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For E. coli, C. thermocellum, Z. mobilis: shotgun proteomics analyses of tryptic digests of cell lysates; direct infusion of cell lysates spiked with isotopically labelled peptides to perform absolute quantification of specific proteins of interest, primarily related to glycolysis
Abstract Monitoring and understanding the variability of heat within cities is important for urban planning and public health, and the number of studies measuring intraurban temperature variability is growing. Recognizing that the physiological effects of heat depend on humidity as well as temperature, measurement campaigns have included measurements of relative humidity alongside temperature. However, the role the spatial structure in humidity, independent from temperature, plays in intraurban heat variability is unknown. Here we use summer temperature and humidity from networks of stationary sensors in multiple cities in the United States to show spatial variations in the absolute humidity within these cities are weak. This variability in absolute humidity plays an insignificant role in the spatial variability of the heat index and humidity index (humidex), and the spatial variability of the heat metrics is dominated by temperature variability. Thus, results from previous studies that considered only intraurban variability in temperature will carry over to intraurban heat variability. Also, this suggests increases in humidity from green infrastructure interventions designed to reduce temperature will be minimal. In addition, a network of sensors that only measures temperature is sufficient to quantify the spatial variability of heat across these cities when combined with humidity measured at a single location, allowing for lower-cost heat monitoring networks. Significance Statement Monitoring the variability of heat within cities is important for urban planning and public health. While the physiological effects of heat depend on temperature and humidity, it is shown that there are only weak spatial variations in the absolute humidity within nine U.S. cities, and the spatial variability of heat metrics is dominated by temperature variability. This suggests increases in humidity will be minimal resulting from green infrastructure interventions designed to reduce temperature. It also means a network of sensors that only measure temperature is sufficient to quantify the spatial variability of heat across these cities when combined with humidity measured at a single location.
Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling many of the practical aspects regarding the preparation of the different thermodynamic end states of complex molecular systems and the numerous processing scripts often remains a burden for successful applications. Here, we present CHARMM-GUI Free Energy Calculator (http://www.charmm-gui.org/input/fec) that provides various alchemical free energy perturbation molecular dynamics (FEP/MD) systems with input and post-processing scripts for NAMD and GENESIS. Four submodules are available: Absolute Ligand Binder (for absolute ligand binding FEP/MD), Relative Ligand Binder (for relative ligand binding FEP/MD), Absolute Ligand Solvator (for absolute ligand solvation FEP/MD), and Relative Ligand Solvator (for relative ligand solvation FEP/MD). Each module is designed to build multiple systems of a set of selected ligands at once for high-throughput FEP/MD simulations. The capability of Free Energy Calculator is illustrated by absolute and relative solvation FEP/MD of a set of ligands and absolute and relative binding FEP/MD of a set of ligands for T4-lysozyme in solution and the adenosine A 2A receptor in a membrane. The calculated free energy values are overall consistent with the experimental and published free energy results (within ~1 kcal/mol). We hope that Free Energy Calculator is useful to carry out high-throughput FEP/MD simulations in the field of biomolecular sciences and drug discovery.
The absolute light yield of a scintillator, defined as the number of scintillation photons produced per unit energy deposited, is a useful quantity for scintillator development, research, and applications. Yet, literature data on the absolute light yield of organic scintillators are limited. The goal of this work is to assess the suitability of the EJ-204 plastic scintillator from Eljen Technology to serve as a reference standard for measurements of the absolute light yield of organic scintillators. Four EJ-204 samples were examined: two manufactured approximately four months prior and stored in high-purity nitrogen, and two aged approximately eleven years and stored in ambient air. The scintillator response was measured using a large-area avalanche photodiode calibrated using low energy $γ$-ray and X-ray sources. The product of the quantum efficiency of the photodetector and light collection efficiency of the housing was characterized using an experimentally-benchmarked optical photon simulation. The average absolute light yield of the fresh samples, 9100 ± 400 photons per MeV, is lower than the manufacturer-reported value of 10400 photons per MeV. Moreover, the aged samples demonstrated significantly lower light yields, deviating from the manufacturer specification by as much as 26%. These results are consistent with recent work showcasing environmental aging in plastic scintillators and suggest that experimenters should use caution when deploying plastic scintillators in photon counting applications.
Neutral particle control is critical for fusion fueling and confinement. Neutral diagnostics for fusion-relevant plasmas are commonly restricted to line-integrated or ex situ methods. A non-perturbative, two-photon absorption laser induced fluorescence (TALIF) diagnostic is implemented on the Prototype Material Plasma Exposure eXperiment (Proto-MPEX) to probe neutral atomic deuterium in a fusion-relevant plasma at 1 cm intervals along the radius of the vacuum vessel. The diagnostic is situated ~20 m from the vacuum vessel, and a signal is collected along the laser injection axis, requiring only one line-of-sight. TALIF measurements are absolutely calibrated using xenon and krypton. Absolute atomic densities derived from xenon calibration are compared to absolute atomic densities derived from krypton calibration. In this work, preliminary measurements of absolute atomic deuterium density, temperature, and local bulk flow dependence on radial location and input power in Proto-MPEX are presented. Neutral atomic deuterium velocity distribution functions are measured throughout a one-second plasma pulse with a time resolution of 250 ms.
The Resolve microcalorimeter spectrometer on the X-ray Imaging and Spectroscopy Mission (XRISM) is designed to have a good timing capability with the mission-level requirement of 1 ms as the absolute time tagging accuracy to suffice the needs for observatory science. In the ground calibration campaign, the absolute and relative timing offsets were measured using pulsed X-rays from the modulated X-ray sources. These offsets were used to determine calibration parameters, the Resolve timing coefficients, which are used in the offline correction of event times. In the orbit, reevaluation of the timing coefficients was carried out using the Crab pulsar, which was observed in two periods, one in the performance verification phase and the other in the guest observation phase. We report the absolute timing calibration of XRISM/Resolve using the ground and in-orbit data. Although the requirement is likely satisfied with the ground parameters, the timing coefficients have been refined using the in-orbit calibration to improve the timing accuracy. In addition, for the first time, we present the interpretation of the absolute timing offset originating from the analog and digital processing of X-ray events unique to a microcalorimeter spectrometer and present a complete view of the timing error of the Resolve instrument.
At the Large Hadron Collider (LHC), absolute luminosity calibrations obtained by the van der Meer (vdM) method are affected by the mutual electromagnetic interaction of the two beams. The colliding bunches experience relative orbit shifts, as well as optical distortions akin to the dynamic-β effect, that both depend on the transverse beam separation and must therefore be corrected for when deriving the absolute luminosity scale. In the vdM regime, the beam–beam parameter is small enough that the orbit shift can be calculated analytically. The dynamic-β corrections to the luminometer calibrations, however, had until the end of Run 2 been estimated in the linear approximation only. In this report, the influence of beam–beam effects on the vdM-based luminosity scale is quantified, together with the associated systematic uncertainties, by means of simulations that fully take into account the non-linearity of the beam–beam force, as well as the resulting non-Gaussian distortions of the transverse beam distributions. Two independent multiparticle simulations, one limited to the weak-strong approximation and one that models strong-strong effects in a self-consistent manner, are found in excellent agreement; both predict a percent-level shift of the absolute pp-luminosity values with respect to those assumed until recently in the physics publications of the LHC experiments. These results also provide guidance regarding further studies aimed at reducing the beam–beam-related systematic uncertainty on beam–beam corrections to absolute luminosity calibrations by the van der Meer method.
A method to reveal low temperature absolute internal quantum efficiency of an InGaN-based light-emitting diode (LED) is reported. Structural (via scanning electron and atomic force microscopies, x-ray diffraction, and Raman spectroscopy) and optical (via temperature- and power-dependent photoluminescence) properties of InGaN-based blue LEDs are coupled with a channel-based recombination model, which reveals the low temperature absolute internal quantum efficiency of the LED on traditional sapphire and emerging Si (111) substrates as 27.5% and 71.1%, respectively. High low-temperature absolute internal quantum efficiency of the former is attributed to its lower defect density and less strain. Furthermore, our results show assuming perfect (i.e., 100%) internal quantum efficiency in an InGaN-based LED at low temperatures could be misleading, and using negative thermal quenching properties of defect luminesce bands with a channel-based recombination model can be a method to quantify LED's less than ideal low temperature internal quantum efficiencies.
Resonant soft X-ray scattering (RSOXS) has become a premier probe to study complex three-dimensional nanostructures in soft matter through combining the robust structural characterization of small-angle scattering with the chemical sensitivity of spectroscopy. This technique borrows many of its analysis methods from alternative small-angle scattering measurements that utilize contrast variation, but thus far RSOXS has been unable to reliably achieve an absolute scattering intensity required for quantitative analysis of domain compositions, volume fraction, or interfacial structure. Here, a novel technique to calibrate RSOXS to an absolute intensity at the carbon absorption edge is introduced. It is shown that the X-ray fluorescence from a thin polymer film can be utilized as an angle-independent scattering standard. Verification of absolute intensity is then accomplished through measuring the Flory–Huggins interaction parameter in a phase-mixed polymer melt. As a result, the necessary steps for users to reproduce this intensity calibration in their own experiments to improve the scientific output from RSOXS measurements are discussed.
Rationale: Spatially resolved and accurate quantitation of drug-related compounds in tissue is a much-needed capability in drug discovery research. In this work, application of an integrated laser ablation-dropletProbe-mass spectrometry surface sampling system (LADP-MS) is reported, which achieved absolute quantitation of propranolol measured from <500 × 500 μm thin tissue samples. Methods: Mouse liver and kidney thin tissue sections were coated with parylene C and analyzed for propranolol by a laser ablation/liquid extraction workflow. Non-coated adjacent sections were microdissected for validation and processed using standard bulk tissue extraction protocols. High-performance liquid chromatography with positive ion mode electrospray ionization tandem mass spectrometry was applied to detect the drug and its metabolites. Results: Absolute propranolol concentration in ~500 × 500 μm tissue regions measured by the two methods agreed within ±8% and had a relative standard deviation within ±17%. Quantitation down to ~400 × 400 μm tissue regions was shown, and this resolution was also used for automated mapping of propranolol and phase II hydroxypropranolol glucuronide metabolites in kidney tissue. Conclusions: This study exemplifies the capabilities of integrated laser ablation-dropletProbe-mass spectrometry (LADP-MS) for high resolution absolute drug quantitation analysis of thin tissue sections. This capability will be valuable for applications needing to quantitatively understand the spatial distribution of small molecules in tissue.
Accurate nuclear data for the decay of 231 Pa is highly important for non-destructive analysis in the areas of radiochronometry and nuclear forensics. However, the evaluated nuclear data for this isotope is lacking; many previous measurements have large uncertainties and only two measurements are used to determine the absolute intensities. In this work, we present modern measurements of the major gamma-ray emissions from the decay of 231 Pa to 227 Ac including the energies and absolute intensities. For many of these measurements, the error envelopes have been significantly decreased compared to previous measurements, while remaining in good agreement. The absolute intensity of the 283 keV reference line was measured as 0.0163(2).
Process-based models have been widely used for hydrologic modeling, and it is a common practice to use sensitivity analysis methods for excluding non-influential hydrologic processes from further investigation and/or model improvement. This study develops a new method called multi-model absolute difference-based sensitivity (MMADS) analysis method to screen non-influential system processes and parameters. MMADS is conceptually similar to the Morris method for addressing parametric uncertainty, but has a unique feature to address both process model uncertainty (i.e., a process may be represented by multiple process models) and process model parameter uncertainty (i.e., parameters associated with a process model are random). MMADS first evaluates absolute differences of a quantity of interest (i.e., a system model output) by varying process models and/or process model parameter values, and then calculates the mean and variance of the differences for investigating process influence. The mean measures overall influence of the process on the quantity of interest, and the variance estimates influence of nonlinear effects of the process and/or its interactions with other processes. MMADS is an extension of the Morris method from a parameter space to a joint parameter-model space for explicitly addressing both process model uncertainty and model parameter uncertainty. The performance of MMADS is evaluated by using two numerical experiments. One experiment is based on Sobol’s G*-function with ten product elements, and has analytical solutions of the MMADS mean and variance of absolute differences. The other experiment is for groundwater flow modeling which considers three processes (i.e., recharge, geology, and snowmelt) that interact with each other. Finally, results indicate that MMADS is computationally efficient and can identify non-influential processes of complex hydrological systems.
Context: We use the phase curves of small bodies to measure absolute magnitudes and, together with complementary theoretical and laboratory results, to understand the micro- and macroscopic properties of their surfaces. Although we can observe asteroids up to phase angles of about 30 deg, the range of phase angles covered by outer Solar System objects usually does not go further than 7-10 deg for centaurs and 2 deg for trans-Neptunian objects, and a linear relation between magnitude and phase angle may be assumed. Aims: We aim to directly compare data taken for objects in the inner Solar System (inside the orbit of Jupiter) with data for centaurs and trans-Neptunian objects. Methods: We use the SLOAN Moving Objects Catalog (MOC) data to construct phase curves restricted to phase angles of less than or equal to 7.5 deg, which is compatible with the angles observed for the trans-Neptunian and Centaur population. We assume a linear model for the photometric behavior to obtain absolute magnitudes and phase coefficients in the ugirz, V, and R filters. Results: We obtain absolute magnitudes in seven filters for over 4000 objects. Our comparison with outer Solar System objects suggests the surfaces have a common property: intrinsically redder objects become blue with increasing phase angle, while the opposite happens for intrinsically bluer objects.
Here, thresholds for the absolute stimulated Raman scattering (SRS) and two-plasma decay (TPD) instabilities driven by multiple broadband laser beams are evaluated using 3-D simulations at conditions relevant to inertial confinement fusion experiments. Multibeam TPD and SRS backscatter are found to be easier to mitigate with bandwidth than the corresponding single-beam instabilities. A relative bandwidth of 1% increases the threshold for absolute SRS backscatter by a factor of 4 at conditions relevant to ongoing National Ignition Facility experiments and should be sufficient to keep all of the absolute instabilities below threshold in experiments with similar conditions.
The LLAMA (Lyman-Alpha Measurement Apparatus) diagnostic was recently installed on the DIII-D tokamak [Rosenthal et al., Rev. Sci. Instrum. (submitted) (2020)]. LLAMA is a pinhole camera system with a narrow band Bragg mirror, a bandpass interference filter, and an absolute extreme ultraviolet photodiode detector array, which measures the Ly-α brightness in the toroidal direction on the inboard, high field side (HFS) and outboard, low field side (LFS). This contribution presents a setup and a procedure for an absolute calibration near the Ly-α line at 121.6 nm. The LLAMA in-vacuum components are designed as a compact, transferable setup that can be mounted in an ex situ vacuum enclosure that is equipped with an absolutely calibrated Ly-α source. The spectral purity and stability of the Ly-α source are characterized using a vacuum ultraviolet spectrometer, while the Ly-α source brightness is measured by a NIST-calibrated photodiode. The non-uniform nature of the Ly-α source emission was overcome by performing a calibration procedure that scans the Ly-α source position and employs a numerical optimization to determine the emission pattern. Nominal and measured calibration factors are determined and compared, showing agreement within their uncertainties. A first conversion of the measured signal obtained from DIII-D indicates that the Ly-α brightness on the HFS and LFS is on the order of 1020 Ph sr-1 m-2 s-1. The established calibration setup and procedure will be regularly used to re-calibrate the LLAMA during DIII-D vents to monitor possible degradation of optical components and detectors.
We present details of a high-accuracy absolute scalar magnetometer based on pulsed proton NMR. The B-field magnitude is determined from the precession frequency of proton spins in a cylindrical sample of water after accounting for field perturbations from probe materials, sample shape, and other corrections. Features of the design, testing procedures, and corrections necessary for qualification as an absolute scalar magnetometer are described. The device was tested at B = 1.45 T but can be modified for a range exceeding 1–3 T. The magnetometer was used to calibrate other NMR magnetometers and measure absolute magnetic field magnitudes to an accuracy of 19 parts per billion as part of a measurement of the muon magnetic moment anomaly at Fermilab.
High precision CCD observations of six totally eclipsing contact binaries were presented and analyzed. It is found that only one target is an A-type contact binary (V429 Cam), while the others are W-type contact ones. By analyzing the times of light minima, we discovered that two of them exhibit secular period increase while three manifest long-term period decrease. For V1033 Her, a cyclic variation superimposed on the long-term increase was discovered. By comparing the Gaia distances with those calculated by the absolute parameters of 173 contact binaries, we found that the Gaia distance can be applied to estimate the absolute parameters for most contact binaries. The absolute parameters of our six targets were estimated using their Gaia distances. The evolutionary status of contact binaries was studied, and we found that the A- and W-subtype contact binaries may have different formation channels. The relationship between the spectroscopic and photometric mass ratios for 101 contact binaries was presented. It was discovered that the photometric mass ratios are in good agreement with the spectroscopic ones for almost all of the totally eclipsing systems, which is corresponding to the results derived by Pribulla et al. and Terrell & Wilson.
Skipper-CCD can achieve deep sub-electron readout noise making possible the absolute determination of the exact number of ionized electrons in a large range, from 0 to above 1900 electrons. In this work we present a novel technique that exploits this unique capability to allow self-calibration and the ultimate determination of silicon properties. We performed an absolute measurement of the variance and the mean number of the charge distribution produced by $^{55}$Fe X-rays, getting a Fano factor absolute measurement in Si at 123K and 5.9 keV. A value of 0.119 $\pm$ 0.002 was found and the electron-hole pair creation energy was determined to be (3.749 $\pm$ 0.001) eV. This technology opens the opportunity for direct measurements of the Fano factor at low energies.