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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Artificial neural network prediction of self-diffusion in pure compounds over multiple phase regimes

Artificial neural networks (ANNs) were developed to accurately predict the self-diffusion constants for pure components in liquid, gas and super critical phases. The ANNs were tested on an experimental database of 6625 self-diffusion constants for 118 different chemical compounds. The presence of multiple phases results in a heavy skew in the distribution of diffusion constants and multiple approaches were used to address this challenge. First, an ANN was developed with the raw diffusion values to assess what the main drawbacks of this direct method were. The first approach for improving the predictions involved taking the log 10 of diffusion to provide a more uniform distribution and reduce the range of target output values used to develop the ANN. The second approach involved developing individual ANNs for each phase using the raw diffusion values. Results show that the log transformation leads to a model with the best self-diffusion constant predictions and an overall average absolute deviation (AAD) of 6.56%. The resultant ANN is a generalized model that can be used to predict diffusion across all three phases and over a diverse group of compounds. The importance of each input feature was ranked using a feature addition method revealing that the density of the compound has the largest impact on the ANN prediction of self-diffusion constants in pure compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A spectrophotometric study of the impact of pH and metal-to-ligand ratio on the speciation of the Pu( vi )-oxalate system

The oxalate ligand is prevalent throughout the nuclear fuel cycle. While the Pu(III)- and Pu(IV)-oxalate systems are well studied due to their use in plutonium metal and PuO 2 production, the effect of oxalate on Pu(VI) remains understudied. Absorption spectroscopy was employed to probe the solution behavior of the Pu(VI)-oxalate system as a function of pH (1, 3, 7) and metal-to-ligand ratio (M/L; 10 : 1–1 : 10). Peak changes in the UV-vis-NIR spectra were associated with the formation of multiple Pu(VI)-oxalate species with increasing oxalate concentration. Some insight into identification of species present in solution was gained from the limited Pu(VI)-oxalate literature and comparisons with the assumed isostructural U(VI)-oxalate system. A peak in the UV-vis-NIR spectrum at 839 nm, which corresponds to the formation of a 1 : 1 PuO 2 (C 2 O 4 )(aq) complex, was observed and used to determine the formation constant (log β° = 4.64 ± 0.06). A higher coordinated Pu(VI)-oxalate peak at 846 nm was tentatively assigned as the 1 : 2 complex PuO 2 (C 2 O 4 ) 2 2₋ and a preliminary formation constant was determined (log β° = 9.30 ± 0.08). In conclusion, the predominance of both complexes was shown in speciation diagrams calculated from the formation constants, illustrating the importance of considering the Pu(VI)-oxalate system in the nuclear fuel cycle.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Physics-based reward driven image analysis in microscopy

The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated (Y, Dy)Ba 2 Cu 3 O 7–δ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.

47 OTHER INSTRUMENTATION↗
DOE OSTI2014

Planck 2013 results. XXVI. Background geometry and topology of the Universe

The new cosmic microwave background (CMB) temperature maps from Planck provide the highest-quality full-sky view of the surface of last scattering available to date. This allows us to detect possible departures from the standard model of a globally homogeneous and isotropic cosmology on the largest scales. We search for correlations induced by a possible non-trivial topology with a fundamental domain intersecting, or nearly intersecting, the last scattering surface (at comoving distance χ rec ), both via a direct search for matched circular patterns at the intersections and by an optimal likelihood search for specific topologies. For the latter we consider flat spaces with cubic toroidal (T3), equal-sided chimney (T2) and slab (T1) topologies, three multi-connected spaces of constant positive curvature (dodecahedral, truncated cube and octahedral) and two compact negative-curvature spaces. These searches yield no detection of the compact topology with the scale below the diameter of the last scattering surface. For most compact topologies studied the likelihood maximized over the orientation of the space relative to the observed map shows some preference for multi-connected models just larger than the diameter of the last scattering surface. Since this effect is also present in simulated realizations of isotropic maps, we interpret it as the inevitable alignment of mild anisotropic correlations with chance features in a single sky realization; such a feature can also be present, in milder form, when the likelihood is marginalized over orientations. Thus marginalized, the limits on the radius R i of the largest sphere inscribed in topological domain (at log-likelihood-ratio Δln L > -5 relative to a simply-connected flat Planck best-fit model) are: in a flat Universe, R i > 0.92χ rec for the T3 cubic torus; R i > 0.71χ rec for the T2 chimney; R i > 0.50χ rec for the T1 slab; and in a positively curved Universe, R i > 1.03χ rec for the dodecahedral space; R i > 1.0χ rec for the truncated cube; and R i > 0.89χ rec for the octahedral space. The limit for a wider class of topologies, i.e., those predicting matching pairs of back-to-back circles, among them tori and the three spherical cases listed above, coming from the matched-circles search, is R i > 0.94χ rec at 99% confidence level. Similar limits apply to a wide, although not exhaustive, range of topologies. We also perform a Bayesian search for an anisotropic global Bianchi VII h geometry. In the non-physical setting where the Bianchi cosmology is decoupled from the standard cosmology, Planck data favour the inclusion of a Bianchi component with a Bayes factor of at least 1.5 units of log-evidence. Indeed, the Bianchi pattern is quite efficient at accounting for some of the large-scale anomalies found in Planck data. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. In the physically motivated setting where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VII h cosmology and constrain the vorticity of such models to (ω/H) 0 < 8.1 × 10 -10 (95% confidence level).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Planck 2015 results: XVIII. Background geometry and topology of the Universe

We report that maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highestquality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance χ rec ), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. We specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius R i of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio ΔlnL > -5 relative to a simply-connected flat Planck best-fit model) are: R i > 0.97 χ rec for the T3 cubic torus; and R i > 0.56 χ rec for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, R i > 0.97 χ rec at 99% confidence level from polarization data alone. We also perform a Bayesian search for an anisotropic global Bianchi VII h geometry. In the non-physical setting, where the Bianchi cosmology is decoupled from the standard cosmology, Planck temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 ± 0.04 compared to the value of + 1 if the model were to be correct. In the physically motivated setting, where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VII h cosmology and constrain the vorticity of such models to (ω/H) 0 < 7.6 × 10 -10 (95% CL).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The eROSITA Final Equatorial-Depth Survey (eFEDS)

Here, we investigate the physical properties – such as the stellar mass (M * ), star-formation rate, infrared (IR) luminosity (L IR ), X-ray luminosity (L X ), and hydrogen column density (N H ) – of mid-IR (MIR) galaxies and active galactic nuclei (AGN) at z < 4 in the 140 deg 2 field observed by eROSITA on SRG using the Performance-and-Verification-Phase program named the eROSITA Final Equatorial Depth Survey (eFEDS). By cross-matching the WISE 22 μm (W4)-detected sample and the eFEDS X-ray point-source catalog, we find that 692 extragalactic objects are detected by eROSITA. We have compiled a multiwavelength dataset extending from X-ray to far-IR wavelengths. We have also performed (i) an X-ray spectral analysis, (ii) spectral-energy-distribution fitting using X-CIGALE, (iii) 2D image-decomposition analysis using Subaru Hyper Suprime-Cam images, and (iv) optical spectral fitting with QSFit to investigate the AGN and host-galaxy properties. For 7088 WISE 22 μm objects that are undetected by eROSITA, we have performed an X-ray stacking analysis to examine the typical physical properties of these X-ray faint and probably obscured objects. We find that (i) 82% of the eFEDS–W4 sources are classified as X-ray AGN with log L X > 42 erg s –1 ; (ii) 67 and 24% of the objects have log(L IR /L ⊙ ) > 12 and 13, respectively; (iii) the relationship between L X and the 6 μm luminosity is consistent with that reported in previous works; and (iv) the relationship between the Eddington ratio and N H for the eFEDS–W4 sample and a comparison with a model prediction from a galaxy-merger simulation indicates that approximately 5.0% of the eFEDS–W4 sources in our sample are likely to be in an AGN-feedback phase, in which strong radiation pressure from the AGN blows out the surrounding material from the nuclear region. Thanks to the wide area coverage of eFEDS, we have been able to constrain the ranges of the physical properties of the WISE 22 μm-selected sample of AGNs at z < 4, providing a benchmark for forthcoming studies on a complete census of MIR galaxies selected from the full-depth eROSITA all-sky survey.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

XXL-HSC: An updated catalogue of high-redshift ( z ≥ 3.5) X-ray AGN in the XMM-XXL northern field

X-rays offer a reliable method to identify active galactic nuclei (AGNs). However, in the high-redshift Universe, X-ray AGNs are poorly sampled due to their relatively low space density and the small areas covered by X-ray surveys. In addition to wide-area X-ray surveys, it is important to have deep optical data in order to locate the optical counterparts and determine their redshifts. Here, in this work, we built a high-redshift (z ≥ 3.5) X-ray-selected AGN sample in the XMM-XXL northern field using the most updated [0.5–2 keV] catalogue along with a plethora of new spectroscopic and multi-wavelength catalogues, including the deep optical Subaru Hyper Suprime-Cam (HSC) data, reaching magnitude limits i ~ 26 mag. We selected all the spectroscopically confirmed AGN and complement this sample with high-redshift candidates that are HSC g- and r-band dropouts. To confirm the dropouts, we derived their photometric redshifts using spectral energy distribution techniques. We obtained a sample of 54 high-z sources (28 with spec-z), the largest in this field so far (almost three times larger than in previous studies), and we estimated the possible contamination and completeness. We calculated the number counts (log N-log S) in different redshift bins and compared our results with previous studies and models. We provide the strongest high-redshift AGN constraints yet at bright fluxes (f 0.5 – 2 keV > 10 –15 erg s –1 cm –2 ). The samples of z ≥ 3.5, z ≥ 4, and z ≥ 5 are in agreement with an exponential decline model similar to that witnessed at optical wavelengths. Our work emphasises the importance of using wide-area X-ray surveys with deep optical data to uncover high-redshift AGNs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Radial velocity variability and the evolution of hot subdwarf stars

Hot subdwarf stars represent a late and peculiar stage in the evolution of low-mass stars, since they are likely formed by close binary interactions. In this work, we perform a radial velocity (RV) variability study of a sample of 646 hot subdwarfs with multi-epoch radial velocities based on spectra from Sloan Digital Sky Survey (SDSS) and Large Sky Area Multi-Object Fibre Spectroscopic Telescope (LAMOST). The atmospheric parameters and RVs were taken from the literature. For stars with archival spectra but without literature values, we determined the parameters by fitting model atmospheres. In addition, we redetermined the atmospheric parameters and RVs for all the He-enriched sdO/Bs. This broad sample allowed us to study RV-variability as a function of the location in theT eff - log g- and T eff - log n (He)/n (H) diagrams in a statistically significant way. We used the fraction of RV-variable stars and the distribution of the maximum RV variations ΔRV max as diagnostics. Both indicators turned out to be quite inhomogeneous across the studied parameter ranges. A striking feature is the completely dissimilar behaviour of He-poor and He-rich hot subdwarfs. While the former have a high fraction of close binaries, almost no significant RV variations could be detected for the latter. This has led us to the conclusion that there is likely no evolutionary connection between these subtypes. On the other hand, intermediate He-rich- and extreme He-rich sdOB/Os are more likely to be related. Furthermore, we conclude that the vast majority of this population is formed via one or several binary merger channels. Hot subdwarfs with temperatures cooler than ~24 000 K tend to show fewer and smaller RV-variations. These objects might constitute a new subpopulation of binaries with longer periods and late-type or compact companions. The RV-variability properties of the extreme horizontal branch (EHB) and corresponding post-EHB populations of the He-poor hot subdwarfs match and confirm the predicted evolutionary connection between them. Stars found below the canonical EHB at somewhat higher surface gravities show large RV variations and a high RV variability fraction. These properties are consistent with most of them being low-mass EHB stars or progenitors of low-mass helium white dwarfs in close binaries.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Lyman continuum leaker candidates among highly ionised, low-redshift dwarf galaxies selected from He II

Contemporary research suggests that the reionisation of the intergalactic medium (IGM) in the early Universe was predominantly realised by star-forming (proto-)galaxies (SFGs). Due to observational constraints, our knowledge on the origins of sufficient amounts of ionising Lyman continuum (LyC) photons and the mechanisms facilitating their transport into the IGM remains sparse. Recent efforts have thus focussed on the study of local analogues to these high-redshift objects. We aim to acquire a set of very low-redshift SFGs that exhibit signs of a hard radiation field being present. A subsequent analysis of their emission line properties is intended to shed light on how the conditions prevalent in these objects compare to those predicted to be present in early SFGs that are thought to be LyC emitters (LCEs). We used archival spectroscopic SDSS DR12 data to select a sample of low-redshift He II 4686 emitters and restricted it to a set of SFGs with an emission line diagnostic sensitive to the presence of an active galactic nucleus, which serves as our only selection criterion. We performed a population spectral synthesis with FADO to reconstruct these galaxies’ star-formation histories (SFHs). Utilising the spectroscopic information at hand, we constrained the predominant ionisation mechanisms in these galaxies and inferred information on interstellar medium (ISM) conditions relevant for the escape of LyC radiation. Our final sample consists of eighteen ionised, metal-poor galaxies (IMPs). These low-mass (6.2 ≤ log(M * /M ⊙ ) ≤ 8.8), low-metallicity (7.54 ≤log(O/H) + 12 ≤ 8.13) dwarf galaxies appear to be predominantly ionised by stellar sources. We find large [OIII] 5007/[OII] 3727 ratios and [SII] 6717,6731/Hα deficiencies, which provide strong indications for these galaxies to be LCEs. At least 40% of these objects are candidates for featuring cosmologically significant LyC escape fractions ≳10%. The IMPs’ SFHs exhibit strong similarities and almost all galaxies appear to contain an old (> 1 Gyr) stellar component, while also harbouring a young, two-stage (~10 Myr and < 1 Myr) starburst, which we speculate might be related to LyC escape. The properties of the compact emission line galaxies presented here align well with those observed in many local LCEs. In fact, our sample may prove as an extension to the rather small catalogue of local LCEs, as the extreme ISM conditions we find are assumed to facilitate LyC leakage. Notably, all of our eighteen candidates are significantly closer (z < 0.1) than most established LCEs. If the inferred LyC photon loss is genuine, this demonstrates that selecting SFGs from He II 4686 is a powerful selection criterion in the search for LCEs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

The SRG/eROSITA All-Sky Survey: Optical identification and properties of galaxy clusters and groups in the western galactic hemisphere

The first SRG/eROSITA All-Sky Survey (eRASS1) provides the largest intracluster medium-selected galaxy cluster and group catalog covering the western Galactic hemisphere. Compared to samples selected purely on X-ray extent, the sample purity can be enhanced by identifying cluster candidates using optical and near-infrared data from the DESI Legacy Imaging Surveys. Using the red-sequence-based cluster findereROMaPPer, we measured individual photometric properties (redshiftz λ , richnessλ, optical center, and BCG position) for 12000 eRASS1 clusters over a sky area of 13 116 deg 2 , augmented by 247 cases identified by matching the candidates with known clusters from the literature. The median redshift of the identified eRASS1 sample isz= 0.31, with 10% of the clusters atz> 0.72. The photometric redshifts have an accuracy ofδz/(1 +z) ≲ 0.005 for 0.05 specand velocity dispersionσ) were measured a posteriori for a subsample of 3210 and 1499 eRASS1 clusters, respectively, using an extensive compilation of spectroscopic redshifts of galaxies from the literature. We infer that the primary eRASS1 sample has a purity of 86% and optical completeness >95% forz> 0.05. For these and further quality assessments of the eRASS1 identified catalog, we applied our identification method to a collection of galaxy cluster catalogs in the literature, as well as blindly on the full Legacy Surveys covering 24069 deg 2 . Using a combination of these cluster samples, we investigated the velocity dispersion-richness relation, finding that it scales with richness as log(λ norm ) = 2.401 × log(σ) − 5.074 with an intrinsic scatter ofδ in = 0.10 ± 0.01 dex. The primary product of our work is the identified eRASS1 cluster catalog with high purity and a well-defined X-ray selection process, opening the path for precise cosmological analyses presented in companion papers.

Astronomy & Astrophysics↗
DOE OSTI2024

Darshan for HEP applications

Modern HEP workflows must manage increasingly large and complex data collections. HPC facilities may be employed to help meet these workflows’ growing data processing needs. However, a better understanding of the I/O patterns and underlying bottlenecks of these workflows is necessary to meet the performance expectations of HPC systems.Darshan is a lightweight I/O characterization tool that captures concise views of HPC application I/O behavior. It intercepts application I/O calls at runtime, records file access statistics for each process, and generates log files detailing application I/O access patterns.Typical HEP workflows include event generation, detector simulation, event reconstruction, and subsequent analysis stages. A study of the I/O behavior of the ATLAS simulation and filtering stage, and the CMS simulation workflow using Darshan is presented, including insights into the I/O operations and data access size.

Wang, Rui↗
DOE OSTI2013

Femtosecond laser diagnostics of the built-in electric field across the p{sup +}-Si/SiO{sub 2} interface and its ultrafast shielding

Ultrafast shielding of the built-in electric field E{sub 0} across the p{sup +}-Si/SiO{sub 2} interface of boron doped Si upon near infrared femtosecond (fs) laser pulse irradiation (73 {+-} 5 fs, 35 GW/cm{sup 2}{<=} I{sub peak}{sup ({omega})} {<=} 115 GW/cm{sup 2}) is shown to be dominated by electron-hole (e-h) pairs generated via two-photon absorption (TPA), whereas contributions from one-photon absorption (OPA) appear negligible. E{sub 0} shows up in the instantaneous signal I{sup (2{omega})}(t Almost-Equal-To 0) Almost-Equal-To I{sup (2{omega})}(E{sub 0}) of the Electric Field Induced Second Harmonic (EFISH). Its power law is derived from the linear log I{sup (2{omega})}(E{sub 0}) vs. log (I{sub peak}{sup ({omega})}){sup n} plots of six fs laser wavelengths 741.2 nm {<=} {lambda} {<=} 801.0 nm for the first time. These reveal 1.2 {<=} n({lambda}) {<=} 2.1 with the minimum at {lambda} = 752.4 nm (2h{nu} = 3.3 eV) related to resonantly enhanced TPA. Shielding of E{sub 0} by e-h pairs from OPA cannot be detected by EFISH in the same fs laser pulse as their generation requires relatively slow electron-phonon coupling.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Chaotic advection at large Péclet number: Electromagnetically driven experiments, numerical simulations, and theoretical predictions

We present a combination of experiment, theory, and modelling on laminar mixing at large Péclet number. The flow is produced by oscillating electromagnetic forces in a thin electrolytic fluid layer, leading to oscillating dipoles, quadrupoles, octopoles, and disordered flows. The numerical simulations are based on the Diffusive Strip Method (DSM) which was recently introduced (P. Meunier and E. Villermaux, “The diffusive strip method for scalar mixing in two-dimensions,” J. Fluid Mech. 662, 134–172 (2010)) to solve the advection-diffusion problem by combining Lagrangian techniques and theoretical modelling of the diffusion. Numerical simulations obtained with the DSM are in reasonable agreement with quantitative dye visualization experiments of the scalar fields. A theoretical model based on log-normal Probability Density Functions (PDFs) of stretching factors, characteristic of homogeneous turbulence in the Batchelor regime, allows to predict the PDFs of scalar in agreement with numerical and experimental results. This model also indicates that the PDFs of scalar are asymptotically close to log-normal at late stages, except for the large concentration levels which correspond to low stretching factors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Role of quantum confinement in luminescence efficiency of group IV nanostructures

Experimental results obtained previously for the photoluminescence efficiency (PL{sub eff}) of Ge quantum dots (QDs) are theoretically studied. A log-log plot of PL{sub eff} versus QD diameter (D) resulted in an identical slope for each Ge QD sample only when E{sub G}∼(D{sup 2}+D){sup −1}. We identified that above D ≈ 6.2 nm: E{sub G}∼D{sup −1} due to a changing effective mass (EM), while below D ≈ 4.6 nm: E{sub G}∼D{sup −2} due to electron/hole confinement. We propose that as the QD size is initially reduced, the EM is reduced, which increases the Bohr radius and interface scattering until eventually pure quantum confinement effects dominate at small D.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Upconversion and pump saturation mechanisms in Er{sup 3+}/Yb{sup 3+} co-doped Y{sub 2}Ti{sub 2}O{sub 7} nanocrystals

The Er{sup 3+}/Yb{sup 3+} co-doped Y{sub 2}Ti{sub 2}O{sub 7} nanocrystals were synthesized by the sol–gel method. X-ray diffraction, transmission electronic microscopy, and photoluminescence spectra were measured to verify the Y{sub 2}Ti{sub 2}O{sub 7} nanocrystalline produced in the sample annealed at 800 °C. The anomalous slopes of the fitted line in the log-log plots for upconversion emissions and the pump-saturation effect of near-infrared emission were observed in the nanocrystalline samples. A theoretical model of practical Er{sup 3+}/Yb{sup 3+} co-doped system based on the rate equations were put forward and explained the experimental phenomena well.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Dynamics of gas phase Ne{sup *} + NH{sub 3} and Ne{sup *} + ND{sub 3} Penning ionisation at low temperatures

Two isotopic chemical reactions, Ne{sup *} + NH{sub 3}, and Ne{sup *} + ND{sub 3}, have been studied at low collision energies by means of a merged beams technique. Partial cross sections have been recorded for the two reactive channels, namely, Ne{sup *} + NH{sub 3} → Ne + NH{sub 3}{sup +} + e{sup −}, and Ne{sup *} + NH{sub 3} → Ne + NH{sub 2}{sup +}+ H + e{sup −}, by detecting the NH{sub 3}{sup +} and NH{sub 2}{sup +} product ions, respectively. The cross sections for both reactions were found to increase with decreasing collision energy, E{sub coll}, in the range 8 μeV < E{sub coll} < 20 meV. The measured rate constant exhibits a curvature in a log(k)-log(E{sub coll}) plot from which it is concluded that the Langevin capture model does not properly describe the Ne{sup *} + NH{sub 3} reaction in the entire range of collision energies covered here. Calculations based on multichannel quantum defect theory were performed to reproduce and interpret the experimental results. Good agreement was obtained by including long range van der Waals interactions combined with a 6-12 Lennard-Jones potential. The branching ratio between the two reactive channels, Γ=([NH{sub 2}{sup +}])/([NH{sub 2}{sup +}]+[NH{sub 3}{sup +}]) , is relatively constant, Γ ≈ 0.3, in the entire collision energy range studied here. Possible reasons for this observation are discussed and rationalized in terms of relative time scales of the reactant approach and the molecular rotation. Isotopic differences between the Ne{sup *} + NH{sub 3} and Ne{sup *} + ND{sub 3} reactions are small, as suggested by nearly equal branching ratios and cross sections for the two reactions.

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

Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET

Photon sequences from single-molecule Förster resonance energy transfer (FRET) experiments can be analyzed using a maximum likelihood method. Parameters of the underlying kinetic model (FRET efficiencies of the states and transition rates between conformational states) are obtained by maximizing the appropriate likelihood function. In addition, the errors (uncertainties) of the extracted parameters can be obtained from the curvature of the likelihood function at the maximum. We study the standard deviations of the parameters of a two-state model obtained from photon sequences with recorded colors and arrival times. The standard deviations can be obtained analytically in a special case when the FRET efficiencies of the states are 0 and 1 and in the limiting cases of fast and slow conformational dynamics. These results are compared with the results of numerical simulations. The accuracy and, therefore, the ability to predict model parameters depend on how fast the transition rates are compared to the photon count rate. In the limit of slow transitions, the key parameters that determine the accuracy are the number of transitions between the states and the number of independent photon sequences. In the fast transition limit, the accuracy is determined by the small fraction of photons that are correlated with their neighbors. The relative standard deviation of the relaxation rate has a “chevron” shape as a function of the transition rate in the log-log scale. The location of the minimum of this function dramatically depends on how well the FRET efficiencies of the states are separated.

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

Comparison of different moment-closure approximations for stochastic chemical kinetics

In recent years, moment-closure approximations (MAs) of the chemical master equation have become a popular method for the study of stochastic effects in chemical reaction systems. Several different MA methods have been proposed and applied in the literature, but it remains unclear how they perform with respect to each other. In this paper, we study the normal, Poisson, log-normal, and central-moment-neglect MAs by applying them to understand the stochastic properties of chemical systems whose deterministic rate equations show the properties of bistability, ultrasensitivity, and oscillatory behaviour. Our results suggest that the normal MA is favourable over the other studied MAs. In particular, we found that (i) the size of the region of parameter space where a closure gives physically meaningful results, e.g., positive mean and variance, is considerably larger for the normal closure than for the other three closures, (ii) the accuracy of the predictions of the four closures (relative to simulations using the stochastic simulation algorithm) is comparable in those regions of parameter space where all closures give physically meaningful results, and (iii) the Poisson and log-normal MAs are not uniquely defined for systems involving conservation laws in molecule numbers. We also describe the new software package MOCA which enables the automated numerical analysis of various MA methods in a graphical user interface and which was used to perform the comparative analysis presented in this paper. MOCA allows the user to develop novel closure methods and can treat polynomial, non-polynomial, as well as time-dependent propensity functions, thus being applicable to virtually any chemical reaction system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗