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We report the complete genome sequence of Acidithiobacillus ferriphilus GT2, an acidophile isolated from gold mill tailings. The circular genome of GT2 contains 2,489 predicted protein-coding units and a single plasmid. Functional analysis indicates the metabolic potential to oxidize iron and reduced sulfur compounds and to fix N 2 and CO 2 .
Dynamical Components Analysis is a Python implementation of the method described in "Unsupervised discovery of temporal structure in noisy data with dynamical components analysis". It implements the method as well as related data analysis functions.
Dynamical Components Analysis is a Python implementation of the method described in "Unsupervised discovery of temporal structure in noisy data with dynamical components analysis". It implements the method as well as related data analysis functions.
SAND2026-23986O EFBMC performs elastic Bayesian model calibration by applying Bayesian statistics and functional analysis. The software provides Python, R, and MATLAB scripts that enable users to calibrate models. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
The data presented herein is inelastic neutron scattering data at Ei=150 meV appropriate for dynamic pair distribution function analysis. The data is an nxspe format which is an hdf5 file following the nexus standard.
Solar materials convert light into other forms of energy through excited state processes occurring on ultrafast time and atomic length scales. Understanding and controlling such nonequilibrium processes is essential for applications ranging from photovoltaics to photocatalysis. These processes are commonly studied by transient optical techniques, which resolve charge carrier dynamics. However, optical spectroscopy does not directly probe the atomic-scale motions that play a central role in the ultimate functionality of these materials. Filling this missing gap, ultrafast electron and x-ray scattering techniques enable monitoring of structural dynamics in materials with femtosecond time resolution. In this work, we focus on the use of ultrafast electron diffraction (UED) techniques to probe photoinduced energy conversion dynamics in solar energy materials. First, we discuss the use of UED as an ultrafast lattice thermometer allowing a direct probe of nonradiative relaxations such as hot carrier cooling and Auger recombination. Second, we present a time-resolved atomic pair distribution function analysis enabled by UED, which uncovers lattice deformations arising from excitation localization in materials. Finally, we provide an outlook looking toward new approaches for resolving in situ energy conversion dynamics and uncovering structure–property relationships in solar energy materials.
We have developed and applied methods of large-scale structure from galaxy redshift surveys to the study of dark energy. This program supported my group's development of the baryon acoustic method and our participation in the Dark Energy Spectroscopic Instrument (DESI) survey. In addition to my leadership role in the DESI collaboration, my group at Harvard focused on several topics addressing key needs of the DESI science program. 1) We continued our design, validation, and documentation of DESI target selection of the luminous red galaxy and emission-line galaxy samples. 2) We applied simulations from our novel and extremely fast N-body code to make DESI catalogs. With these, we will search for possible systematic shifts in the acoustic scale due to clustering bias with an unprecedented volume of simulations. 3) We extended our method for the fast construction of covariance matrices for correlation functions. 4) We developed new large-scale structure methods, including density-field reconstruction and three-point function analysis.
Between 2017 and 2019, a series of injection tests were performed at pilot vertical well 58-32 at the Utah FORGE site. These injection activities were conducted in three distinct zones, isolated with packers and bridge plugs during the tests. Zone 1 consists of an open-hole section at the toe of the well, whereas Zones 2 and 3 are three-meter long cased and perforated sections. Several injection cycles were conducted in each zone. A detailed description of the geology of the FORGE site, of well 58-32 and of all injection cycles can be found in (Xing et al., 2020). The injection cycles included Diagnostic Fracture Injection Tests (DFITs). DFITs comprise two primary stages: an injection (pump-in) phase, where controlled fluid injection is employed to create a small hydraulic fracture in the surrounding rock, followed by a shut-in phase, where injection ceases, allowing observation of the formation’s pressure response. Utilizing methodologies such as the G-function analysis, DFITs provide valuable insights, including fracture closure pressure and the Instantaneous Shut-in Pressure (ISIP) and can be employed to estimate the minimum horizontal stress.
The Fixed-Energy Response-Function Analysis with Multiple Efficiency (FRAM) code was developed at Los Alamos National Laboratory to measure the gamma-ray spectrometry of the isotopic composition of plutonium, uranium, and other actinides. For FRAM versions 4 and earlier, the reported uncertainties of the results come from the propagation of the statistics in the peak areas only. No systematic error components are included in the reported uncertainties. For FRAM versions 5 and 6, we examined the FRAM analytical results of both the archival plutonium data and the data specifically acquired for the isotopic uncertainty analysis project and found the relationship between the bias and other parameters. We worked out the equations representing the biases of the measured isotopes from each measurement using internal spectral parameters, such as peak resolution and shape, region of analysis, and burnup (for plutonium) or enrichment (for uranium). The resulting biases were included in the reported uncertainties of FRAM v.5 and v.6.
Fixed-energy Response-function Analysis with Multiple efficiency (FRAM) is a software code designed primarily for plutonium and uranium isotopic analysis. It is widely used in both the domestic and international safeguards community. FRAM can quickly and accurately determine the isotopic compositions of plutonium, uranium, and mixed oxides (MOX) when measuring with a high-purity germanium (HPGe), cadmium zinc telluride (CZT), or lanthanum bromide (LaBr3) detector. The capabilities of FRAM have been enhanced to analyze the data of the pixelated CZT detector (made by H3D) and to measure the mass of plutonium, uranium, and MOX. Both the isotopic composition and mass of the item can be quickly determined with one measurement using a gamma detector with FRAM v.7.1.
Characterizing in situ stress is essential in Enhanced Geothermal System (EGS) for both risk assessment and operation design. Standard stress measurement techniques such as diagnostic fracture injection tests (DFITs) require creating hydraulic fractures and apply analytical methods such as the G -function analysis to estimate the stress. These classical approaches rely on several assumptions, including but not limited to: (i) the induced fracture is planar and persistent, and (ii) the fracture plane is normal to the minimum horizontal stress. However, these assumptions may not hold in EGS environments like Utah FORGE, where thermo-hydro-mechanical (THM) coupling, wellbore deviation, and rock heterogeneity can alter the local stress condition and consequently lead to fracture complexities in both near-well and far-field regions.
Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design. However, few user-friendly tools leveraging the latest deep learning technology for inter-chain contact prediction and the distance-based modelling to predict protein quaternary structures are available. To address this gap, we develop DeepComplex, a web server for predicting structures of dimeric protein complexes. It uses deep learning to predict inter-chain contacts in a homodimer or heterodimer. The predicted contacts are then used to construct a quaternary structure of the dimer by the distance-based modelling, which can be interactively viewed and analysed. The web server is freely accessible and requires no registration. It can be easily used by providing a job name and an email address along with the tertiary structure for one chain of a homodimer or two chains of a heterodimer. The output webpage provides the multiple sequence alignment, predicted inter-chain residue-residue contact map, and predicted quaternary structure of the dimer.
Here, we employ a combination of advanced synchrotron-based scattering characterization techniques to understand and unravel the atomic origins of the colossal stored energy release in neutron irradiated silicon carbide. The quantification of the neutron irradiation-induced defects, and their impact on the structureproperty relationship is important for the design and safe operation of advanced fission and fusion reactors. Our experimental results show that the atomic structure in the as irradiated samples is significantly perturbed due to a large fraction of vacancy and interstitial type defects that lead to complex microstructures and additional components in the x-ray diffraction and pair distribution function results. We directly correlate the stored energy release to the recovery of the sub-lattices, with pair distribution function analysis highlighting that the carbon interstitial and vacancy-type defects contribute to stored energy more than those of silicon. We find these results to be striking and believe our discoveries to be timely and noteworthy given the technological importance of silicon carbide to the nuclear fission and fusion communities.
While we have made significant progress in probing nuclear structure at low Bjorken x and high Q 2 , we still have gaps in our knowledge regarding the high Bjorken x and intermediate Q 2 kinematic region. This is not an accident, but instead due to the diffculty in assessing the non-perturbative region of nuclear physics. For this reason, the E12-10-002 experiment measured the H(e,e') and D(e,e') inclusive cross section in the resonance region. This will allow us to study both perturbative and non-perturbative physics in a kinematic region that lacks precision measurements. Measurements were made up to a Bjorken x of 0.99 and Q 2 up to 17 GeV 2 . These measurements are made using the independent HMS and SHMS spectrometers at the upgraded beam energy of 11 GeV in Hall C at Jefferson Lab. Further, we extract F 2 structure functions from the measured data and study the effect of their inclusion in a global Parton Distribution Function analysis.
Disclosed herein are barcoded expression libraries comprising a plurality of expression vectors, wherein each expression vector comprises a nucleic acid fragment flanked by a first barcode and a second barcode. Further disclosed herein are methods of making the barcoded expression libraries and methods of conducting functional analysis using the barcoded expression libraries.
We make use of individual (epoch) detection data from the Pan-STARRS “3π” survey for 2863 optical ICRF3 counterparts in the five wavelength bands g, r, i, z, and y, published as part of the Data Release 2. A dedicated method based on the Functional Principal Component Analysis is developed for these sparse and irregularly sampled data. With certain regularization and normalization constraints, it allows us to obtain uniform and compatible estimates of the variability amplitudes and average magnitudes between the passbands and objects. We find that the starting assumption of affinity of the light curves for a given object at different wavelengths is violated for several percent of the sample. The distributions of rms variability amplitudes are strongly skewed toward small values, peaking at ∼0.1 mag with tails stretching to 2 mag. Statistically, the lowest variability is found for the r band and the largest for the reddest y band. A small “brighter-redder” effect is present, with amplitudes in y greater than amplitudes in g in 57% of the sample. The variability versus redshift dependence shows a strong decline with z toward redshift 3, which we interpret as the time dilation of the dominant time frequencies. The colors of radio-loud ICRF3 quasars are correlated with redshift in a complicated, wavy pattern governed by the emergence of brightest emission lines within the five passbands.
The Gaia optical reference frame is intrinsically undefined with respect to global orientation and spin, so it needs to be anchored in the radio-based International Celestial Reference Frame (ICRF) to provide a referenced and quasi-inertial celestial coordinate system. The link between the two fundamental frames is realized through two samples of distant extragalactic sources, mostly active galactic nuclei and quasars, but only the smaller sample of radio-loud ICRF sources with optical counterparts is available to determine the mutual orientation. The robustness of this link can be mathematically formulated in the framework of functional principal component analysis using a set of vector spherical harmonics to represent the differences in celestial positions of the common objects. The weakest eigenvectors are computed, which describe the greatest deficiency of the link. The deficient or poorly determined terms are specific vector fields on the sphere that carry the largest errors of absolute astrometry using Gaia in reference to the ICRF. This analysis provides guidelines for the future development of the ICRF maximizing the accuracy of the link over the entire celestial sphere. A measure of the robustness of a least-squares solution, which can be applied to any linear model fitting problem, is introduced to help discriminate between reference frame tie models of different degrees.
Goals: What is Analysis of Variance (ANOVA); Extending Analysis of Variance to Function Data (F-ANOVA); The role of stochastic processes in F-ANOVA; One and Two Sample Problems for F-ANOVA; One-Way F-ANOVA.