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At least 955 records · Page 53

On the Bayesian calibration of computer model mixtures through experimental data, and the design of predictive models

For many real systems, several computer models may exist with different physics and predictive abilities. To achieve more accurate simulations/predictions, it is desirable for these models to be properly combined and calibrated. Here, we propose the Bayesian calibration of computer model mixture method which relies on the idea of representing the real system output as a mixture of the available computer model outputs with unknown input dependent weight functions. The method builds a fully Bayesian predictive model as an emulator for the real system output by combining, weighting, and calibrating the available models in the Bayesian framework. Moreover, it fits a mixture of calibrated computer models that can be used by the domain scientist as a mean to combine the available computer models, in a flexible and principled manner, and perform reliable simulations. It can address realistic cases where one model may be more accurate than the others at different input values because the mixture weights, indicating the contribution of each model, are functions of the input. Inference on the calibration parameters can consider multiple computer models associated with different physics. The method does not require knowledge of the fidelity order of the models. We provide a technique able to mitigate the computational overhead due to the consideration of multiple computer models that is suitable to the mixture model framework. We implement the proposed method in a real-world application involving the Weather Research and Forecasting large-scale climate model.

97 MATHEMATICS AND COMPUTING↗

Structural and functional consequences of the STAT5B N642H driver mutation

Hyper-activated STAT5B variants are high value oncology targets for pharmacologic intervention. STAT5B N642H , a frequently-occurring oncogenic driver mutation, promotes aggressive T-cell leukemia/lymphoma in patient carriers, although the molecular origins remain unclear. Herein, we emphasize the aggressive nature of STAT5B N642H in driving T-cell neoplasia upon hematopoietic expression in transgenic mice, revealing evidence of multiple T-cell subset organ infiltration. Notably, we demonstrate STAT5B N642H -driven transformation of γδ T-cells in in vivo syngeneic transplant models, comparable to STAT5B N642H patient γδ T-cell entities. Importantly, we present human STAT5B and STAT5B N642H crystal structures, which propose alternative mutation-mediated SH2 domain conformations. Our biophysical data suggests STAT5B N642H can adopt a hyper-activated and hyper-inactivated state with resistance to dephosphorylation. MD simulations support sustained interchain cross-domain interactions in STAT5B N642H , conferring kinetic stability to the mutant anti-parallel dimer. This study provides a molecular explanation for the STAT5B N642H activating potential, and insights into pre-clinical models for targeted intervention of hyper-activated STAT5B.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗

Lead and Arsenic Bioaccessibility and Speciation as a Function of Soil Particle Size

Bioavailability research of soil metals has advanced considerably from default values to validated in vitro bioaccessibility (IVBA) assays for site‐specific risk assessment. Previously, USEPA determined that the soil‐size fraction representative of dermal adherence and consequent soil ingestion was <250 μm. This size fraction was widely used in testing efforts for both in vivo and in vitro experiments. However, recent studies indicate the <150‐μm size fraction better represents the particle size that adheres to skin for potential ingestion. At issue is the relevance of validated in vivo and in vitro methods developed with <250 μm moving to the <150‐μm fraction. The objectives of this study were to investigate <250‐μm versus <150‐μm particle size and particle size groups for evaluating lead (Pb) and arsenic (As) IVBA and speciation. Soils with different properties were homogenized, oven dried, and sieved: <250 to > 150, <150 to >75, <75 to >38, and <38 μm. Sieved versus ground subsamples of <250‐μm and <150‐μm bulk soils were also used for IVBA and synchrotron‐based Pb and As speciation. Although we observed an increase in total and IVBA‐extractable Pb and As with decreased soil particle size, changes in %IVBA of Pb and As (dependent on the ratio extractable:total) remained consistent in all of the tested soils. No significant changes in Pb and As speciation were observed across the soil fractions. The results suggest that using the more relevant <150‐μm fraction will not undermine currently validated IVBA protocols in future bioavailability studies. Core Ideas Identified critical knowledge gaps regarding the <250‐μm vs. <150‐μm particle size used for IVBA. Wider implementation of the <150‐μm size fraction maintains past validation with <‐250 μm fraction. Regardless of increase in total and extractable Pb and As, %IVBA results remained consistent. Using <150‐μm particle size for IVBA requires much higher volumes/masses of soils. Synchrotron‐based speciation is significant in bioavailability studies to understand the fate and transport of contaminants.

Karna, Ranju R.↗

Optimal mass variables for semivisible jets

Strongly coupled hidden sector theories predict collider production of invisible, composite dark matter candidates mixed with standard model hadrons in the form of semivisible jets. Classical mass reconstruction techniques may not be optimal for these unusual topologies, in which the missing transverse momentum comes from massive particles and has a nontrivial relationship to the visible jet momentum. We apply the artificial event variable network, a semisupervised, interpretable machine learning technique that uses an information bottleneck, to derive superior mass reconstruction functions for several cases of resonant semivisible jet production. We demonstrate that the technique can extrapolate to unknown signal model parameter values. We further demonstrate the viability of conducting an actual search for new physics using this method, by applying the learned functions to standard model background events from quantum chromodynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Arrhenian to non-Arrhenian crossover in glass melt viscosity

The activation energy for glass melt viscosity is a function of temperature, i.e., non-Arrhenian, within a middle range of viscosity values (typically, between 10 2 and 10 10 Pa s) and constant, i.e., Arrhenian, outside this range. At the low-viscosity end, the Arrhenian to non-Arrhenian transition (termed the crossover) falls within the glass processing range: glass melting and fining occur within the Arrhenian range while glass forming occurs within the non-Arrhenian range. By the Adam-Gibbs equation, the configuration entropy is nearly constant at high temperatures (low viscosities), where the glass melt turns into a simple liquid, and decreases with decreasing temperature (increasing viscosity) as the glass is increasingly polymerized. In the present study, the power-law function and hyperbolic tangent function are used to express the configuration entropy as a function of temperature. The viscosity crossover is defined as the point at which onset of structural grouping is causing the configuration entropy to deviate from its high-temperature value. In conclusion, it appears that the limited range of the configuration entropy of the fully depolymerized melt imposes a restriction on the crossover viscosity; for well-defined glass families, such as float glasses or nuclear waste glasses, the crossover point can be defined using a fixed, i.e., composition-independent, viscosity value.

36 MATERIALS SCIENCE↗

Shale as a Source of Organic Carbon in Floodplain Sediments of a Mountainous Watershed

Abstract Shales contain high levels of organic carbon (OC) and represent a large fraction of the Earth's reduced carbon stocks. While recent evidence suggests that shale‐derived OC may be actively cycled in riverine systems, this process is poorly understood and not currently considered in global C models. Through the use of sediment density fractionations, extractions, radiocarbon measurements, and chemical characterization, we provide information on the abundance, chemistry, and mobility of shale‐derived OC in floodplain sediments of a shale‐rich mountainous watershed. The heavy fraction of the sediment, representing mineral‐associated OC, is the largest (84 ± 6% of TOC) and oldest (Δ 14 C values −224 to −853‰) OC pool. Evidence of shale‐derived OC is observed in all sediment C pools (i.e., occluded light fraction, water‐soluble, and pyrophosphate‐extractable) except the free light fraction, which is entirely modern. Relatively consistent chemistry was observed across samples for extracted and density‐separated OC, despite wide ranges of Δ 14 C values. Carbon spectroscopy revealed that floodplain sediments had a higher degree of functionalized aromatic groups and lower carbonate content compared to shale collected nearby, consistent with chemical alteration and mixing with other C sources in the floodplain. We estimate that approximately 23–34% of sediment OC is derived from shale, with implications for other shale‐derived elements (e.g., N). This study demonstrates the important contribution of shale‐OC, particularly in environments with low litter inputs. The large impact of radiocarbon‐dead shale‐OC, which has a thermally altered chemical structure distinct from plant litter, on Δ 14 C values and reactivity of sediment‐OC must be considered.

Fox, Patricia M.↗

Polarizabilities of neutral atoms and atomic ions with a noble gas electron configuration

Atomic polarizabilities play an important role in the development of force fields for molecular simulations, as well as for the development of qualitative concepts of atomic and molecular behavior. Coupled cluster theory at the coupled cluster singles doubles triples level with very large correlation-consistent basis sets with extended diffuse functions has been used to predict the polarizabilities of the atomic neutrals, mono-cations and mono-anions with a noble gas configuration. Additional corrections for scalar relativistic and spin–orbit effects were also included for the electron configurations of Kr, Xe, and Rn. The results are in excellent agreement with experiment or with other high level calculations where available. The current results for most of these species represent the best available values for the polarizabilities. The results show that the polarizability of H - is very difficult to calculate without extremely diffuse functions. The polarizability of H - is the largest value, 34.05 Å 3 , calculated for all species in the current study. The polarizabilities of the remaining halogen anions are also the best available values. The polarizabilities of the halogen anions (excluding F - ) and H - have a linear correlation with the electron affinity of the neutral atom. Spin– orbit effects, even for closed shell species, cannot be ignored for quantitative accuracy, and the inclusion of spin–orbit effects for Fr + , Rn, and At - increases the polarizability by 4%, 6%, and 15%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Taming the fixed-node error in diffusion Monte Carlo via range separation

By combining density-functional theory (DFT) and wave function theory via the range separation (RS) of the interelectronic Coulomb operator, we obtain accurate fixed-node diffusion Monte Carlo (FN-DMC) energies with compact multi-determinant trial wave functions. In particular, we combine here short-range exchange-correlation functionals with a flavor of selected configuration interaction known as configuration interaction using a perturbative selection made iteratively (CIPSI), a scheme that we label RS-DFT-CIPSI. One of the take-home messages of the present study is that RS-DFT-CIPSI trial wave functions yield lower fixed-node energies with more compact multi-determinant expansions than CIPSI, especially for small basis sets. Indeed, as the CIPSI component of RS-DFT-CIPSI is relieved from describing the short-range part of the correlation hole around the electron-electron coalescence points, the number of determinants in the trial wave function required to reach a given accuracy is significantly reduced as compared to a conventional CIPSI calculation. Importantly, by performing various numerical experiments, we evidence that the RS-DFT scheme essentially plays the role of a simple Jastrow factor by mimicking short-range correlation effects, hence avoiding the burden of performing a stochastic optimization. Considering the 55 atomization energies of the Gaussian-1 benchmark set of molecules, we show that using a fixed value of mu = 0.5 bohr(-1) provides effective error cancellations as well as compact trial wave functions, making the present method a good candidate for the accurate description of large chemical systems.

Scemama, Anthony↗

An evaluation of tri-valent oxide (Cr 2 O 3 ) as a grain enlarging dopant for UO 2 nuclear fuels fabricated under reducing environment

A study was performed to evaluate the microstructure and crystallography of nominally 500–2000 Cr 2 O 3 -doped UO 2 fabricated in a temperature range of 1150–1750°C under reducing experimental conditions. We observed an increase in grain size of the samples with the increase in heat treating temperature as expected. For a given sintering temperature (1700–1750°C), an increase in the grain size was also observed with the increase in Cr 2 O 3 concentration up to a value of ~1000–1200 wppm. A decrease in fission gas release as a function of grain size was estimated for the Cr 2 O 3 -doped UO 2 samples assuming specified post-irradiation annealing conditions. A nearly linear decrease was obtained in the lattice parameter of the Cr 2 O 3 -doped UO 2 fcc phase with the increase in Cr 2 O 3 concentration, especially up to a nominal value of 1000 wppm. The lattice parameter decrease was also persistent with the increase in the average grain size as a result of addition of Cr 2 O 3 into the UO 2 lattice. An increase in the crystallite size and a decrease in the microstrain of the $fcc$ phase were observed with the increase in the average grain size of the samples, indicating a higher crystallinity of the Cr 2 O 3 -doped samples than that of the undoped UO 2 sample.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis

High-content imaging of embryonic zebrafish behavior can be used as a screening approach to rapidly evaluate the relative potential for chemicals to cause toxicity. However, most statistical methods applied to these data so far transform movement values to incidence-based “hits” and calculate lowest effect levels (LELs), which loses individual fish resolution of behavior and defies hazard ranking due to reliance on applied dose levels. Here, we have developed and parallelized a workflow to calculate benchmark dose (BMD) values from dynamic, high-content zebrafish behavior data that scales for high-throughput chemical screening. To appropriately capture the dynamics of zebrafish response from light to dark stimulus, we summarized time-dependent data using both area under the curve and immediate change at the transition point into two novel metrics that characterized abnormal behavior as a function of chemical concentration. The BMD workflow was applied to calculate BMD 10 values of 1,060 ToxCast chemicals for 24 zebrafish endpoints, including behavior, mortality and morphology. The BMD 10 values provided better precision and separation than LELs for clustering chemicals since they were derived from models that best-fit their concentration-response curves. Clustering analysis revealed behavioral signatures as the most sensitive endpoints. High concordance in chemical activity was observed between ToxCast assays and zebrafish behavioral endpoints, however ToxPi analysis indicated that rankings based on in vitro data was not a reliable predictor of in vivo rankings for lower potency chemicals. The methods developed in this work will enable the use of high-content zebrafish behavioral screening data for BMD analysis in toxicological hazard assessment.

59 BASIC BIOLOGICAL SCIENCES↗

Bifurcation of avoided crossing at an exceptional point in the dispersion of sound and light in locally resonant media

The avoided crossing behavior in the interaction of propagating sound or light waves with resonant inclusions is analyzed using a simple model of an acoustic medium containing damped mass-spring oscillators, which is shown to be equivalent to the Lorentz oscillator model in the elementary dispersion theory in optics. Two classes of experimental situations dictating the choice in the analysis of the dispersion relation are identified. If the wavevector is regarded as the independent variable and frequency as a complex function of the wavevector, then the avoided crossing bifurcates at an exceptional point at a certain value of the parameter γβ -1/2 , where γ and β characterize the oscillator damping and interaction strength, respectively. This behavior is not observed if the wavevector is regarded as a complex function of frequency.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Development of the self-consistent approximation and its application to the problem of magnetoelastic resonance in an inhomogeneous medium

Our previously proposed approximation involving both the first and second terms of the expansion of the vertex function is generalized to the system of two interacting wavefields of different physical nature. A system of self-consistent equations for the matrix Green’s function and matrix vertex function is derived. On the basis of this matrix generalization of the new self-consistent approximation, a theory of magnetoelastic resonance is developed for a ferromagnetic model, where the magnetoelastic coupling parameter ε(x) is inhomogeneous. Equations for magnetoelastic resonance are analyzed for one-dimensional inhomogeneities of the coupling parameter. The diagonal and off-diagonal elements of the matrix Green’s function of the system of coupled spin and elastic waves are calculated with the change in the ratio between the average value ε and rms fluctuation Δε of the coupling parameter between waves from the homogeneous case (ε ≠ 0, Δε = 0) to the extremely randomized case (ε = 0, Δε ≠ 0) at various correlation wavenumbers of inhomogeneities k{sub c}. For the limiting case of infinite correlation radius (k{sub c} = 0), in addition to approximate expressions, exact analytical expressions corresponding to the summation of all diagrams of elements of the matrix Green’s function are obtained. The results calculated for an arbitrary k{sub c} value in the new self-consistent approximation are compared to the results obtained in the standard self-consistent approximation, where only the first term of the expansion of the vertex function is taken into account. It is shown that the new approximation corrects disadvantages of the Green’s functions calculated in the standard approximation such as the dome shape of resonances and bends on the sides of resonance peaks. The appearance of a fine structure of the spectrum in the form of a narrow resonance on the Green’s function of spin waves and a narrow antiresonance on the Green’s function of elastic waves, which was previously predicted in the standard self-consistent approximation, is confirmed. With an increase in the parameter k{sub c}, the Green’s functions calculated in the standard and new approximations approach each other and almost coincide with each other at k{sub c}/k ≥ 0.5. At the same time, the results of this work indicate that the new self-consistent approximation has a certain advantage for studying the problems of stochastic radiophysics in media with long-wavelength inhomogeneities (small k{sub c} values), because it describes both the shape and width of peaks much better than the standard approximation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multiplicity dependence of light-flavor hadron production in p p collisions at s = 7 TeV

Comprehensive results on the production of unidentified charged particles, $π^±, K^±, K^0_S, K^*(892)^0, p,$ $\bar{p}$, $\phi$ (1020), Λ, $\bar{Λ}$, $\Xi^-$, $\bar{\Xi}^+$, $Ω^-$, and $\bar{Ω}^+$ hadrons in proton-proton ($pp$) collisions at $\sqrt{s}$ = 7 TeV at midrapidity ($|y|$ < 0.5) as a function of charged-particle multiplicity density are presented. In order to avoid autocorrelation biases, the actual transverse momentum ($p$ T ) spectra of the particles under study and the event activity are measured in different rapidity windows. In the highest multiplicity class, the charged-particle density reaches about 3.5 times the value measured in inelastic collisions. While the yield of protons normalized to pions remains approximately constant as a function of multiplicity, the corresponding ratios of strange hadrons to pions show a significant enhancement that increases with increasing strangeness content. Furthermore, all identified particle-to-pion ratios are shown to depend solely on charged-particle multiplicity density, regardless of system type and collision energy. The evolution of the spectral shapes with multiplicity and hadron mass shows patterns that are similar to those observed in $p$-Pb and Pb-Pb collisions at Large Hadron Collider energies. The obtained $p$ T distributions and yields are compared to expectations from QCD-based $pp$ event generators as well as to predictions from thermal and hydrodynamic models. These comparisons indicate that traces of a collective, equilibrated system are already present in high-multiplicity $pp$ collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hexadecapole strength in the rare isotopes 74,76 Kr

In the Ge-Sr mass region, isotopes with neutron number N ≤ 40 are known to feature rapid shape changes with both nucleon number and angular momentum. To gain new insights into their structure, inelastic proton scattering experiments in inverse kinematics were performed on the rare isotopes 74,76 Kr. This work focuses on observables related to the J π = $4$$^{+}_{1}$ states of the Kr isotopes and, in particular, on the hexadecapole degree of freedom. By performing coupled-channels calculations, hexadecapole deformation parameters β 4 were determined for the J π = $4$$^{+}_{1}$ states of 74,76 Kr from inelastic proton scattering cross sections. Two possible coupled-channels solutions were found. A comparison to predictions from nuclear energy density functional theory, employing both non-relativistic and relativistic functionals, clearly favors the large, positive β 4 solutions. These β 4 values are unambiguously linked to the well deformed prolate configuration. Given the β 2 - β 4 trend, established in this work, it appears that β 4 values could provide a sensitive measure of the nuclear shell structure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Comprehensive Stress Drop Map From Trench to Depth in the Northern Chilean Subduction Zone

We compute stress drops for earthquakes in Northern Chile recorded between 2007 and 2021. By applying two analysis techniques, (a) the spectral ratio (SR) method and (b) the spectral decomposition (SDC) method, a stress drop map for the subduction zone consisting of 51,510 stress drop values is produced. We build an extended set of empirical Green’s functions (EGF) for the SR method by systematic template matching. Outputs are used to compare with results from the SDC approach, where we apply cell-wise obtained global EGF's to compensate for the structural heterogeneity of the subduction zone. We find a good consistency of results of the two methods. The increased spatial coverage and quantity of stress drop estimates from the SDC method facilitate a consistent stress drop mapping of the different seismotectonic domains. Albeit only small differences of median stress drop, strike-perpendicular depth sections clearly reveal systematic variations, with earthquakes at different seismotectonic locations exhibiting distinct values. In particular, interface seismicity is characterized by the lowest observed median value, whereas upper plate earthquakes show noticeably higher stress drop values. Intermediate depth earthquakes show comparatively high average stress drop and a rather strong depth-dependent increase of median stress drop. Additionally, we observe spatio-temporal variability of stress drops related to the occurrence of the two megathrust earthquakes in the study region. The presented study is the first coherent large scale 3D stress drop mapping of the Northern Chilean subduction zone. It provides an important component for further detailed analysis of the physics of earthquake ruptures.

58 GEOSCIENCES↗

The frequency-dependent response of single aerosol particles to vapour phase oscillations and its application in measuring diffusion coefficients

A new method for measuring diffusion in the condensed phase of single aerosol particles is proposed and demonstrated. The technique is based on the frequency-dependent response of a binary particle to oscillations in the vapour phase of one of its chemical components. Here, we discuss how this physical situation allows for what would typically be a non-linear boundary value problem to be approximately reduced to a linear boundary value problem. For the case of aqueous aerosol particles, we investigate the accuracy of the closed-form analytical solution to this linear problem through a comparison with the numerical solution of the full problem. Then, using experimentally measured whispering gallery modes to track the frequency-dependent response of aqueous particles to relative humidity oscillations, we determine diffusion coefficients as a function of water activity. The measured diffusion coefficients are compared to previously reported values found using the two common experiments: (i) the analysis of the sorption/desorption of water from a particle after a step-wise change to the surrounding relative humidity and (ii) the isotopic exchange of water between a particle and the vapour phase. The technique presented here has two main strengths: first, when compared to the sorption/desorption experiment, it does not require the numerical evaluation of a boundary value problem during the fitting process as a closed-form expression is available. Second, when compared to the isotope exchange experiment, it does not require the use of labeled molecules. Therefore, the frequency-dependent experiment retains the advantages of these two commonly used methods but does not suffer from their drawbacks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Measurement of the infrared optical constants for spectral modeling: n and k values for (NH4)2SO4 via single-angle reflectance and ellipsometric methods

The optical constants n and k can be used to model infrared spectra, including refraction, absorption, reflectance, and emissivity, but obtaining reliable values for solid materials (pure or otherwise) presents a challenge: In the past, the best results for n and k have been obtained from bulk, homogeneous materials, free of defects. That is, materials where the Fresnel equations are operant since there is no light scattering. Since it is often not possible to obtain a pure macroscopic (crystalline) material, it may be possible to press the material into a (uniform, void-free) disk. We have recently been able to do this with ammonium sulfate powder and then measured the n & k values via two independent methods: 1) Ellipsometry - which measures the changes in amplitude and phase of light reflected from the material of interest as a function of wavelength and angle of incidence, and 2) Single angle specular reflectance with an FT spectrometer using a specular reflectance device within an FT instrument which measures the change in amplitude of light reflected from the material of interest as a function of wavelength and angle of incidence over a wide wavelength range. The quality of the derived n & k values was tested by generating the reflectance spectra of the pellet and comparing to the calculated to measured reflectance spectra of the pure material which has been previously published. The comparison to literature values showed good accuracy and good agreement, indicating promise to measure other materials by such methods.

ammonium sulfate↗