Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model
Code repository for aneuploidy model and gene machine learning model
aneuploidy↗
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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
YPS1009-derivative strain genome assembly in NCBI, BioProject
aneuploidy↗
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↗
Fitting improved accretion disk models to the multiwavelength continua of quasars and active galactic nuclei
Fits to the ultraviolet-optical-infrared spectra of 60 quasars and active galactic nuclei (AGNs) are investigated, using black hole accretion disk models. The disk is assumed to be geometrically thin and optically thick. The observed spectrum from a black hole accretion disk, rotating (Kerr) or nonrotating (Schwarzschild), is transformed by the geometric inclination effect, Doppler shifts, gravitational redshifts, and gravitational focusing. These effects alter the locally emitted fluxes and produce harder spectra for an observer at higher inclination angles. The relativistic corrections are much more significant in the Kerr geometry since the inner edge of the disk is much closer to the rotating black hole. A simple inverse relation between the inferred black hole mass and the assumed inclination angle was found in the Kerr case, while the inferred accretion rate (solar masses/yr) remains independent of the angle. In the Schwarzschild case, the ratio of the inferred accretion rate to the black hole mass remains roughly constant when the viewing angle changes. In both geometries, low-redshift Seyfert galaxies have relatively low accretion rates, only a few percent of their Eddington luminosities, while the most luminous quasars are accreting near their Eddington limits.
Sun, Wei-Hsin↗
Relativistic Iron Emission and Disk Reflection in Galactic Microquasar XTE J1748-288
We report evidence for an Fe K-alpha fluorescence line feature and disk reflection in the very high, high-, and low-state X-ray spectra of the Galactic microquasar XTE J1748 - 288 during its 1998 June outburst. Spectral analyses are made on data gathered throughout the outburst by the Rossi X-Ray Timing Explorer Proportional Counter Array. Gaussian line, relativistic disk emission line, and ionized disk reflection models are fitted to the data. In the very high state the line profile appears strongly redshifted, consistent with disk emission from the innermost stable orbits around a maximally rotating Kerr black hole. In the high state the line profile is less redshifted and increasingly prominent. The low-state line profile is very strong (approx. 0.5 keV equivalent width) and centered at 6.7 +/- 0.10 keV; disk line emission model fits indicate that the inner edge of the disk fluctuates between approx. 20R(sub g) and - approx. 100R(sub g) in this state. The disk reflection fraction is traced through the outburst; reflection from an ionized disk is preferred in the very high and high states, and reflection from a relatively neutral disk is preferred in the low state. We discuss the implications of our findings for the binary system dynamics and accretion flow geometry in XTE J1748 - 288.
Miller, J. M.↗
Relativistic Iron Emission and Disk Reflection in Galactic Microquasar XTE J1748-288
We report evidence for an Fe K(alpha) fluorescence line feature and disk reflection in the very high, high-, and low-state X-ray spectra of the Galactic microquasar XTE J1748-288 during its 1998 June outburst. Spectral analyses are made on data gathered throughout the outburst by the Rossi X-Ray Timing Explorer Proportional Counter Array. Gaussian line, relativistic disk emission line, and ionized disk reflection models are fitted to the data. In the very high state the line profile appears strongly redshifted, consistent with disk emission from the innermost stable orbits around a maximally rotating Kerr black hole. In the high state the line profile is less redshifted and increasingly prominent. The low-state line profile is very strong (approx. 0.5 keV equivalent width) and centered at 6.7 +/- 0.10 keV; disk line emission model fits indicate that the inner edge of the disk fluctuates between approx. 20Rg and approx. 100Rg in this state. The disk reflection fraction is traced through the outburst; reflection from an ionized disk is preferred in the very high and high states, and reflection from a relatively neutral disk is preferred in the low state. We discuss the implications of our findings for the binary system dynamics and accretion flow geometry in XTE J1748-288.
Miller, J. M.↗
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↗
The energy spectra of solar flare electrons
A survey of 50 electron energy spectra from .1 to 100 MeV originating from solar flares was made by the combination of data from two spectrometers onboard the International Sun Earth Explorer-3 spacecraft. The observed spectral shapes of flare events can be divided into two classes through the criteria of fit to an acceleration model. This standard two step acceleration model, which fits the spectral shape of the first class of flares, involves an impulsive step that accelerates particles up to 100 keV and a second step that further accelerates these particles up to 100 MeV by a single shock. This fit fails for the second class of flares that can be characterized as having excessively hard spectra above 1 MeV relative to the predictions of the model. Correlations with soft X-ray and meter radio observations imply that the acceleration of the high energy particles in the second class of flares is dominated by the impulsive phase of the flares.
Evenson, P. A.↗
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↗
The Atacama Cosmology Telescope: Cosmological Parameters from the 2008 Power Spectrum
We present cosmological parameters derived from the angular power spectrum of the cosmic microwave background (CMB) radiation observed at 148 GHz and 218 GHz over 296 deg(exp 2) with the Atacama Cosmology Telescope (ACT) during its 2008 season. ACT measures fluctuations at scales 500 < l < 10,000. We fit a model for the lensed CMB, Sunyaev-Zel'dovich (SZ), and foreground contribution to the 148 GHz and 218 GHz power spectra, including thermal and kinetic SZ, Poisson power from radio and infrared point sources, and clustered power from infrared point sources. At l = 3000, about half the power at 148 GHz comes from primary CMB after masking bright radio sources. The power from thermal and kinetic SZ is estimated to be Beta(sub 3000) is identical to 6.8 +/- 2.9 mu K (exp 2), where Beta (sub l) is identical to l(l + 1) C(sub l)/2pi. The IR Poisson power at 148 GHz is Bewta(sub 3000) 7.8 +/- 0.7 muK(exp 2) (C(sub l) = 5.5 +/- 0.5 nK(exp 2)), and a clustered IR component is required with Beta (sub 3000) = 4.6 +/- 0.9 muK(exp 2), assuming an analytic model for its power spectrum shape. At 218 GHz only about 15% of the power, approximately 27 mu K(exp 2), is CMB anisotropy at l = 3000. The remaining 85% is attributed to IR sources (approximately 50% Poisson and 35% clustered), with spectral index alpha = 3.69 +/- 0.14 for flux scaling as S(nu) varies as nu(sup alpha). We estimate primary cosmological parameters from the less contaminated 148 GHz spectrum, marginalizing over SZ and source power. The ACDM cosmological model is a good fit to the data (chi square/dof = 29/46), and ACDM parameters estimated from ACT+Wilkinson Microwave Anisotropy Probe (WMAP) are consistent with the seven-year WMAP limits, with scale invariant n(sub s) = 1 excluded at 99.7% confidence level (CL) (3 sigma). A model with no CMB lensing is disfavored at 2.8 sigma. By measuring the third to seventh acoustic peaks, and probing the Silk damping regime, the ACT data improve limits on cosmological parameters that affect the small-scale CMB power. The ACT data combined with WMAP give a 6 sigma detection of primordial helium, with Y(sub p) = 0.313 +/- 0.044, and a 4 sigma detection of relativistic species, assumed to be neutrinos, with N(sub eff) = 5.3 +/- 1.3 (4.6 +/- 0.8 with BAO+H(sub 0) data). From the CMB alone the running of the spectral index is constrained to be d(sub s) / d ln k = -0,034 +/- 0,018, the limit on the tensor-to-scalar ratio is r < 0,25 (95% CL), and the possible contribution of Nambu cosmic strings to the power spectrum is constrained to string tension G(sub mu) < 1.6 x 10(exp -7) (95% CL),
Dunkley, J.↗
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↗
Backus Effect on a Perpendicular Errors in Harmonic Models of Real vs. Synthetic Data
Measurements of geomagnetic scalar intensity on a thin spherical shell alone are not enough to separate internal from external source fields; moreover, such scalar data are not enough for accurate modeling of the vector field from internal sources because of unmodeled fields and small data errors. Spherical harmonic models of the geomagnetic potential fitted to scalar data alone therefore suffer from well-understood Backus effect and perpendicular errors. Curiously, errors in some models of simulated 'data' are very much less than those in models of real data. We analyze select Magsat vector and scalar measurements separately to illustrate Backus effect and perpendicular errors in models of real scalar data. By using a model to synthesize 'data' at the observation points, and by adding various types of 'noise', we illustrate such errors in models of synthetic 'data'. Perpendicular errors prove quite sensitive to the maximum degree in the spherical harmonic expansion of the potential field model fitted to the scalar data. Small errors in models of synthetic 'data' are found to be an artifact of matched truncation levels. For example, consider scalar synthetic 'data' computed from a degree 14 model. A degree 14 model fitted to such synthetic 'data' yields negligible error, but amplifies 4 nT (rmss) added noise into a 60 nT error (rmss); however, a degree 12 model fitted to the noisy 'data' suffers a 492 nT error (rmms through degree 12). Geomagnetic measurements remain unaware of model truncation, so the small errors indicated by some simulations cannot be realized in practice. Errors in models fitted to scalar data alone approach 1000 nT (rmss) and several thousand nT (maximum).
Voorhies, C. V.↗
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↗