Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model
YPS1009-derivative strain genome assembly in NCBI, BioProject
aneuploidy↗
SEARCH · Engineering Papers
Results for “Model fitting”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model
gene duplication screen raw sequencing and barcode counts, on GEO
aneuploidy↗
Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps
Abstract Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and fitting into cryo-EM maps. In this work, we designed a protein model-building workflow, which combines a deep-learning cryo-EM map feature enhancement tool, CryoFEM (Cryo-EM Feature Enhancement Model) and AlphaFold. A benchmark test using 36 cryo-EM maps shows that CryoFEM achieves state-of-the-art performance in optimizing the Fourier Shell Correlations between the maps and the ground truth models. Furthermore, in a subset of 17 datasets where the initial AlphaFold predictions are less accurate, the workflow significantly improves their model accuracy. Our work demonstrates that the integration of modern deep learning image enhancement and AlphaFold may lead to automated model building and fitting for the atomistic interpretation of cryo-EM maps.
59 BASIC BIOLOGICAL SCIENCES↗
Theoretical justification for heat flux limiter 0.15
In this section, we describe a semi-nonlocal kinetic model for the electron heat flux. The model has no free parameters. It takes the more physically motivated approach of placing a limiter on the perturbation to the electron distribution function, rather than the usual ad-hoc limiter on the heat flux. If the kinetic model is fitted by a heat flux limiter model, we find that the higher value of f e = 0.15 is a much closer fit than other models with f e ≃ 0.02.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
OPTICAL SPECTROSCOPY OF SDSS J004054.65-0915268: THREE POSSIBLE SCENARIOS FOR THE CLASSIFICATION. A z ∼ 5 BL LACERTAE, A BLUE FSRQ, OR A WEAK EMISSION LINE QUASAR
The haunt of high-redshift BL Lacerate objects is day by day more compelling to firmly understand their intrinsic nature and evolution. SDSS J004054.65-0915268 is, at the moment, one of the most distant BL Lac candidates, at z ∼ 5. We present a new optical-near-IR spectrum obtained with ALFOSC-NOT with a new, custom designed dispersive grating aimed to detect broad emission lines that could disprove this classification. In the obtained spectra, we do not detect any emission features and we provide an upper limit to the luminosity of the C iv broad emission line. Therefore, the nature of the object is then discussed, building the overall spectral energy distribution (SED) and fitting it with three different models. Our fits, based on SED modeling with different possible scenarios, cannot rule out the possibility that this source is indeed a BL Lac object, though the absence of optical variability and the lack of strong radio flux seem to suggest that the observed optical emission originates from a thermalized accretion disk.
79 ASTRONOMY AND ASTROPHYSICS↗
Training material models using gradient descent algorithms
High temperature design requires accurate constitutive models to describe material inelastic deformation and failure behavior. Oftentimes, calibrating accurate models devolves into the problem of fitting the model parameters against experimental test data. Here, we present the pyopmat package, an open source framework for calibrating constitutive models against experiment data subjected to various loading conditions using machine learning techniques. The package calculates the exact gradient of the model response with respect to the parameters using a combination of automatic differentiation and the adjoint method. Given this exact gradient, we compare the performance of several gradient-based optimization techniques in fitting realistic constitutive models against data. Here, we demonstrate the efficiency and accuracy of our package through example problems using both synthetic data, generated using known parameter sets, under monotonic and cyclic loading conditions and also with an example applying the techniques developed here to actual high temperature creep-fatigue test data.
36 MATERIALS SCIENCE↗
ML Pipeline (Machine Learning Pipeline) [SWR-22-35]
The Machine Learning Pipeline (ML Pipeline) allows the user to fit a model to predict a dependent variable, y, based on a feature set, X. ML Pipeline gives the ability to automatically generate features with its Feature Engineering function, automatically select the most important features with its Feature Selection function, fit the model with its Fit function, and evaluate the model with its Evaluate function. ML Pipeline's functionality can not only help the user predict values for the desired variable it also gives the user a better understanding of which features are important and how effective the model is. ML Pipeline accomplishes all this, while remaining simple to use and interpret.
Schiek, Andrew↗
Fourier-like Thermal Relaxation of Nanoscale Explosive Hot Spots
Hot spots are local regions of high temperature that are widely considered to govern explosive initiation. Hot spot dynamics rests on a delicate balance between heat generation due to chemical reactions and heat loss through thermal conduction, making accurate determinations of the conductivity under extreme conditions a key component of predictive explosive models. We develop here an approach to directly determine the thermal transport properties of explosive hot spots with realistic initial structures through a combination of molecular dynamics (MD) and diffusive heat equation (HEq) modeling. Effective thermal conductivity values are determined by fitting HEq models to MD predictions of long timescale hot spot relaxation. The approach is applied to model hot spots in the molecular crystalline explosive 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) for a range of shock strengths and two limiting cases for impact orientation. Isotropic and anisotropic HEq models yield similar results, despite TATB exhibiting some of the largest and most anisotropic thermal conductivity values for explosive near normal conditions. The conductivity is found to be a strong function of density, which parametrically captures dependence on temperature, pressure, and material state. The associated root-mean-square errors of the fitted HEq models are approximately 5% of MD predicted final equilibrium temperatures. Here, the conductivity values determined here for TATB hot spots are considerably larger than those used in a prior hot spot criticality study, which may significantly impact predictions for critical hot spot sizes. The approach provides a convenient foundation for determining the effective thermal conductivity for hot spot problems in other explosives and directly yields information on reasonable approximations that might be taken in higher-level models for those materials.
36 MATERIALS SCIENCE↗
Measurement of the black hole mass in NGC 1332 from ALMA observations at 0.044 arcsecond resolution
We present Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 3 observations of CO(2–1) emission from the circumnuclear disk in the E/S0 galaxy NGC 1332 at 0.″044 resolution. The disk exhibits regular rotational kinematics and central high-velocity emission (±500 km s{sup −1}) consistent with the presence of a compact central mass. We construct models for a thin, dynamically cold disk in the gravitational potential of the host galaxy and black hole and fit the beam-smeared model line profiles directly to the ALMA data cube. Model fits successfully reproduce the disk kinematics out to r = 200 pc. Fitting models just to spatial pixels within projected r = 50 pc of the nucleus (two times larger than the black hole’s gravitational radius of influence), we find M{sub BH}=(6.64{sub −0.63}{sup +0.65})×10{sup 8} M{sub ⊙}. This observation demonstrates ALMA’s powerful capability to determine the masses of supermassive black holes by resolving gas kinematics on small angular scales in galaxy nuclei.
79 ASTRONOMY AND ASTROPHYSICS↗
On readout of vibrational qubits using quantum beats
Readout of the final states of qubits is a crucial step towards implementing quantum computation in experiment. Although not scalable to large numbers of qubits per molecule, computational studies show that molecular vibrations could provide a significant (factor 2–5 in the literature) increase in the number of qubits compared to two-level systems. In this theoretical work, we explore the process of readout from vibrational qubits in thiophosgene molecule, SCCl{sub 2}, using quantum beat oscillations. The quantum beats are measured by first exciting the superposition of the qubit-encoding vibrational states to the electronically excited readout state with variable time-delay pulses. The resulting oscillation of population of the readout state is then detected as a function of time delay. In principle, fitting the quantum beat signal by an analytical expression should allow extracting the values of probability amplitudes and the relative phases of the vibrational qubit states. However, we found that if this procedure is implemented using the standard analytic expression for quantum beats, a non-negligible phase error is obtained. We discuss the origin and properties of this phase error, and propose a new analytical expression to correct the phase error. The corrected expression fits the quantum beat signal very accurately, which may permit reading out the final state of vibrational qubits in experiments by combining the analytic fitting expression with numerical modelling of the readout process. The new expression is also useful as a simple model for fitting any quantum beat experiments where more accurate phase information is desired.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
HerMES: Spectral energy distributions of submillimeter galaxies at z > 4
We present a study of the infrared properties for a sample of seven spectroscopically confirmed submillimeter galaxies (SMGs) at z > 4.0. By combining ground-based near-infrared, Spitzer IRAC and MIPS, Herschel SPIRE, and ground-based submillimeter/millimeter photometry, we construct their spectral energy distributions (SEDs) and a composite model to fit the SEDs. The model includes a stellar emission component at λ{sub rest} < 3.5 μm, a hot dust component peaking at λ{sub rest} ∼ 5 μm, and cold dust component which becomes significant for λ{sub rest} > 50 μm. Six objects in the sample are detected at 250 and 350 μm. The dust temperatures for the sources in this sample are in the range of 40-80 K, and their L {sub FIR} ∼ 10{sup 13} L {sub ☉} qualifies them as hyper-luminous infrared galaxies. The mean FIR-radio index for this sample is around (q) = 2.2 indicating no radio excess in their radio emission. Most sources in the sample have 24 μm detections corresponding to a rest-frame 4.5 μm luminosity of Log{sub 10}(L {sub 4.5}/L {sub ☉}) = 11 ∼ 11.5. Their L {sub 4.5}/L {sub FIR} ratios are very similar to those of starburst-dominated SMGs at z ∼ 2. The L {sub CO} – L {sub FIR} relation for this sample is consistent with that determined for local ULIRGs and SMGs at z ∼ 2. We conclude that SMGs at z > 4 are hotter and more luminous in the FIR but otherwise very similar to those at z ∼ 2. None of these sources show any sign of the strong QSO phase being triggered.
79 ASTRONOMY AND ASTROPHYSICS↗
Glass Property-Composition Models for Support of Hanford WTP LAW Facility Operation
Current plans for the River Protection Project envision starting to vitrifying low-activity waste (LAW) by 2023 using a Direct Feed Low-Activity Waste (DFLAW) approach and subsequently using a full-pretreatment approach. The Hanford Tank Waste Treatment and Immobilization Plant (WTP) LAW Facility will be operated and controlled using a LAW glass formulation algorithm (GFA), which requires several inputs based on research and development results. LAW glass property-composition models for several product quality and processing properties are key inputs for the LAW GFA. It is envisioned that the preliminary LAW GFA discussed by Kim and Vienna (2012) will be used for commissioning and initial radioactive operations of the WTP LAW Facility under Bechtel National, Inc. using the DFLAW approach. Then, an updated LAW GFA will be developed for implementation by the WTP operating contractor that takes over after WTP LAW Facility commissioning. This report documents the enhanced LAW glass property-composition models developed for use in the updated LAW GFA. The properties for which models were developed include Product Consistency Test (PCT) response, Vapor Hydration Test (VHT) response, viscosity at 1150 °C, electrical conductivity at 1150 °C, melter SO 3 tolerance at 1150 °C, and K-3 refractory corrosion at 1208 °C. Table S.1 lists the tables in this report that contain the recommended models for each of these properties. The model types recommended include partial quadratic mixture (PQM) models for viscosity, electrical conductivity, melter SO 3 tolerance and K-3 corrosion, bias corrected PQM model (bcPQM) for PCT, and logistic PQM model for VHT. The fits of model and validation subsets were found to be well predicted by the recommended models.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Glass Property-Composition Models for Support of Hanford WTP LAW Facility Operation
Current plans for the River Protection Project envision starting to vitrifying low-activity waste (LAW) by 2023 using a Direct Feed Low-Activity Waste (DFLAW) approach and subsequently using a full-pretreatment approach. The Hanford Tank Waste Treatment and Immobilization Plant (WTP) LAW Facility will be operated and controlled using a LAW glass formulation algorithm (GFA), which requires several inputs based on research and development results. LAW glass property-composition models for several product quality and processing properties are key inputs for the LAW GFA. It is envisioned that the preliminary LAW GFA discussed by Kim and Vienna (2012) will be used for commissioning and initial radioactive operations of the WTP LAW Facility under Bechtel National, Inc. using the DFLAW approach. Then, an updated LAW GFA will be developed for implementation by the WTP operating contractor that takes over after WTP LAW Facility commissioning. This report documents the enhanced LAW glass property-composition models developed for use in the updated LAW GFA. The properties for which models were developed include Product Consistency Test (PCT) response, Vapor Hydration Test (VHT) response, viscosity at 1150 °C, electrical conductivity at 1150 °C, melter SO3 tolerance at 1150 °C, and K-3 refractory corrosion at 1208 °C. Table S.1 lists the tables in this report that contain the recommended models for each of these properties. The model types recommended include partial quadratic mixture (PQM) models for viscosity, electrical conductivity, melter SO 3 tolerance and K-3 corrosion, bias corrected PQM model (bcPQM) for PCT, and logistic PQM model for VHT. The fits of model and validation subsets were found to be well predicted by the recommended models.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
First Sagittarius A* Event Horizon Telescope Results. IV. Variability, Morphology, and Black Hole Mass
In this paper we quantify the temporal variability and image morphology of the horizon-scale emission from Sgr A*, as observed by the EHT in 2017 April at a wavelength of 1.3 mm. We find that the Sgr A* data exhibit variability that exceeds what can be explained by the uncertainties in the data or by the effects of interstellar scattering. The magnitude of this variability can be a substantial fraction of the correlated flux density, reaching ~100% on some baselines. Through an exploration of simple geometric source models, we demonstrate that ring-like morphologies provide better fits to the Sgr A* data than do other morphologies with comparable complexity. We develop two strategies for fitting static geometric ring models to the time-variable Sgr A* data; one strategy fits models to short segments of data over which the source is static and averages these independent fits, while the other fits models to the full data set using a parametric model for the structural variability power spectrum around the average source structure. Both geometric modeling and image-domain feature extraction techniques determine the ring diameter to be 51.8 ± 2.3 μas (68% credible intervals), with the ring thickness constrained to have an FWHM between ~30% and 50% of the ring diameter. To bring the diameter measurements to a common physical scale, we calibrate them using synthetic data generated from GRMHD simulations. This calibration constrains the angular size of the gravitational radius to be ${4.8}_{-0.7}^{+1.4}$ μas, which we combine with an independent distance measurement from maser parallaxes to determine the mass of Sgr A* to be ${4.0}_{-0.6}^{+1.1}\times {10}^{6}$ M⊙.
79 ASTRONOMY AND ASTROPHYSICS↗
DES14X3taz: A TYPE I SUPERLUMINOUS SUPERNOVA SHOWING A LUMINOUS, RAPIDLY COOLING INITIAL PRE-PEAK BUMP
We present DES14X3taz, a new hydrogen-poor superluminous supernova (SLSN-I) discovered by the Dark Energy Survey (DES) supernova program, with additional photometric data provided by the Survey Using DECam for Superluminous Supernovae. Spectra obtained using Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy on the Gran Telescopio CANARIAS show DES14X3taz is an SLSN-I at z = 0.608. Multi-color photometry reveals a double-peaked light curve: a blue and relatively bright initial peak that fades rapidly prior to the slower rise of the main light curve. Our multi-color photometry allows us, for the first time, to show that the initial peak cools from 22,000 to 8000 K over 15 rest-frame days, and is faster and brighter than any published core-collapse supernova, reaching 30% of the bolometric luminosity of the main peak. No physical Ni-56-powered model can fit this initial peak. We show that a shock-cooling model followed by a magnetar driving the second phase of the light curve can adequately explain the entire light curve of DES14X3taz. Models involving the shock-cooling of extended circumstellar material at a distance of similar or equal to 400 R-circle dot are preferred over the cooling of shock-heated surface layers of a stellar envelope. We compare DES14X3taz to the few double-peaked SLSN-I events in the literature. Although the rise. times and characteristics of these initial peaks differ, there exists the tantalizing possibility that they can be explained by one physical interpretation
general↗
Evaluation of Deep Subsurface Resistivity Imaging for Hydrofracture Monitoring
This report describes the results of the first of its kind monitoring of a hydrofracture operation with electromagnetic measurements. The researchers teamed with oil and gas producer Encana Corporation to design and execute a borehole to surface monitoring of three fracture stages at a well pad in central Colorado. The field project consisted of an equipment upgrade, a survey design and modeling phase, several weeks of data collection, and data processing and interpretation. Existing Depth to Surface Resistivity (DSR) instrumentation was upgraded to allow for continuous high precision recording from downhole sources. The full system can now collect data continuously for up to 72 hours, which is sufficient to measure data for 10 frac stages. Next we used numerical modeling and frac treatment data supplied by Encana to design a field survey to detect EM signal from induced fractures. Prior to modeling we developed a novel technique for using well casing as an antenna for a downhole source. Modeling shows that 1) a measurable response for an induced fracture could be achieved if the facture fluid was of high salinity 2) an optimum fracture response is created when the primary source field is parallel to the well casing but perpendicular to the fracture direction. In mid-July, 2014 we installed an array of more than 100 surface sensors, distributed above the treatment wells and extending for approximately 1 km north and 750 m eastward. We applied a 0.6 Hz square wave signal to a downhole current electrode located in a horizontal well 200 m offset from the treatment well with a return electrode on the surface. The data were transmitted to a recording trailer via Wi-Fi where we monitored receiver and transmitter channels continuously in a 72-hour period which covered 7 frac stages, three of which were high salinity. Although the background conditions were very noisy we were able to extract a clear signal from the high salinity stages. Initial data interpretation attempts consisting of trying to directly invert collected data using a simple background starting model did not produce reasonable models. We next used a simulated data set to develop a constrained inversion workflow that places the downhole fracture in the correct location. Finally, we used a combination of forward and inverse models to fit the collected data to a model that incorporated 3 frac stages. This project provided a first-of-its-kind application of EM technology to map an induced fracture. The results demonstrated a clear anomaly during the operation that can be fit to a reasonable model of an induced fracture.
42 ENGINEERING↗
eXtremeMAT: Uncertainty Quantification of the LApx Model
Presentation on the uncertainty quantification efforts to parameterize and fit the LApx model for ferritic-martensitic steels and austenitic stainless steels. These workflows support ease of adoption of the code to new materials and enable rapid model fitting and understanding of the level of confidence in predictions.
mechanical properties↗
An analysis of parameter compression and Full-Modeling techniques with Velocileptors for DESI 2024 and beyond
In anticipation of forthcoming data releases of current and future spectroscopic surveys, we present the validation tests and analysis of systematic effects within velocileptors modeling pipeline when fitting mock data from the AbacusSummit N-body simulations. We compare the constraints obtained from parameter compression methods to the direct fitting (Full-Modeling) approaches of modeling the galaxy power spectra, and show that the ShapeFit extension to the traditional template method is consistent with the Full-Modeling method within the standard ΛCDM parameter space. We show the dependence on scale cuts when fitting the different redshift bins using the ShapeFit and Full-Modeling methods. We test the ability to jointly fit data from multiple redshift bins as well as joint analysis of the pre-reconstruction power spectrum with the post-reconstruction BAO correlation function signal. We further demonstrate the behavior of the model when opening up the parameter space beyond ΛCDM and also when combining likelihoods with external datasets, namely the Planck CMB priors. Finally, we describe different parametrization options for the galaxy bias, counterterm, and stochastic parameters, and employ the halo model in order to physically motivate suitable priors that are necessary to ensure the stability of the perturbation theory.
79 ASTRONOMY AND ASTROPHYSICS↗