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DOE OSTI2020

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis -element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Microtubules as key cytoskeletal elements in cellular transport and shape changes: their expected responses to space environments

Application of reference standard reagents to alternatively depolymerize or stabilize microtubules in a cell that undergoes very regular cytoskeleton-dependent shape changes provides a model system in which some expected components of the environments of spacecraft and space can be tested on Earth for their effects on the cytoskeleton. The fertilized eggs of Ilyanassa obsoleta undergo polar lobe formation by repeated, dramatic, constriction and relaxation of a microfilamentous band localized in the cortical cytoplasm and activated by microtubules.

NASA Discipline Number 93-10↗

DOE OSTI2021

PV Reference Cells for Outdoor Use: An Investigation of Calibration Factors

Reference cells are widely used in the photovoltaic (PV) industry to measure irradiance. For field applications and outdoor use, a variety of products are on the market, and they are often perceived as a low-cost alternative to thermopile radiometers. But reference cell characteristics differ substantially from the latter, therefore measurements made by one category of instrument cannot be substituted for or directly compared with the other. The National Renewable Energy Laboratory's (NREL's) Solar Radiation Research Laboratory is currently in a multiyear effort to develop guidance and recommendations for the design and use of outdoor reference cells, with a view to reducing inconsistencies and measurement uncertainty. The core of this effort is the long-term deployment of 39 units of 10 distinct types made by 6 manufacturers. This report compares the calibration factors provided by manufacturers - which most users rely upon - to those measured at a high level of accuracy by NREL's Cell Lab. It also reports on the application of the Broadband Outdoor Radiometer Calibration (BORCAL) method to reference cells. As a group, the factory calibrations for the crystalline silicon cells showed a small positive bias of +0.7%, with a tight distribution around this value. This is a very good result for the manufacturers. The two World Photovoltaic Scale cells constituted outliers, with a mean deviation of -0.8%, which is still within the reported uncertainty ranges. The data collected during the BORCAL procedures show a strong and systematic fluctuation of the apparent responsivity of the reference cells over the course of a day, which was anticipated. Consequently, the standard BORCAL R@45 calibration factors underestimated the reference cell responsivities by 1%-4%. An alternate responsivity indicator was developed, R'@30, incorporating adjustments for temperature response, spectral response, and directional response. This reduced the mean deviation to -0.4% compared to the Cell Lab. Further, two independent BORCAL sessions were able to produce the same values to within ±0.2%. This could be a viable approach for verifying reference cells using existing BORCAL infrastructure, for example, to evaluate their long-term stability. The daily profiles of responsivity obtained during the BORCAL sessions (provided in Appendix A) show clear patterns of differences between models, which provides evidence that their directional responses differ from each other; thus, two sensors that are calibrated correctly might give the same reading at 30° zenith angle but systematically different readings at 60°. The impact of these inconsistencies in field operation will be quantified using the long-term observations started in 2020.

14 SOLAR ENERGY↗

DOE OSTI2017

Efficient Safety and Degradation Modeling of Automotive Lithium-ion Cells and Packs

This document is intended to give an overall synopsis of the activities and accomplishments of the EC Power CAEBAT2 project over the course of four years. The reader is referred to the previously submitted quarterly reports, review presentations, and AMR presentations for further technical details. As highlighted by the numerous results shown herein and the volume and quality of the publications and presentations made in the course of this project, we feel that we have made a strong impact in the community.

25 ENERGY STORAGE↗

NASA NTRS2018

Computational Model Prediction and Biological Validation Using Simplified Mixed Field Exposures for the Development of a GCR Reference Field

The yield of chromosomal aberrations has been shown to increase in the lymphocytes of astronauts after long-duration missions of several months in space. Chromosome exchanges, especially translocations, are positively correlated with many cancers and are therefore a potential biomarker of cancer risk associated with radiation exposure. Although extensive studies have been carried out on the induction of chromosomal aberrations by low- and high-LET radiation in human lymphocytes, fibroblasts, and epithelial cells exposed in vitro, there is a lack of data on chromosome aberrations induced by low dose-rate chronic exposure and mixed field beams such as those expected in space. Chromosome aberration studies at NSRL will provide the biological validation needed to extend the computational models over a broader range of experimental conditions (more complicated mixed fields leading up to the galactic cosmic rays (GCR) simulator), helping to reduce uncertainties in radiation quality effects and dose-rate dependence in cancer risk models. These models can then be used to answer some of the open questions regarding requirements for a full GCR reference field, including particle type and number, energy, dose rate, and delivery order. In this study, we designed a simplified mixed field beam with a combination of proton, helium, oxygen, and iron ions with shielding or proton, helium, oxygen, and titanium without shielding. Human fibroblasts cells were irradiated with these mixed field beam as well as each single beam with acute and chronic dose rate, and chromosome aberrations (CA) were measured with 3-color fluorescent in situ hybridization (FISH) chromosome painting methods. Frequency and type of CA induced with acute dose rate and chronic dose rates with single and mixed field beam will be discussed. A computational chromosome and radiation-induced DNA damage model, BDSTRACKS (Biological Damage by Stochastic Tracks), was updated to simulate various types of CA induced by acute exposures of the mixed field beams used for the experiments. The chromosomes were simulated by a polymer random walk algorithm with restrictions to their respective domains in the nucleus [1]. The stochastic dose to the nucleus was calculated with the code RITRACKS [2]. Irradiation of a target volume by a mixed field of ions was implemented within RITRACKs, and the fields of ions can be delivered over specific periods of time, allowing the simulation of dose-rate effects. Similarly, particles of various types and energies extracted from a pre-calculated spectra of galactic cosmic rays (GCR) can be used in RITRACKS. The number and spatial location of DSBs (DNA double-strand breaks) were calculated in BDSTRACKS using the simulated chromosomes and local (voxel) dose. Assuming that DSBs led to chromosome breaks, and simulating the rejoining of damaged chromosomes occurring during repair, BDSTRACKS produces the yield of various types of chromosome aberrations as a function of time (only final yields are presented). A comparison between experimental and simulation results will be shown.

Hada, M.↗

NASA NTRS2010

TERRA Battery Thermal Control Anomaly - Simulation and Corrective Actions

The TERRA spacecraft was launched in December 1999 from Vandenberg Air Force Base, becoming the flagship of NASA's Earth Observing System program to gather data on how the planet's processes create climate. Originally planned as a 5 year mission, it still provides valuable science data after nearly 10 years on orbit. On October 13th, 2009 at 16:23z following a routine inclination maneuver, TERRA experienced a battery cell failure and a simultaneous failure of several battery heater control circuits used to maintain cell temperatures and gradients within the battery. With several cells nearing the minimum survival temperature, preventing the electrolyte from freezing was the first priority. After several reset attempts and power cycling of the control electronics failed to reestablish control authority on the primary side of the controller, it was switched to the redundant side, but anomalous performance again prevented full heater control of the battery cells. As the investigation into the cause of the anomaly and corrective action continued, a battery thermal model was developed to be used in determining the control ability remaining and to simulate and assess corrective actions. Although no thermal model or detailed reference data of the battery was available, sufficient information was found to allow a simplified model to be constructed, correlated against pre-anomaly telemetry, and used to simulate the thermal behavior at several points after the anomaly. It was then used to simulate subsequent corrective actions to assess their impact on cell temperatures. This paper describes the rapid development of this thermal model, including correlation to flight data before and after the anomaly., along with a comparative assessment of the analysis results used to interpret the telemetry to determine the extent of damage to the thermal control hardware, with near-term corrective actions and long-term operations plan to overcome the anomaly.

Grob, Eric W.↗

DOE OSTI2016

Stable discrete representation of relativistically drifting plasmas

Representing the electrodynamics of relativistically drifting particle ensembles in discrete, co-propagating Galilean coordinates enables the derivation of a Particle-In-Cell algorithm that is intrinsically free of the numerical Cherenkov instability for plasmas flowing at a uniform velocity. Application of the method is shown by modeling plasma accelerators in a Lorentz-transformed optimal frame of reference.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2010

Evaluation of PV performance models and their impact on project risk.

Photovoltaic systems are often priced in $/W{sub p}, where Wp refers to the DC power rating of the modules at Standard Test Conditions (1000 W/m{sup 2}, 25 C cell temperature) and $ refers to the installed cost of the system. However, the true value of the system is in the energy it will produce in kWhs, not the power rating. System energy production is a function of the system design and location, the mounting configuration, the power conversion system, and the module technology, as well as the solar resource. Even if all other variables are held constant, the annual energy yield (kWh/kW{sup p}) will vary among module technologies because of differences in response to low-light levels and temperature. Understanding energy yield is a key part of understanding system value. System performance models are used during project development to estimate the expected output of PV systems for a given design and location. Performance modeling is normally done by the system designer/system integrator. Often, an independent engineer will also model system output during a due diligence review of a project. A variety of system performance models are available. The most commonly used modeling tool for project development and due diligence in the United States is probably PVsyst, while those seeking a quick answer to expected energy production may use PVWatts. In this paper, we examine the variation in predicted energy output among modeling tools and users and compare that to measured output.

14 SOLAR ENERGY↗

DOE OSTI2016

Zero-Kelvin Compression Isotherms of the Elements 1 ≤ Z ≤ 92 to 100 GPa

Most of the chemical elements have now been compressed close to or above 100 GPa (1 Mbar) pressure in diamond-anvil cells and the pressure–volume room-temperature isotherms have been measured. We collect these data and use simple lattice-dynamics models to reduce the isotherms to 0 K. We have extended the published work by making new diamond-anvil-cell measurements on Cr and Rh, and by conducting density-functional calculations on the elements Po, At, Rn, Fr, Ra, and Ac. The 0 K data are tabulated for all elements 1 ≤ Z ≤ 92 and 0 ≤ P ≤ 100 GPa. These data are useful for generating wide-range equation of state models and for studying the stability of chemical compounds at high pressure (“Megabar chemistry”). The tables presented here are intended to be reference thermodynamic tables for use in high-pressure research. Further experimental and theoretical work will be needed to extend the tables to higher pressure and to improve accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

DECENTRALIZED APPROACH TO MULTI-ZONE GREY-BOX MODELING FOR MODEL-BASED PREDICTIVE CONTROL

This study aims to improve the easiness of utilizing the grey-box model (i.e., Resistance-Capacitance circuit) for Model-based Predictive Control (MPC). The primary barrier of implementing the MPC is estimating the control-oriented building model that needs to be computationally inexpensive and quick but reasonably precise in predicting building load and indoor conditions. The estimating of the model parameters becomes more complicated when the building scale is larger; e.g., multi-zone building. In this study, a decentralized approach is introduced; each zone is split and individually estimated with measured boundary temperature from adjacent zones integrated into one single system model. The proposed decentralized method is demonstrated with experimental data from a full-scale multi-zone test cell compared with the centralized reference case.

Joe, Jaewan↗

DOE OSTI2022

Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation detection approach, and demonstrated performance advantages on in silico data. In this study, we use the first comprehensive and well-characterized somatic reference data sets from the SEQC2 consortium to investigate best practices for using a deep learning framework in cancer mutation detection. Using the high-confidence somatic mutations established for a cancer cell line by the consortium, we identify the best strategy for building robust models on multiple data sets derived from samples representing real scenarios, for example, a model trained on a combination of real and spike-in mutations had the highest average performance. The strategy identified in our study achieved high robustness across multiple sequencing technologies for fresh and FFPE DNA input, varying tumor/normal purities, and different coverages, with significant superiority over conventional detection approaches in general, as well as in challenging situations such as low coverage, low variant allele frequency, DNA damage, and difficult genomic regions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping

Abstract High-throughput transcriptomics (HTTr) uses gene expression profiling to characterize the biological activity of chemicals in in vitro cell-based test systems. As an extension of a previous study testing 44 chemicals, HTTr was used to screen an additional 1,751 unique chemicals from the EPA’s ToxCast collection in MCF7 cells using 8 concentrations and an exposure duration of 6 h. We hypothesized that concentration-response modeling of signature scores could be used to identify putative molecular targets and cluster chemicals with similar bioactivity. Clustering and enrichment analyses were conducted based on signature catalog annotations and ToxPrint chemotypes to facilitate molecular target prediction and grouping of chemicals with similar bioactivity profiles. Enrichment analysis based on signature catalog annotation identified known mechanisms of action (MeOAs) associated with well-studied chemicals and generated putative MeOAs for other active chemicals. Chemicals with predicted MeOAs included those targeting estrogen receptor (ER), glucocorticoid receptor (GR), retinoic acid receptor (RAR), the NRF2/KEAP/ARE pathway, AP-1 activation, and others. Using reference chemicals for ER modulation, the study demonstrated that HTTr in MCF7 cells was able to stratify chemicals in terms of agonist potency, distinguish ER agonists from antagonists, and cluster chemicals with similar activities as predicted by the ToxCast ER Pathway model. Uniform manifold approximation and projection (UMAP) embedding of signature-level results identified novel ER modulators with no ToxCast ER Pathway model predictions. Finally, UMAP combined with ToxPrint chemotype enrichment was used to explore the biological activity of structurally related chemicals. The study demonstrates that HTTr can be used to inform chemical risk assessment by determining in vitro points of departure, predicting chemicals’ MeOA and grouping chemicals with similar bioactivity profiles.

Toxicology↗

NASA NTRS1982

Reduction of solar cell efficiency by bulk defects across the back-surface-field junction

The degradation of solar cell performance due to bulk defects distributed across the back-surface field junction is analyzed in terms of a three-region developed-perimeter model. Families of curves are computed and their physical significance is discussed in detail with reference to three parameters used to characterize the defects: defect area, defect density, and defect surface recombination velocity. A reduction in the open-circuit voltage due to the presence of a defect is expressed as a function of the defect area, density, cell thickness, and defect surface recombination velocity. Numerical examples are presented to illustrate the importance of the particular defect parameters.

Sah, C. T.↗

DOE OSTI2016

Lipid bilayer thickness determines cholesterol's location in model membranes

Cholesterol is an essential biomolecule of animal cell membranes, and an important precursor for the biosynthesis of certain hormones and vitamins. It is also thought to play a key role in cell signaling processes associated with functional plasma membrane microdomains (domains enriched in cholesterol), commonly referred to as rafts. In all of these diverse biological phenomena, the transverse location of cholesterol in the membrane is almost certainly an important structural feature. Using a combination of neutron scattering and solid-state 2 H NMR, we have determined the location and orientation of cholesterol in phosphatidylcholine (PC) model membranes having fatty acids of different lengths and degrees of unsaturation. The data establish that cholesterol reorients rapidly about the bilayer normal in all the membranes studied, but is tilted and forced to span the bilayer midplane in the very thin bilayers. The possibility that cholesterol lies flat in the middle of bilayers, including those made from PC lipids containing polyunsaturated fatty acids (PUFAs), is ruled out. Finally, these results support the notion that hydrophobic thickness is the primary determinant of cholesterol's location in membranes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Building predictive signaling models by perturbing yeast cells with time-varying stimulations resulting in distinct signaling responses

This protocol provides a step-by-step approach to perturb single cells with time-varying stimulation profiles, collect distinct signaling responses, and use these to infer a system of ordinary differential equations to capture and predict dynamics of protein-protein regulation in signal transduction pathways. The models are validated by predicting the signaling activation upon new cell stimulation conditions. In comparison to using standard step-like stimulations, application of diverse time-varying cell stimulations results in better inference of model parameters and substantially improves model predictions. For complete details on the use and results of this protocol, please refer to Jashnsaz et al. (2020).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Toward “optimal” integration of terrestrial biosphere models

Multimodel ensembles (MME) are commonplace in Earth system modeling. Here we perform MME integration using a 10-member ensemble of terrestrial biosphere models (TBMs) from the Multiscale synthesis and Terrestrial Model Intercomparison Project (MsTMIP). We contrast optimal (skill based for present-day carbon cycling) versus naive (one model-one vote) integration. MsTMIP optimal and naive mean land sink strength estimates (-1.16 versus -1.15 Pg C per annum respectively) are statistically indistinguishable. This holds also for grid cell values and extends to gross uptake, biomass, and net ecosystem productivity. TBM skill is similarly indistinguishable. The added complexity of skill-based integration does not materially change MME values. This suggests that carbon metabolism has predictability limits and/or that all models and references are misspecified. Finally, resolving this issue requires addressing specific uncertainty types (initial conditions, structure, and references) and a change in model development paradigms currently dominant in the TBM community.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

SU-E-T-398: Evaluation of Radiobiological Parameters Using Serial Tumor Imaging During Radiotherapy as An Inverse Ill-Posed Problem

Purpose: Combination of serial tumor imaging with radiobiological modeling can provide more accurate information on the nature of treatment response and what underlies resistance. The purpose of this article is to improve the algorithms related to imaging-based radiobilogical modeling of tumor response. Methods: Serial imaging of tumor response to radiation therapy represents a sum of tumor cell sensitivity, tumor growth rates, and the rate of cell loss which are not separated explicitly. Accurate treatment response assessment would require separation of these radiobiological determinants of treatment response because they define tumor control probability. We show that the problem of reconstruction of radiobiological parameters from serial imaging data can be considered as inverse ill-posed problem described by the Fredholm integral equation of the first kind because it is governed by a sum of several exponential processes. Therefore, the parameter reconstruction can be solved using regularization methods. Results: To study the reconstruction problem, we used a set of serial CT imaging data for the head and neck cancer and a two-level cell population model of tumor response which separates the entire tumor cell population in two subpopulations of viable and lethally damage cells. The reconstruction was done using a least squared objective function and a simulated annealing algorithm. Using in vitro data for radiobiological parameters as reference data, we shown that the reconstructed values of cell surviving fractions and potential doubling time exhibit non-physical fluctuations if no stabilization algorithms are applied. The variational regularization allowed us to obtain statistical distribution for cell surviving fractions and cell number doubling times comparable to in vitro data. Conclusion: Our results indicate that using variational regularization can increase the number of free parameters in the model and open the way to development of more advanced algorithms which take into account tumor heterogeneity, for example, related to hypoxia.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

Non-Linear Luminescent Coupling in Series-Connected Multijunction Solar Cells

The assumption of superposition or linearity of photocurrent with solar flux is widespread for calculations and measurements of solar cells. The well-known effect of luminescent coupling in multijunction solar cells has also been assumed to be linear with excess current. Here we show significant non-linearities in luminescent coupling in III-V multijunction solar cells and propose a simple model based on competition between radiative and nonradiative processes in the luminescent junction to explain these non-linearities. We demonstrate a technique for accurately measuring the junction photocurrents under a specified reference spectrum, that accounts for and quantifies luminescent coupling effects.

14 SOLAR ENERGY↗