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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Exciton correlations and input-output relations in non-equilibrium exciton superfluids

The photoluminescence (PL) measurements on photons and the transport measurements on excitons are the two types of independent and complementary detection tools to search for possible exciton superfluids in electron-hole semi-conductor bilayer systems. In fact, it was believed that the transport measurements can provide more direct evidences on superfluids than the spectroscopic measurements. It is important to establish the relations between the two kinds of measurements. In this paper, using quantum Heisenberg-Langevin equations, we establish such a connection by calculating various exciton correlation functions in the putative exciton superfluids. These correlation functions include both normal and anomalous greater, lesser, advanced, retarded, and time-ordered exciton Green functions and also various two exciton correlation functions. We also evaluate the corresponding normal and anomalous spectral weights and the Keldysh distribution functions. We stress the violations of the fluctuation and dissipation theorem among these various exciton correlation functions in the non-equilibrium exciton superfluids. We also explore the input-output relations between various exciton correlation functions and those of emitted photons such as the angle resolved photon power spectrum, phase sensitive two mode squeezing spectrum and two photon correlations. Applications to possible superfluids in the exciton-polariton systems are also mentioned. For a comparison, using conventional imaginary time formalism, we also calculate all the exciton correlation functions in an equilibrium dissipative exciton superfluid in the electron-electron coupled semi-conductor bilayers at the quantum Hall regime at the total filling factor {nu}{sub T}=1. We stress the analogies and also important differences between the correlations functions in the two exciton superfluid systems. - Highlights: Black-Right-Pointing-Pointer Establish the relations between photoluminescence and transport measurements. Black-Right-Pointing-Pointer Stress the violations of the fluctuation-dissipation theorem in non-equilibrium systems. Black-Right-Pointing-Pointer Explore the input-output relations between excitons and photons. Black-Right-Pointing-Pointer Discuss differences between non-equilibrium systems and dissipative ones.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Formation of Fe2Al5-xZnx intermetallic crystals at the Fe-Zn interface in hot-dip galvanizing

Highlights: • Interstitial-free steels were galvanized in Zn baths containing 0.14-0.28 wt% Al. • The Fe-Al layer formed in a 0.14 wt% Al bath is composed of equiaxed Fe{sub 2}Al{sub 5-x}Zn{sub x} crystals without preferred orientations. • The layers formed in baths containing 0.18 wt% Al or more are composed of orientated domains. • Each domain contains 4-12 Fe{sub 2}Al{sub 5-x}Zn{sub x} crystal variants of specific orientations. • A layer of a single variant crystal can grow epitaxially on the α-Fe grains as the Al content reaches 0.28 wt%. - Abstract: The formation of Fe{sub 2}Al{sub 5-x}Zn{sub x} inhibition layer at the Fe-Zn interface has been characterized by scanning electron microscopy/electron backscatter diffraction and transmission electron microscopy for interstitial-free steels galvanized in Zn baths containing 0.14–0.28 wt% Al. The inhibition layer formed in the 0.14 wt% Al bath is composed of fine, equiaxed Fe{sub 2}Al{sub 5-x}Zn{sub x} crystals without preferred orientations. The inhibition layers formed in the baths containing 0.18 wt% Al or more are composed of orientated domains and each domain contains 4–12 Fe{sub 2}Al{sub 5-x}Zn{sub x} crystal variants of specific orientations. All the variants follow the same Fe{sub 2}Al{sub 5-x}Zn{sub x}/Fe orientation relationship of [110]{sub Fe2Al5-xZnx}//[1 1-bar 1]{sub Fe} and (001){sub Fe2Al5-xZnx}//(110){sub Fe}. Therefore, each domain is formed on a single α-Fe grain and the number of variants in the domain is determined by the orientation of the α-Fe grain. The fraction of the area of epitaxial growth increases with increasing Al content in bath. When the Al content reaches 0.28 wt%, a layer of a single variant (SV) crystal can grow epitaxially on the α-Fe grains having orientations distributed from <110> to <113> parallel to the normal direction of the sheet surface. The formation of a dense SV inhibition layer is the major reason for the drastic reductions in both the Al-pickup rate and the inhibition layer thickness at high Al content baths.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Leptodermic corrections to the TOV equations and nuclear astrophysics within the effective surface approximation

The macroscopic model for a neutron star (NS) as a liquid drop at the equilibrium is used to extend the Tolman-Oppenheimer-Volkoff (TOV) equations taking into account the gradient terms responsible for the system surface. The parameters of the Schwarzschild metric in the spherical case are found with these surface corrections to the known leading (zero) order of the leptodermic approximation a/R << 1, where a is the NS effective-surface (ES) thickness, and R is the effective NS radius. The energy density $\mathscr{E}$ is considered in a general form including the functions of the particle number density and of its gradient terms. The macroscopic gravitational component $Φ$(ρ) of the energy density is taken into account in the simplest form as expansion in powers of $ρ$ – $\overline{ρ}$, where $\overline{ρ}$ is the saturation density, up to second order, in terms of its contributions to the separation particle energy and incompressibility. Density distributions ρ across the NS ES in the normal direction to the ES, which are derived in the simple analytical form at the same leading approximation, was used for the derivation of the modified TOV (MTOV) equations by accounting for their NS surface corrections. As a result, the MTOV equations are analytically solved at first order and the results are compared with the standard TOV approach of the zero order.

Magner, A. G. [Institute for Nuclear Research, Kyi↗
DOE OSTI2014

Probing the photochemistry of chemisorbed oxygen on TiO2(110) with Kr and other co-adsorbates

Weakly bound (physisorbed) atoms and molecules such as Ar, Kr, Xe, CO, CH4, CH3OH, CO2 and N2 are used to probe the photochemical interactions of O2 on rutile TiO2(110). UV irradiation of chemisorbed O2 along with the physisorbed probe species leads to photon-stimulated desorption (PSD) of Ar, Kr, CO, CH4 and N2. Without co-adsorbed O2, the PSD yields of the probe species are very low or not observed. No PSD was observed for CO2, N2O, CH3OH and the PSD yield for Xe is very low compared to the other probe atoms or molecules. The angular distribution of the photo-desorbing Kr, which is broad and cosine, is quite different from the O2 PSD angular distribution, which is sharply peaked along the surface normal. The Kr PSD yields increase with increasing coverage of Kr and of chemisorbed O2. We propose a mechanism for the observed phenomena where the chemisorbed O2 serves as photoactive center, excited via electronic excitations (electrons and/or holes) created in the TiO2 substrate by UV photon irradiation. The photo-excited O2 may transfer its energy to neighboring co-adsorbed atom or molecule resulting in desorption of the latter. Simple momentum transfer considerations suggest that heavier adsorbates (like Xe) and adsorbates with higher binding energy (like CO2) should desorb less efficiently according to the proposed mechanism. Various forms of chemisorbed O2 appeared photoactive in such stimulated desorption of Kr atoms: molecular anions (O22-, O2-), adatoms (Oa), and others. The observed phenomenon provides a new tool for study of photocatalysis.

photochemistry↗
DOE OSTI2025

Energy supply time in an islanded grid portion re-energized by local renewable sources

When a portion of the low-voltage distribution network, typically a village, is disconnected from the upstream network, due to a fault or maintenance, it can be re-energized temporarily by the distribution system operator. Usually, if closing of a normally open tie-switch connected to a neighboring feeder is not possible, a diesel generator is conveyed to the islanded grid portion and used towards temporary energy supply. This solution though can be costly, environmentally detrimental or n

Marchand, Jane [University Grenoble Alpes]↗
DOE OSTI2013

Growth of tungsten nanoparticles in direct-current argon glow discharges

The growth of nanoparticles from the sputtering of a tungsten cathode in DC argon glow discharges is reported. The study was performed at fixed argon pressure and constant discharge current. The growth by successive agglomerations is evidenced. First, tungsten nanocrystallites agglomerate into primary particles, the most probable size of which being {approx}30 nm. Primary particles of this size are observed for all plasma durations and always remain the most numerous in the discharge. Primary particles quickly agglomerate to form particles with size up to {approx}150 nm. For short plasma duration, log-normal functions describe accurately the dust particle size distributions. On the contrary, for long discharge durations, a second hump appears in the distributions toward large particle sizes. In the meantime, the discharge voltage, electron density, and emission line intensities strongly evolve. Their evolutions can be divided in four separate phases and exhibit unusual distinctive features compared to earlier observations in discharges in which particles were growing. The evolution of the different parameters is explained by a competition between the surface state of the tungsten cathode and the influence of the growing nanoparticles. The differences with sputtering glow discharges and chemically active plasmas suggest that the nanoparticle growth and its influence on discharge parameters is system and material dependent.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Flow annealed importance sampling bootstrap meets differentiable particle physics

High-energy physics requires the generation of large numbers of simulated data samples from complex but analytically tractable distributions called matrix elements. Surrogate models, such as normalizing flows, are gaining popularity for this task due to their computational efficiency. We adopt an approach based on flow annealed importance sampling bootstrap (FAB) that evaluates the differentiable target density during training and helps avoid the costly generation of training data in advance. We show that FAB reaches higher sampling efficiency with fewer target evaluations in high dimensions in comparison to other methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Empirical radius formulas for canonical neutron stars from bidirectionally selecting features of equations of state in extended Bayesian analyses of observational data

Significant advancement in Bayesian inference of nuclear equation of state (EOS) from gravitational wave and x-ray observations of neutron stars (NSs) has been made by the nuclear astrophysics community especially since GW170817. By extending the traditional Bayesian analysis which normally ends at presenting the marginalized posterior probability distribution functions (PDFs) of individual EOS parameters and their correlations (or sometimes only the Pearson correlation coefficients which are only reliably useful when the variables are linearly correlated while they are actually often not), we search for a data-driven and robust empirical formula for the radius 𝑅 1.4 of canonical NSs in terms of the characteristic EOS parameters (features). We also identify the single most important but currently poorly known EOS parameter for determining the 𝑅 1.4 . Using three regression-model-building methodologies: bidirectional stepwise feature selection, least absolute shrinkage selection operator (LASSO) regression, and neural network regression on a large set of posterior EOSs and the corresponding 𝑅 1.4 values inferred from earlier comprehensive Bayesian analyses of NS observational data, we systematically and rigorously develop the most probable 𝑅 1.4 formulas with varying statistical accuracy and technical complexity. Here, the most important EOS parameters for determining 𝑅 1.4 are found consistently in each of the feature selection processes to be (in order of decreasing importance): curvature 𝐾 sym , slope 𝐿, skewness 𝐽 sym of nuclear symmetry energy, skewness 𝐽 0 , incompressibility 𝐾 0 of symmetric nuclear matter, and the magnitude 𝐸 sym ⁡(𝜌 0 ) of symmetry energy at the saturation density 𝜌 0 of nuclear matter.

Bayesian methods↗
DOE OSTI2023

Strong lensing of high-energy neutrinos

Here, we consider the effects of strong gravitational lensing by galaxy-scale deflectors on the observations of high-energy ( E $\gg$ GeV ) neutrinos (HENs). For HENs at cosmological distances, the optical depth for multiple imaging is ~10 –3 , implying that while we do not expect any multiply imaged HENs with present samples, next-generation experiments should be able to detect the first such event. We then present the distribution of expected time delays to aid in the identification of such events, in combination with directional and energy information. In order to assist in the evaluation of HEN production mechanisms, we illustrate how lensing affects the observed number counts for a variety of intrinsic luminosity functions of the source population. Finally, we see that the lensing effects on the cosmic neutrino background flux calculation would be negligible by taking kiloparsec-scale jets as an example.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

SU-D-BRB-01: A Comparison of Learning Methods for Knowledge Based Dose Prediction for Coplanar and Non-Coplanar Liver Radiotherapy

Purpose: The predictive power of knowledge based planning (KBP) has considerable potential in the development of automated treatment planning. Here, we examine the predictive capabilities and accuracy of previously reported KBP methods, as well as an artificial neural networks (ANN) method. Furthermore, we compare the predictive accuracy of these methods on coplanar volumetric-modulated arc therapy (VMAT) and non-coplanar 4π radiotherapy. Methods: 30 liver SBRT patients previously treated using coplanar VMAT were selected for this study. The patients were re-planned using 4π radiotherapy, which involves 20 optimally selected non-coplanar IMRT fields. ANNs were used to incorporate enhanced geometric information including liver and PTV size, prescription dose, patient girth, and proximity to beams. The performance of ANN was compared to three methods from statistical voxel dose learning (SVDL), wherein the doses of voxels sharing the same distance to the PTV are approximated by either taking the median of the distribution, non-parametric fitting, or skew-normal fitting. These three methods were shown to be capable of predicting DVH, but only median approximation can predict 3D dose. Prediction methods were tested using leave-one-out cross-validation tests and evaluated using residual sum of squares (RSS) for DVH and 3D dose predictions. Results: DVH prediction using non-parametric fitting had the lowest average RSS with 0.1176(4π) and 0.1633(VMAT), compared to 0.4879(4π) and 1.8744(VMAT) RSS for ANN. 3D dose prediction with median approximation had lower RSS with 12.02(4π) and 29.22(VMAT), compared to 27.95(4π) and 130.9(VMAT) for ANN. Conclusion: Paradoxically, although the ANNs included geometric features in addition to the distances to the PTV, it did not perform better in predicting DVH or 3D dose compared to simpler, faster methods based on the distances alone. The study further confirms that the prediction of 4π non-coplanar plans were more accurate than VMAT. NIH R43CA183390 and R01CA188300.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-R-08: Can Normalization of Brain MRI Texture Features Reduce Scanner-Dependent Effects in Unsupervised Machine Learning?

Purpose: To reduce differences in features calculated from MRI brain scans acquired at different field strengths with or without Gadolinium contrast. Methods: Brain scans were processed for 111 epilepsy patients to extract hippocampus and thalamus features. Scans were acquired on 1.5 T scanners with Gadolinium contrast (group A), 1.5T scanners without Gd (group B), and 3.0 T scanners without Gd (group C). A total of 72 features were extracted. Features were extracted from original scans and from scans where the image pixel values were rescaled to the mean of the hippocampi and thalami values. For each data set, cluster analysis was performed on the raw feature set and for feature sets with normalization (conversion to Z scores). Two methods of normalization were used: The first was over all values of a given feature, and the second by normalizing within the patient group membership. The clustering software was configured to produce 3 clusters. Group fractions in each cluster were calculated. Results: For features calculated from both the non-rescaled and rescaled data, cluster membership was identical for both the non-normalized and normalized data sets. Cluster 1 was comprised entirely of Group A data, Cluster 2 contained data from all three groups, and Cluster 3 contained data from only groups 1 and 2. For the categorically normalized data sets there was a more uniform distribution of group data in the three Clusters. A less pronounced effect was seen in the rescaled image data features. Conclusion: Image Rescaling and feature renormalization can have a significant effect on the results of clustering analysis. These effects are also likely to influence the results of supervised machine learning algorithms. It may be possible to partly remove the influence of scanner field strength and the presence of Gadolinium based contrast in feature extraction for radiomics applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Analyzing the Validity of Brazilian Testing Using Digital Image Correlation and Numerical Simulation Techniques

Characterizing the mechanical behavior of rocks plays a crucial role to optimize the fracturing process in unconventional reservoirs. However, due to the intrinsic anisotropy and heterogeneity in unconventional resources, fracture process prediction remains the most significant challenge for sustainable and economic hydrocarbon production. During the deformation tracking under compression, deploying conventional methods (strain gauge, extensometer, etc.) is insufficient to measure the deformation since the physical attachment of the device is restricted to the size of the sample, monitoring limited point-wise deformation, producing difficulties in data retrieval, and a tendency to lose track in failure points, etc. Where conventional methods are limited, the application of digital image correlation (DIC) provides detailed and additional information of strain evolution and fracture patterns under loading. DIC is an image-based optical method that records an object with a camera and monitors the random contrast speckle pattern painted on the facing surface of the specimen. To overcome the existing limitations, this paper presents numerical modeling of Brazilian disc tests under quasi-static conditions to understand the full-field deformation behaviors and finally, it is validated by DIC. As the direct tensile test has limitations in sample preparation and test execution, the Brazilian testing principle is commonly used to evaluate indirectly the tensile strength of rocks. The two-dimensional numerical model was built to predict the stress distribution and full-field deformation on Brazilian disc under compression based on the assumptions of a homogenous, isotropic and linear elastic material. The uniaxial compression test was conducted using the DIC technique to determine the elastic properties of Spider Berea sandstone, which were used as inputs for the simulation model. The model was verified by the analytical solution and compared with the digital image correlation. The numerical simulation results showed that the solutions matched reasonably with the analytical solutions where the maximum deviation of stress distribution was obtained as 14.59%. The strain evolution (normal and shear strains) and displacements along the central horizontal and vertical planes were investigated in three distinguishable percentages of peak loads (20%, 40%, and 90%) to understand the deformation behaviors in rock. The simulation results demonstrated that the strain evolution contours consistently matched with DIC generated contours with a reasonable agreement. The changes in displacement along the central horizontal and vertical planes showed that numerical simulation and DIC generated experimental results were repeatable and matched closely. In terms of validation, Brazilian testing to measure the indirect tensile strength of rocks is still an issue of debate. The numerical model of fracture propagation supported by digital image correlation from this study can be used to explain the fracturing process in the homogeneous material and can be extended to non-homogeneous cases by incorporating heterogeneity, which is essential for rock mechanics field applications.

58 GEOSCIENCES↗
DOE OSTI2022

A Hybrid Data-Driven and Model-Based Anomaly Detection Scheme for DER Operation: Preprint

This paper proposes a hybrid data and model-based anomaly detection for securing the operation of distributed energy resources (DERs) in distribution grids. Data-driven autoencoders (AE) are set up at the edge level by taking local DER data and detect anomalous operations by leveraging the reconstruction ability. In parallel, model-based state estimation (SE) is running at the system level by taking system models and measurements, the anomalies are identified by analyzing the measurements residual. The hybrid scheme preserves the benefits of both data-driven and model-based analysis and thus improves the robustness and accuracy of anomaly detection. It can be established by getting full use of the existing infrastructures in distribution grids. Numerical tests on a realistic distribution feeder in Southern California highlight the effectiveness as well as benefits of the proposed scheme.

anomaly detection↗
DOE OSTI2022

Background Information on the Protection Requirements in IEEE Std 1547-2018

As the DER penetration level has risen significantly in recent times, parameter settings and configuration of installed DERs are having direct impact on local electric distribution utilities as well as bulk power systems during normal and abnormal grid conditions. On the other hand, all grid-connected DERs in the United States of America must conform to the interconnection requirements prescribed in the IEEE Std 1547-2018. Because of these reasons, it is crucial to understand the expected DER performance during abnormal grid conditions considering the requirements of the IEEE Std 1547-2018. The aim of this document is twofold: (1) to summarize requirements in IEEE Std 1547-2018 having direct implications in distribution network protection, and (2) to provide the reader with knowledge and information that will be required for users to apply the requirements specified. Since the focus of this document is on distribution network protection in the presence of DERs, it is assumed that the readers have basic understanding of distribution network protection as well as working principles of DERs. This document starts with a brief introduction on protection systems for distribution network followed by a discussion on the impact of DER on the protection systems. Current practices to provide network protection in the presence of DER is briefly discussed. The document then explores the DER performance requirements in IEEE Std. 1547-2018; especially on those related to distribution network protection. Section 6.1 in IEEE Std. 1547-2018 provides an overview of capabilities and control requirements for DER under abnormal operating conditions. This section also introduces abnormal operating performance categories I, II, III. The DER response to various types of faults and grid conditions such as short-circuit faults and open phase conditions are discussed in section 6.2 in the standard while requirements for coordination with the Area EPS reclosing scheme are provided in section 6.3. Section 6.4 in the IEEE Std 1547-2018 specifies requirements for mandatory voltage tripping and ride-through requirements during low and high voltage disturbances and section 6.5 specifies similar requirements for low and high frequency disturbances. IEEE Std. 1547 requires that the conformance of the DERs to IEEE Std 1547-2018 requirements should be verified in accordance with IEEE Std. 1547. 1. There are several parameters and settings of DERs that need to be properly selected for reliable operation during abnormal grid condition while applying the requirements of IEEE Std 1547-2018. Key decisions for proper selections of parameter and settings are: 1. Determination of required DER abnormal operating performance category, 2. Determination of DER response (shall trip) to abnormal voltages and 3. Determination of DER response (shall trip) to abnormal frequency.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

A possible mass distribution of primordial black holes implied by LIGO-Virgo

The LIGO-Virgo Collaboration has so far detected around 90 black holes, some of which have masses larger than what were expected from the collapse of stars. The mass distribution of LIGO-Virgo black holes appears to have a peak at ~ 30 M ⊙ and two tails on the ends. By assuming that they all have a primordial origin, we analyze the GWTC-1 (O1&O2) and GWTC-2 (O3a) datasets by performing maximum likelihood estimation on a broken power law mass function f ( m ), with the result f ∝ m 1.2 for m < 35 M ⊙ and f ∝ m -4 for m > 35 M ⊙ . This appears to behave better than the popular log-normal mass function. Surprisingly, such a simple and unique distribution can be realized in our previously proposed mechanism of PBH formation, where the black holes are formed by vacuum bubbles that nucleate during inflation via quantum tunneling. Moreover, this mass distribution can also provide an explanation to supermassive black holes formed at high redshifts.

Astronomy & Astrophysics↗
DOE OSTI2014

Quantifying the Combined Effect of Radiation Therapy and Hyperthermia in Terms of Equivalent Dose Distributions

Purpose: To develop a method to quantify the therapeutic effect of radiosensitization by hyperthermia; to this end, a numerical method was proposed to convert radiation therapy dose distributions with hyperthermia to equivalent dose distributions without hyperthermia. Methods and Materials: Clinical intensity modulated radiation therapy plans were created for 15 prostate cancer cases. To simulate a clinically relevant heterogeneous temperature distribution, hyperthermia treatment planning was performed for heating with the AMC-8 system. The temperature-dependent parameters α (Gy{sup −1}) and β (Gy{sup −2}) of the linear–quadratic model for prostate cancer were estimated from the literature. No thermal enhancement was assumed for normal tissue. The intensity modulated radiation therapy plans and temperature distributions were exported to our in-house-developed radiation therapy treatment planning system, APlan, and equivalent dose distributions without hyperthermia were calculated voxel by voxel using the linear–quadratic model. Results: The planned average tumor temperatures T90, T50, and T10 in the planning target volume were 40.5°C, 41.6°C, and 42.4°C, respectively. The planned minimum, mean, and maximum radiation therapy doses were 62.9 Gy, 76.0 Gy, and 81.0 Gy, respectively. Adding hyperthermia yielded an equivalent dose distribution with an extended 95% isodose level. The equivalent minimum, mean, and maximum doses reflecting the radiosensitization by hyperthermia were 70.3 Gy, 86.3 Gy, and 93.6 Gy, respectively, for a linear increase of α with temperature. This can be considered similar to a dose escalation with a substantial increase in tumor control probability for high-risk prostate carcinoma. Conclusion: A model to quantify the effect of combined radiation therapy and hyperthermia in terms of equivalent dose distributions was presented. This model is particularly instructive to estimate the potential effects of interaction from different treatment modalities.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Insights into acetone photochemistry on rutile TiO₂(110). 2. new photodesorption channel with CH₃ ejection along the surface normal

Angle-resolved photon stimulated desorption (PSD) combined with infrared reflection-adsorption spectroscopy and temperature programmed desorption reveal two distinct channels in the photochemistry of acetone on rutile TiO₂(110) surface. During UV irradiation of co-adsorbed oxygen and acetone molecules, methyl radicals (CH₃) are ejected in two different directions: i) normal to the surface and ii) off-normal at ~±66° to the surface normal in the azimuth (i.e. perpendicular to the rows of bridging oxygen and Ti atoms). Both components are relatively narrow and non-cosine, indicating non-thermal evolution of CH₃ radicals. The direction of the “off-normal” PSD component is consistent with orientation of the C–CH₃ bonds in the n²-acetone diolate—a photoactive form of acetone chemisorption on the oxidized TiO₂(110) surface proposed earlier from experimental and theoretical studies. The direction of the “normal” PSD component requires an orientation of a C–CH₃ bond which is not consistent with the n²-acetone diolate structure. The angular distribution of the CH₃ PSD depends on the acetone coverage. The “off-normal” PSD component dominates at lower acetone coverage (< 0.2 ML), but does not increase at higher coverages in accord with the acetone diolate peak intensity in the infrared reflection-absorption spectra. The “normal” PSD component grows with the acetone coverage up to 0.6 ML. The newly discovered “normal” PSD channel is tentatively assigned to a photo-produced n²- acetone enolate as a potential precursor based on the H/D exchange experiments

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson’s R and Spearman’s ρ coefficients as well as Kendall’s τ and Top–Down correlation. We also test the behavior of association measures, including the coefficient of determination R 2 , Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spear man’s ρ, Kendall’s τ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R 2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.

59 BASIC BIOLOGICAL SCIENCES↗