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DOE OSTI2024

Predicting transcription factor activity using prior biological information

Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Source of Processable Vitrimer Viscosities: Swap Frequencies and Steric Factors

Vitrimers exhibit high, processable viscosities, where other polymers do not, and are among the most promising polymers for closed-loop material circularity. We sought to investigate the underlying chemical kinetic factors that result in high viscosities for vitrimers, which are crucial to designing vitrimers with tunable viscosity. To interrogate these factors, we achieved the first simulated predictions of real vitrimer viscosities, using a novel kinetic Monte Carlo molecular dynamics method, overcoming the time and length scale gaps to predict experimental bulk viscosities. The vitrimer architecture investigated is based on poly(dimethylsiloxane) chains and vinylogous urethane bond swaps. We probed the effects of the extent of free swapping groups, %F, the activation energy, E A , and the steric factor, ρ. The steric factor is related to the intrinsic reaction probability for molecules with sufficient energy. All three factors were found to be significant, but the role of ρ was found to be the biggest and also the most underappreciated. The results show that the inclusion of accurate ρ is of critical importance for viscosity predictions, with the evidence suggesting that the typical assumption of ρ = 1 is not valid for vitrimers and that, indeed, very low steric factors are present in bond-swap vitrimers such that values of ρ < 10 –10 may be typical. This greatly influences the bond exchange rates and, ultimately, the viscosities. Recognition of this result is necessary for the prediction of vitrimer viscosities from molecular simulations and to make vitrimers by design from molecular dynamics. We also investigated the effects that E A , ρ, and the number of free swapping groups have upon vitreous range temperatures, TV, with respect to achieving a specific viscosity (η V = 1 × 10 8 Pa·s), as well as for a commonly reported higher viscosity extrapolation (η V = 1 × 10 12 Pa·s). The evidence suggests that vitrimers may follow universal curves for E A vs T V , as a function of ρ. Finally, this study achieves the first of these comparisons of molecular simulations to experiments and reveals critical insights toward creating vitrimers by design, while providing a route for the prediction of T V from kinetic Monte Carlo molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Local self-interaction correction method with a simple scaling factor

A recently proposed local self-interaction correction (LSIC) method [Zope et al., J. Chem. Phys., 2019, 151, 214108] when applied to the simplest local density approximation provides a significant improvement over standard Perdew–Zunger SIC (PZSIC) for both equilibrium properties such as total or atomization energies as well as properties involving stretched bond such as barrier heights. The method uses an iso-orbital indicator to identify the single-electron regions. To demonstrate the LSIC method, Zope et al. used the ratio z σ of von Weizsäcker τ W σ and total kinetic energy densities τ σ , (z σ = τ W σ /τ σ ) as a scaling factor to scale the self-interaction correction. The present work further explores the LSIC method using a ratio of orbital and spin densities as a simpler scaling factor in place of the ratio of kinetic energy densities. We compute a wide array of both, equilibrium and non-equilibrium properties using LSIC and orbital scaling methods using this simple scaling factor and compare them with previously reported results. Our study shows that LSIC with the simple scaling factor performs better than PZSIC, with results comparable to those obtained by LSIC( z σ ) for most properties, but has slightly larger errors than LSIC( z σ ). Furthermore, we study the binding energies of small water clusters using both scaling factors. Our results show that LSIC with zσ has limitations in predicting the cluster binding energies of weakly bonded systems due to the inability of z σ to distinguish weakly bonded regions from slowly varying density regions. LSIC when used with the density ratio as a scaling factor, on the other hand, provides a good description of water cluster binding energies, thus highlighting the appropriate choice of the iso-orbital indicator.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites

Abstract Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Measurement of the sodium and iodine scintillation quenching factors across multiple NaI(Tl) detectors to identify systematics

The amount of light produced by nuclear recoils in scintillating targets is strongly quenched compared to that produced by electrons. A precise understanding of the quenching factor is particularly interesting for weakly interacting massive particles (WIMP) searches and coherent elastic neutrino-nucleus scattering ( CE ν NS ) measurements since both rely on nuclear recoils, whereas energy calibrations are more readily accessible from electron recoils. There is a wide variation among the current measurements of the quenching factor in sodium iodide (NaI) crystals, especially below 10 keV, the energy region of interest for dark matter and CE ν NS studies. A better understanding of the quenching factor in NaI(Tl) is of particular interest for resolving the decades-old puzzle in the field of dark matter between the null results of most WIMP searches and the claim for dark matter detection by the DAMA/LIBRA collaboration. In this work, we measured sodium and iodine quenching factors for five small NaI(Tl) crystals grown with similar thallium concentrations and growth procedures. Unlike previous experiments, multiple crystals were tested, with measurements made in the same experimental setup to control systematic effects. The quenching factors agree in all crystals we investigated, and both sodium and iodine quenching factors are smaller than those reported by DAMA/LIBRA. The dominant systematic effect was due to the electron equivalent energy calibration originating from the nonproportional behavior of the NaI(Tl) light yield at lower energies, potentially the cause for the discrepancies among the previous measurements. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Individual tree damage dominates mortality risk factors across six tropical forests

Summary The relative importance of tree mortality risk factors remains unknown, especially in diverse tropical forests where species may vary widely in their responses to particular conditions. We present a new framework for quantifying the importance of mortality risk factors and apply it to compare 19 risks on 31 203 trees (1977 species) in 14 one‐year periods in six tropical forests. We defined a condition as a risk factor for a species if it was associated with at least a doubling of mortality rate in univariate analyses. For each risk, we estimated prevalence (frequency), lethality (difference in mortality between trees with and without the risk) and impact (‘excess mortality’ associated with the risk, relative to stand‐level mortality). The most impactful risk factors were light limitation and crown/trunk loss; the most prevalent were light limitation and small size; the most lethal were leaf damage and wounds. Modes of death (standing, broken and uprooted) had limited links with previous conditions and mortality risk factors. We provide the first ranking of importance of tree‐level mortality risk factors in tropical forests. Future research should focus on the links between these risks, their climatic drivers and the physiological processes to enable mechanistic predictions of future tree mortality.

Zuleta, Daniel↗

DOE OSTI2023

Combining Sparse Approximate Factorizations with Mixed-precision Iterative Refinement

The standard LU factorization-based solution process for linear systems can be enhanced in speed or accuracy by employing mixed-precision iterative refinement. Most recent work has focused on dense systems. We investigate the potential of mixed-precision iterative refinement to enhance methods for sparse systems based on approximate sparse factorizations. In doing so, we first develop a new error analysis for LU- and GMRES-based iterative refinement under a general model of LU factorization that accounts for the approximation methods typically used by modern sparse solvers, such as low-rank approximations or relaxed pivoting strategies. We then provide a detailed performance analysis of both the execution time and memory consumption of different algorithms, based on a selected set of iterative refinement variants and approximate sparse factorizations. Our performance study uses the multifrontal solver MUMPS, which can exploit block low-rank factorization and static pivoting. We evaluate the performance of the algorithms on large, sparse problems coming from a variety of real-life and industrial applications showing that mixed-precision iterative refinement combined with approximate sparse factorization can lead to considerable reductions of both the time and memory consumption.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

The Prediction Model of Risk Factors for COVID-19 Developing into Severe Illness Based on 1046 Patients with COVID-19

This study analyzed the risk factors for patients with COVID-19 developing severe illnesses and explored the value of applying the logistic model combined with ROC curve analysis to predict the risk of severe illnesses at COVID-19 patients’ admissions. The clinical data of 1046 COVID-19 patients admitted to a designated hospital in a certain city from July to September 2020 were retrospectively analyzed, the clinical characteristics of the patients were collected, and a multivariate unconditional logistic regression analysis was used to determine the risk factors for severe illnesses in COVID-19 patients during hospitalization. Based on the analysis results, a prediction model for severe conditions and the ROC curve were constructed, and the predictive value of the model was assessed. Logistic regression analysis showed that age (OR = 3.257, 95% CI 10.466–18.584), complications with chronic obstructive pulmonary disease (OR = 7.337, 95% CI 0.227–87.021), cough (OR = 5517, 95% CI 0.258–65.024), and venous thrombosis (OR = 7322, 95% CI 0.278–95.020) were risk factors for COVID-19 patients developing severe conditions during hospitalization. When complications were not taken into consideration, COVID-19 patients’ ages, number of diseases, and underlying diseases were risk factors influencing the development of severe illnesses. The ROC curve analysis results showed that the AUC that predicted the severity of COVID-19 patients at admission was 0.943, the optimal threshold was −3.24, and the specificity was 0.824, while the sensitivity was 0.827. The changes in the condition of severe COVID-19 patients are related to many factors such as age, clinical symptoms, and underlying diseases. This study has a certain value in predicting COVID-19 patients that develop from mild to severe conditions, and this prediction model is a useful tool in the quick prediction of the changes in patients’ conditions and providing early intervention for those with risk factors.

Lian, Zhichuang↗

DOE OSTI2020

Calculation of Friction Factors in Heat Pipes Using CFD in Support of the Sockeye Code

A heat pipe is two-phase heat transfer device which relies on surface tension and capillary pressure to provide a very efficient heat transfer mechanism. Currently, there is interest in designing micro nuclear power reactors using high temperature heat pipes to provide totally passive cooling. To support this, Sockeye is being developed as a heat pipe simulation capability. To support the development of Sockeye, individual phenomena must be tested. This work focuses on applying a CFD model to evaluate friction factors for use in Sockeye. A CFD model has been developed in Nek5000 which simulates each component fluid, i.e. sodium liquid and vapor, independently and captures the effects of the wick on friction factor. The model tests the effect of the wick permeability and the thickness of the wick occupied by each fluid component. The thickness of the wick occupied by each component can be directly related to the local vapor volume fraction from the Sockeye heat pipe model. Results from the CFD model indicate that friction factor in the liquid flow decreases with increasing wick permeability, while the friction factor in the vapor flow increases with increasing wick permeability. In the liquid, this is likely a direct result of the increased cross sectional area available for the flow. For the vapor, this is explained as the wick acting like a rough wall, while the increased area has only a negligible impact. Results for the tests of the thickness of the wick occupied by each fluid showed a thresholding behavior for both liquid and vapor. When the thickness of the wick occupied by each fluid was increased, it increased the effect of the wick, but only up to a certain point. Once a certain thickness was reached, the friction factors remained constant. When the fluid occupied only a very small fraction of the wick, friction factors returned to nominal values.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Update to the Finite Cloud Dose Correction Factors in MACCS

In WASH - 1400, external exposure from the finite radioactive cloud (cloudshine) is calculated by assuming that the cloud is semi-infinite, the concentration of radioactive material is uniform, and by using a correction factor to account for these approximations. This correction factor is originally based upon formulations by Healy and depends on the effective size of the plume and the distance from the plume center to the receptor. The range of the finite cloud dose correction factor table from WASH - 1400 developed using Healy formulations can be exceeded in certain situations. When the range of the table is exceeded, no extrapolation is performed; rather interpolation at the edge of the table is performed per WASH - 1400. The tabulated values of these finite cloud dose correction factors from WASH - 1400 and the interpolation at the edge of the table have been used in MACCS since its creation. An expanded table of finite cloud dose correction factors is one way to reduce the need of using interpolation at the edge of the table. The generation of an expanded finite cloud dose correction factor table for future use in MACCS is documented in this report.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Impact of K-factor on Short Circuit Program Convergence for Inverter-Based Resources during Faults

Classical short-circuit programs that linearize the power network are no longer applicable for inverter based resources (IBRs), necessitating an iterative approach. Phasor domain programs can model the IBRs using an iterative approach considering nonlinear fault responses. In phasor domain models, the IBR can be modeled as a voltage controlled current source (VCCS) in tabular form with positive, negative, and zero sequence information for balanced and unbalance short-circuit faults. In the VCCS modeling of the IBR, positive and negative incremental reactive current, also known as the k-factor, plays an important role in short circuit program convergence. In this work, a few approaches: conventional VCCS modeling with a k-factor of 2, conventional VCCS modeling with a k-factor of 2 with modified pre-fault voltages, VCCS characteristics based on the power flow solution with a k-factor of 2, and VCCS characteristics based on the power flow solution with a k-factor of 1 are investigated for short circuit program convergence under higher IBR penetration. The IEEE 39 bus New England Test System is taken as the test system, and simulations are carried out in PSS®CAPE 15.0.26 simulation software. Simulation results demonstrate that IBR penetration is higher for the VCCS model, which corresponds to the power flow solution with k-factor 1, compared to other approaches.

42 ENGINEERING↗

DOE OSTI2024

SAGAbg. I. A Near-unity Mass-loading Factor in Low-mass Galaxies via Their Low-redshift Evolution in Stellar Mass, Oxygen Abundance, and Star Formation Rate

Measuring the relation between star formation and galactic winds is observationally difficult. In this work we make an indirect measurement of the mass-loading factor (the ratio between the mass outflow rate and star formation rate) in low-mass galaxies using a differential approach to modeling the low-redshift evolution of the star-forming main sequence and mass–metallicity relation. We use Satellites Around Galactic Analogs (SAGA) background galaxies, i.e., spectra observed by the SAGA Survey that are not associated with the main SAGA host galaxies, to construct a sample of 11,925 spectroscopically confirmed low-mass galaxies from 0.01 ≲ z ≤ 0.21 and measure auroral line metallicities for 120 galaxies. The crux of the method is to use the lowest-redshift galaxies as the boundary condition of our model, and to infer a mass-loading factor for the sample by comparing the expected evolution of the low-redshift reference sample in stellar mass, gas-phase metallicity, and star formation rate against the observed properties of the sample at higher redshift. We infer a mass-loading factor of η m = $0.92^{+1.76}_{-0.74}$, which is in line with direct measurements of the mass-loading factor from the literature despite the drastically different sets of assumptions needed for each approach. While our estimate of the mass-loading factor is in good agreement with recent galaxy simulations that focus on resolving the dynamics of the interstellar medium, it is smaller by over an order of magnitude than the mass-loading factor produced by many contemporary cosmological simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1972

Investigation of Structural Factors of Safety for the Space Shuttle

A study was made of the factors governing the structural design of the fully reusable space shuttle booster to establish a rational approach to select optimum structural factors of safety. The study included trade studies of structural factors of safety versus booster service life, weight, cost, and reliability. Similar trade studies can be made on other vehicles using the procedures developed. The major structural components of a selected baseline booster were studied in depth, each being examined to determine the fatigue life, safe-life, and fail-safe capabilities of the baseline design. Each component was further examined to determine its reliability and safety requirements, and the change of structural weight with factors of safety. The apparent factors of safety resulting from fatigue, safe-life, proof test, and fail-safe requirements were identified. The feasibility of reduced factors of safety for design loads such as engine thrust, which are well defined, was examined.

Source record↗

NASA NTRS1973

View factor computer program (program view) user's manual

The purpose of program VIEW is to compute view factors between specified surfaces and to be compatible with level 15.5 of the NASTRAN structural analysis program. Program VIEW is a modification of a (finite element) view factor computation program called RAVFAC. VIEW is designed to run on an IBM System/360 operating under OS (operating system), with a minimum region size of 110 K bytes. The actual computation of view factors is still performed exactly as it was in the original version of RAVFAC. In developing VIEW, RAVFAC was modified to satisfy the following compatibility requirements: (1) accept finite element input which can also be used as input to NASTRAN, (2) produce output (view factors) in a format which can be used as input to NASTRAN, and (3) follow NASTRAN program design so that in the future VIEW can be incorporated into NASTRAN as a subroutine. The VIEW program permits computation of the view factors between surfaces, taking into account the presence of any intermediate surfaces. VIEW also computes these view factors either by contour integration or by finite difference (double summation) methods.

Puccinelli, E. F.↗

NASA NTRS1989

OH A 2Sigma - X 2Pi (0,0) band rotational line emission rate factors

This paper presents the results of the emission-rate factor (g factor) calculations for the (0,0) band of the OH (A 2Sigma - X 2Pi) system, for the temperatures 200.0, 240.0, 296.0, 300.0, and 500.0 K, as well as for the individual g factors for each rotational line of the band. The derived g factor at 240 K for the entire band is 0.00055 + or - 0.00011 photon/sec. The g factor for the entire band was found to decrease with increasing temperature, but the difference in the change was less than 10 percent for the temperature range studied. The data on the individual rotational line g factors are valuable for future work on determining OH concentration profiles in the atmosphere, through the observation of the UV fluorescence in the OH (A 2Sigma - X 2Pi) (0,0) band using high-resolution spectrometers of a low-scattered-light design.

Fennelly, J. A.↗

NASA NTRS1991

Key factors limiting the open circuit voltage of n(+)pp(+) indium phosphide solar cells

Solar cells made from gallium arsenide (GaAs), with a room temperature bandgap of E(sub g) = 1.43 eV have exhibited the best measured open circuit voltage (V sub OC) of 1.05 V at 1 AMO, 25 C. The material InP is in many ways similar to GaAs. A simple calculation comparing InP to GaAs then shows that solar cells made from InP, with E(sub g) = 1.35 at 300 K, should exhibit the best measured (V sub OC) of approximately 950 mV at 1 AMO, 300 K. However, to date, the best measured V(sub OC) for InP solar cells made by any fabrication method is 899 mV at AM1.5, 25 C which would translate to 912 mV at 1 AMO, 25 C. The V(sub OC) of an n(+)pp(+) InP solar cell is governed by several factors. Of these, some factors, such as the thickness and doping of the emitter and base regions, are easily controlled and can be adjusted to desired values dictated by a good performance optimizing model. Such factors were not considered. There are other factors which also govern V(sub OC), and their values are not so easily controlled. The primary ones among these are (1) the indirect or Hall-Shockley-Read lifetimes in the various regions of the cell, (2) the low-doping intrinsic carrier concentration n(sub i) of the InP material, (3) the heavy doping factors in the emitter and BSF regions, and (4) the front surface recombination velocity S(sub F). The influence of these latter factors on the V(sub OC) of the n(+)pp(+) InP solar cell and the results were used to produce a near-optimum design of the n(+)pp(+) InP solar cell.

Goradia, Chandra↗

NASA NTRS1990

Key factors limiting the open circuit voltage of n(+)pp(+) indium phosphide solar cells

Solar cells made from gallium arsenide (Gaas), with a room temperature bandgap of E(sub g) = 1.43 eV have exhibited the best measured open circuit voltage (V sub oc) of 1.05 V at 1 AM0, 25 C. The material InP is in many ways similar to GaAs. A simple calculation comparing InP to GaAs then shows that solar cells made from InP, with E(sub g) = 1.35 at 300 K, should exhibit the best measured V sub oc of approximately 950 mV at 1 AM0, 300 K. However, to date, the best measured V sub oc for InP solar cells made by any fabrication method is 899 mV at AM1.5, 25 C which would translate to 912 mV at 1 AM0, 25 C. The V sub oc of an n(+)pp(+) InP solar cell is governed by several factors. Of these, some factors, such as the thickness and doping of the emitter and base regions, are easily controlled and can be adjusted to desired values dictated by a good performance optimizing model. Such factors were not considered. There are other factors which also govern V sub oc, and their values are not so easily controlled. The primary ones among these are (1) the indirect or Hall-Shockley-Read lifetimes in the various regions of the cell, (2) the low-doping intrinsic carrier concentration n(sub i) of the InP material, (3) the heavy doping factors in the emitter and BSF regions, and (4) the front surface recombination velocity S(sub F). The influence of these latter factors on the V sub oc of the n(+)pp(+) InP solar cell and the results were used to produce a near-optimum design of the n(+)pp(+) InP solar cell.

Goradia, Chandra↗

NASA NTRS1993

On the stability analysis of approximate factorization methods for 3D Euler and Navier-Stokes equations

The convergence characteristics of various approximate factorizations for the 3D Euler and Navier-Stokes equations are examined using the von-Neumann stability analysis method. Three upwind-difference based factorizations and several central-difference based factorizations are considered for the Euler equations. In the upwind factorizations both the flux-vector splitting methods of Steger and Warming and van Leer are considered. Analysis of the Navier-Stokes equations is performed only on the Beam and Warming central-difference scheme. The range of CFL numbers over which each factorization is stable is presented for one-, two-, and three-dimensional flow. Also presented for each factorization is the CFL number at which the maximum eigenvalue is minimized, for all Fourier components, as well as for the high frequency range only. The latter is useful for predicting the effectiveness of multigrid procedures with these schemes as smoothers. Further, local mode analysis is performed to test the suitability of using a uniform flow field in the stability analysis. Some inconsistencies in the results from previous analyses are resolved.

Demuren, A. O.↗