model calibration, uncertainty propagation, and optimization under uncertainty, typically require several thousand evaluations of the underlying computer codes. To cope with the cost of simulations, one replaces the real response surface with a cheap surrogate based, e.g., on polynomial chaos expansions, neural networks, support vector machines, or Gaussian processes (GP). However, the number of simulations required to learn a generic multivariate response grows exponentially as the input dimension increases. This curse of dimensionality can only be addressed, if the response exhibits some special structure that can be discovered and exploited. A wide range of physical responses exhibit a special structure known as an active subspace (AS). An AS is a linear manifold of the stochastic space characterized by maximal response variation. The idea is that one should first identify this low dimensional manifold, project the high-dimensional input onto it, and then link the projection to the output. If the dimensionality of the AS is low enough, then learning the link function is a much easier problem than the original problem of learning a high-dimensional function. The classic approach to discovering the AS requires gradient information, a fact that severely limits its applicability. Furthermore, and partly because of its reliance to gradients, it is not able to handle noisy observations. The latter is an essential trait if one wants to be able to propagate uncertainty through stochastic simulators, e.g., through molecular dynamics codes. In this work, we develop a probabilistic version of AS which is gradient-free and robust to observational noise. Our approach relies on a novel Gaussian process regression with built-in dimensionality reduction. In particular, the AS is represented as an orthogonal projection matrix that serves as yet another covariance function hyper-parameter to be estimated from the data. To train the model, we design a two-step maximum likelihood optimization procedure that ensures the orthogonality of the projection matrix by exploiting recent results on the Stiefel manifold, i.e., the manifold of matrices with orthogonal columns. The additional benefit of our probabilistic formulation, is that it allows us to select the dimensionality of the AS via the Bayesian information criterion. We validate our approach by showing that it can discover the right AS in synthetic examples without gradient information using both noiseless and noisy observations. We demonstrate that our method is able to discover the same AS as the classical approach in a challenging one-hundred-dimensional problem involving an elliptic stochastic partial differential equation with random conductivity. Finally, we use our approach to study the effect of geometric and material uncertainties in the propagation of solitary waves in a one dimensional granular system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2014

A three-dimensional metal–organic framework for selective sensing of nitroaromatic compounds

A 3D metal–organic framework [NH{sub 2}(CH{sub 3}){sub 2}][Cd{sub 6}(L){sub 4}(DMF){sub 6}(HCOO)](DMF = N,N-dimethylformamide) (1) has been synthesized using a tripodal ligand H{sub 3}L (2,4,6-tris[1-(3-carboxylphenoxy)ylmethyl]mesitylene). The obtained complex exhibits a 3D framework containing hexanuclear (Cd{sub 6}) building units formed by two trinuclear (Cd{sub 3}) clusters that are connected via HCOO{sup −} anions. For complex 1, the participation of the fluorescent ligand H{sub 3}L not only gives rise to a strong photoluminescence emission as expected, but more interestingly, that ligand originated characteristic band could be quenched selectively by nitrobenzene with a low detection limit, showing its potential as a highly sensitive and selective sensor for nitrobenzene. Based on an electron transfer quenching mechanism, the fluorescence sensing ability of 1 is also applicable for other electron-deficient nitroaromatic compounds with high selectivity and sensitivity, i.e., 1,4-dinitrobenzene, 1,3-dinitrobenzene, 2,4-dinitrotoluene, and 4-nitrotoluene, suggesting 1 a promising fluorescence sensor for detecting and recognizing the same kind of chemicals.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Optimal Stop Word Selection for Text Mining in Critical Infrastructure Domain

Eliminating all stop words from the feature space is a standard practice of preprocessing in text mining, regardless of the domain which it is applied to. However, this may result in loss of important information, which adversely affects the accuracy of the text mining algorithm. Therefore, this paper proposes a novel methodology for selecting the optimal set of domain specific stop words for improved text mining accuracy. First, the presented methodology retains all the stop words in the text preprocessing phase. Then, an evolutionary technique is used to extract the optimal set of stop words that result in the best classification accuracy. The presented methodology was implemented on a corpus of open source news articles related to critical infrastructure hazards. The first step of mining geo-dependencies among critical infrastructures from text is text classification. In order to achieve this, article content was classified into two classes: 1) text content with geo-location information, and 2) text content without geo-location information. Classification accuracy presented methodology was compared to accuracies of four other test cases. Experimental results with 10-fold cross validation showed that the presented method yielded an increase of 1.76% or higher in True Positive (TP) rate and a 2.27% or higher increase in the True Negative (TN) rate compared to the other techniques.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Fast dynamics of a hydrogen-bonding glass forming liquid: Chemical exchange-induced spectral diffusion in 2D IR spectroscopy

Polarization-selective Two Dimensional Infrared (2D IR) and IR pump-probe spectroscopies have been performed on the hydrogen bonding glass forming liquid 2-biphenylmethanol doped with the long-lived vibrational probe phenylselenocyanate over a wide range of temperatures. The spectral diffusion seen in the 2D spectra was found to have a large polarization dependence, in large excess of what is predicted by standard theory. This anomaly was explained by decomposing the 2D spectra into hydrogen-bonding and non-bonding components, which exchange through large-angle orientational motion. By adapting chemical exchange theories, parameters for the component peaks were then calculated by fitting the polarization-dependent spectral diffusion and the pump-probe anisotropy. A model of highly heterogeneous exchange and orientational dynamics was used to explain the observed time dependences as a function of temperature on fast time scales. The experimental observations, the kinetic modeling, and physical arguments lead to the determination of the times for interconversion of slow dynamics structural domains to fast dynamics structural domains in the supercooled liquid as a function of temperature. The slow to fast domain interconversion times range from 40 ps at 355 K to 5000 ps at 270 K.

14 SOLAR ENERGY↗

DOE OSTI2015

SU-E-T-630: Predictive Modeling of Mortality, Tumor Control, and Normal Tissue Complications After Stereotactic Body Radiotherapy for Stage I Non-Small Cell Lung Cancer

Purpose: While rates of local control have been well characterized after stereotactic body radiotherapy (SBRT) for stage I non-small cell lung cancer (NSCLC), less data are available characterizing survival and normal tissue toxicities, and no validated models exist assessing these parameters after SBRT. We evaluate the reliability of various machine learning techniques when applied to radiation oncology datasets to create predictive models of mortality, tumor control, and normal tissue complications. Methods: A dataset of 204 consecutive patients with stage I non-small cell lung cancer (NSCLC) treated with stereotactic body radiotherapy (SBRT) at the University of Pennsylvania between 2009 and 2013 was used to create predictive models of tumor control, normal tissue complications, and mortality in this IRB-approved study. Nearly 200 data fields of detailed patient- and tumor-specific information, radiotherapy dosimetric measurements, and clinical outcomes data were collected. Predictive models were created for local tumor control, 1- and 3-year overall survival, and nodal failure using 60% of the data (leaving the remainder as a test set). After applying feature selection and dimensionality reduction, nonlinear support vector classification was applied to the resulting features. Models were evaluated for accuracy and area under ROC curve on the 81-patient test set. Results: Models for common events in the dataset (such as mortality at one year) had the highest predictive power (AUC = .67, p < 0.05). For rare occurrences such as radiation pneumonitis and local failure (each occurring in less than 10% of patients), too few events were present to create reliable models. Conclusion: Although this study demonstrates the validity of predictive analytics using information extracted from patient medical records and can most reliably predict for survival after SBRT, larger sample sizes are needed to develop predictive models for normal tissue toxicities and more advanced machine learning methodologies need be consider in the future.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2014

DOE-RCT-0003641 Final Technical Report

This program studied novel concepts for an Axial Flux Reluctance Machine to capture energy from marine hydrokinetic sources and compared their attributes to a Radial Flux Reluctance Machine which was designed under a prior Department of Energy program for the same application. Detailed electromagnetic and mechanical analyses were performed to determine the validity of the concept and to provide a direct comparison with the existing conventional Radial Flux Switched Reluctance Machine designed during the Advanced Wave Energy Conversion Project, DE-EE0003641. The alternate design changed the machine topology so that the flux that is switched flows axially rather than radially and the poles themselves are long radially, as opposed to the radial flux machine that has pole pieces that are long axially. It appeared possible to build an axial flux machine that should be considerably more compact than the radial machine. In an “apples to apples” comparison, the same rules with regard to generating magnetic force and the fundamental limitations of flux density hold, so that at the heart of the machine the same torque equations hold. The differences are in the mechanical configuration that limits or enhances the change of permeance with rotor position, in the amount of permeable iron required to channel the flux via the pole pieces to the air-gaps, and in the sizing and complexity of the electrical winding. Accordingly it was anticipated that the magnetic component weight would be similar but that better use of space would result in a shorter machine with accompanying reduction in housing and support structure. For the comparison the pole count was kept the same at 28 though it was also expected that the radial tapering of the slots between pole pieces would permit a higher pole count machine, enabling the generation of greater power at a given speed in some future design. The baseline Radial Flux Machine design was established during the previous DOE program. Its characteristics were tabulated for use in comparing to the Axial Flux Machine. Three basic conceptual designs for the Axial Flux Machine were considered: (1) a machine with a single coil at the inner diameter of the machine, (2) a machine with a single coil at the outside diameter of the machine, and (3) a machine with a coil around each tooth. Slight variations of these basic configurations were considered during the study. Analysis was performed on these configurations to determine the best candidate design to advance to preliminary design, based on size, weight, performance, cost and manufacturability. The configuration selected as the most promising was the multi-pole machine with a coil around each tooth. This configuration provided the least complexity with respect to the mechanical configuration and manufacturing, which would yield the highest reliability and lowest cost machine of the three options. A preliminary design was performed on this selected configuration. For this first ever axial design of the multi rotor configuration the 'apples to apples' comparison was based on using the same length of rotor pole as the axial length of rotor pole in the radial machine and making the mean radius of the rotor in the axial machine the same as the air gap radius in the radial machine. The tooth to slot ratio at the mean radius of the axial machine was the same as the tooth to slot ratio of the radial machine. The comparison between the original radial flux machine and the new axial flux machine indicates that for the same torque, the axial flux machine diameter will be 27% greater, but it will have 30% of the length, and 76% of the weight. Based on these results, it is concluded that an axial flux reluctance machine presents a viable option for large generators to be used for the capture of wave energy. In the analysis of Task 4, below, it is pointed out that our selection of dimensional similarity for the 'apples to apples' comparison did not produce an optimum axial flux design. There is torque capability to spare, implying we could reduce the magnetic structure, but the winding area, constrained by the pole separation at the inner pole radius has a higher resistance than desirable, implying we need more room for copper. The recommendation is to proceed via one cycle of optimization and review to correct this unbalance and then proceed to a detailed design phase to produce manufacturing drawings, followed by the construction of a prototype to test the performance of the machine against predicted results.

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

Investigation of Numerical Methods for Performance Improvement of MOOSE-based System Analysis Codes

The main objective of this study is to investigate the feasibility of implementation of staggered-grid finite volume method (SG-FVM) using the MOOSE framework to support the development of the advanced system analysis code SAM. This study successfully demonstrated the integration of staggered-grid finite volume method in the application level using the MOOSE framework, although not in the framework level which should be investigated in the future. Several important properties of the implemented SG-FVM, e.g., high-order spatial accuracy and monotonicity preserving, have been demonstrated with selected numerical test cases. The superior performance in execution time was also evident based on a selected one- dimensional flow problem in a loop configuration.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1978

Perturbation solutions for transonic flow on the blade-to-blade surface of compressor blade rows

A preliminary investigation was conducted to establish the theoretical basis of perturbation techniques with the objective of minimizing computational requirements associated with parametric studies of transonic flows in turbomachines. The theoretical analysis involved the development of perturbation methods for determining first order changes in the flow solution due to variations of one or more geometrical or flow parameters. The formulation is primarily directed toward transonic flows on the blade to blade surface of a single blade row compressor. Two different perturbation approaches were identified and studied. Applications and results of these methods for various perturbations are presented for selected two dimensional transonic cascade flows to illustrate the advantages and disadvantages of each technique. Additionally, it was found that, for flows with shock waves, proper account of shock displacement was crucial.

Stahara, S. S.↗

NASA NTRS2000

Selected contribution: a three-dimensional model for assessment of in vitro toxicity in balaena mysticetus renal tissue

This study established two- and three-dimensional renal proximal tubular cell cultures of the endangered species bowhead whale (Balaena mysticetus), developed SV40-transfected cultures, and cloned the 61-amino acid open reading frame for the metallothionein protein, the primary binding site for heavy metal contamination in mammals. Microgravity research, modulations in mechanical culture conditions (modeled microgravity), and shear stress have spawned innovative approaches to understanding the dynamics of cellular interactions, gene expression, and differentiation in several cellular systems. These investigations have led to the creation of ex vivo tissue models capable of serving as physiological research analogs for three-dimensional cellular interactions. These models are enabling studies in immune function, tissue modeling for basic research, and neoplasia. Three-dimensional cellular models emulate aspects of in vivo cellular architecture and physiology and may facilitate environmental toxicological studies aimed at elucidating biological functions and responses at the cellular level. Marine mammals occupy a significant ecological niche (72% of the Earth's surface is water) in terms of the potential for information on bioaccumulation and transport of terrestrial and marine environmental toxins in high-order vertebrates. Few ex vivo models of marine mammal physiology exist in vitro to accomplish the aforementioned studies. Techniques developed in this investigation, based on previous tissue modeling successes, may serve to facilitate similar research in other marine mammals.

Whales/genetics/physiology↗

NASA NTRS2000

Cellular Responses to Mechanical Stress Selected Contribution: A Three-Dimensional Model for Assessment of in Vitro Toxicity in Balaena Mysticetus Renal Tissue

Goodwin, T. J.↗

DOE OSTI2013

Tile-Based Fisher-Ratio Software for Improved Feature Selection Analysis of Comprehensive Two-Dimensional Gas Chromatography Time-of-Flight Mass Spectrometry Data

Two-dimensional (2D) gas chromatography coupled with time-of-flight mass spectrometry (GC × GC – TOFMS) is a highly capable instrumental platform that produces complex and information-rich multi-dimensional chemical data. The complex data can be overwhelming, especially when many samples (of various sample classes) are analyzed with multiple injections for each sample. Thus, the data must be analyzed in such a way to extract the most meaningful information. The pixel-based and peak table-based algorithmic use of Fisher ratios has been used successfully in the past to reduce the multi-dimensional data down to those chemical compounds that are changing between classes relative to those that are not (i.e., chemical feature selection). We report on the initial development of a computationally fast novel tile-based Fisher-ratio software that addresses challenges due to 2D retention time misalignment without explicitly aligning the data, which is a problem for both pixel-based and peak table- based methods. Concurrently, the tile-based Fisher-ratio software maximizes the sensitivity contrast of true positives against a background of potential false positives and noise. To study this software, eight compounds, plus one internal standard, were spiked into diesel at various concentrations. The tile-based F-ratio software was able to discover all spiked analytes, within the complex diesel sample matrix with thousands of potential false positives, in each possible concentration comparison, even at the lowest absolute spiked analyte concentration ratio of 1.06.

chemometrics↗

NASA NTRS1986

Improved numerical methods for turbulent viscous recirculating flows

The objective of the present study is to improve both the accuracy and computational efficiency of existing numerical techniques used to predict viscous recirculating flows in combustors. A review of the status of the study is presented along with some illustrative results. The effort to improve the numerical techniques consists of the following technical tasks: (1) selection of numerical techniques to be evaluated; (2) two dimensional evaluation of selected techniques; and (3) three dimensional evaluation of technique(s) recommended in Task 2.

Vandoormaal, J. P.↗

DOE OSTI2016

Orbital-selective Mott phases of a one-dimensional three-orbital Hubbard model studied using computational techniques

A recently introduced one-dimensional three-orbital Hubbard model displays orbital-selective Mott phases with exotic spin arrangements such as spin block states [J. Rincón et al., Phys. Rev. Lett. 112, 106405 (2014)]. In this paper we show that the constrained-path quantum Monte Carlo (CPQMC) technique can accurately reproduce the phase diagram of this multiorbital one-dimensional model, paving the way to future CPQMC studies in systems with more challenging geometries, such as ladders and planes. The success of this approach relies on using the Hartree-Fock technique to prepare the trial states needed in CPQMC. In addition, we study a simplified version of the model where the pair-hopping term is neglected and the Hund coupling is restricted to its Ising component. The corresponding phase diagrams are shown to be only mildly affected by the absence of these technically difficult-to-implement terms. This is confirmed by additional density matrix renormalization group and determinant quantum Monte Carlo calculations carried out for the same simplified model, with the latter displaying only mild fermion sign problems. Lastly, we conclude that these methods are able to capture quantitatively the rich physics of the several orbital-selective Mott phases (OSMP) displayed by this model, thus enabling computational studies of the OSMP regime in higher dimensions, beyond static or dynamic mean-field approximations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

Investigating vibrational relaxation in cyanide-bridged transition metal mixed-valence complexes using two-dimensional infrared and infrared pump-probe spectroscopies

Using polarization-selective two-dimensional infrared (2D IR) and infrared pumpprobe spectroscopies, we study vibrational relaxation of the four cyanide stretching (CN) vibrations found in [(NH3)5RuIIINCFeII(CN)5] (FeRu) dissolved in D2O or formamide and [(NC)5FeIICNPtIV(NH3)4NCFeII(CN)5] 4 (FePtFe) dissolved in D2O. These cyanide-bridged transition metal complexes serve as models for understanding the role high frequency vibrational modes play in metal-to-metal charge transfers over a bridging ligand. However, there is currently little information about vibrational relaxation and dephasing dynamics of the anharmonically coupled CN modes in the electronic ground state of these complexes. IR pump-probe experiments reveal that the vibrational lifetimes of the CN modes are 2 times faster when FeRu is dissolved in D2O versus formamide. They also reveal that the vibrational lifetimes of the CN modes of FePtFe in D2O are almost four times as long as for FeRu in D2O. Combined with mode-specific relaxation dynamics measured from the 2D IR experiments, the IR pump-probe experiments also reveal that intramolecular vibrational relaxation is occurring in all three systems on 1 ps timescale. Center line slope dynamics, which have been shown to be a measure of the frequency-frequency correlation function, reveal that the radial, axial, and trans CN modes exhibit a 3 ps timescale for frequency fluctuations. This timescale is attributed to the forming and breaking of hydrogen bonds between each mode and the solvent. The results presented here along with our previous work on FeRu and FePtFe reveal a picture of coupled anharmonic CN modes where the spectral diffusion and vibrational relaxation dynamics depend on the spatial localization of the mode on the molecular complex and its specific interaction with the solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Full-dimensional and reduced-dimensional calculations of initial state-selected reaction probabilities studying the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction on a neural network PES

Initial state-selected reaction probabilities of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C{sub 3v} symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f{sub 2}-symmetric) stretching, or e-symmetric bending excited states of methane.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗