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DOE OSTI2014

Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits

Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

CICE on a C-grid: new momentum, stress, and transport schemes for CICEv6.5

Abstract. This article presents the C-grid implementation of the CICE sea ice model, including the C-grid discretization of the momentum equation, the boundary conditions (BCs), and the modifications to the code required to use the incremental remapping transport scheme. To validate the new C-grid implementation, many numerical experiments were conducted and compared to the B-grid solutions. In idealized experiments, the standard advection method (incremental remapping with C-grid velocities interpolated to the cell corners) leads to a checkerboard pattern. A modal analysis demonstrates that this computational noise originates from the spatial averaging of C-grid velocities at corners. The checkerboard pattern can be eliminated by adjusting the departure regions to match the divergence obtained from the solution of the momentum equation. We refer to this novel approach as the edge flux adjustment (EFA) method. The C-grid discretization with edge flux adjustment allows for transport in channels that are one grid cell wide – a capability that is not possible with the B-grid discretization nor with the C-grid and standard remapping advection. Simulation results match the predicted values of a novel analytical solution for one-grid-cell-wide channels.

Lemieux, Jean-François (ORCID:0000000320845759)↗

DOE OSTI2025

Cooper-pair density modulation state in an iron-based superconductor

Superconducting (SC) states that break space-group symmetries of the underlying crystal can exhibit nontrivial spatial modulation of the order parameter. Previously, such states were intimately associated with the breaking of translational symmetry, resulting in the density-wave orders, with wavelengths spanning several unit cells. However, a related basic concept has long been overlooked: when only intra-unit-cell symmetries of the space group are broken, the SC states can show a distinct type of nontrivial modulation preserving long-range lattice translation. Here, in this study, we refer to this new concept as the pair density modulation (PDM) and report the first observation of a PDM state in exfoliated thin flakes of the iron-based superconductor FeTe 0.55 Se 0.45 . Using scanning tunnelling microscopy (STM), we discover robust SC gap modulation with the wavelength corresponding to the lattice periodicity and the amplitude exceeding 30% of the gap average. Notably, we find that the observed modulation originates from the large difference in SC gaps on the two nominally equivalent iron sublattices. The experimental findings, backed up by model calculations, suggest that, in contrast to the density-wave orders, the PDM state is driven by the interplay of sublattice symmetry breaking and a peculiar nematic distortion specific to the thin flakes. Our results establish new frontiers for exploring the intertwined orders in strong-correlated electronic systems and open a new chapter for iron-based superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Quantitative Methods for Comparing Different Polyline Stream Network Models

Two techniques for exploring relative horizontal accuracy of complex linear spatial features are described and sample source code (pseudo code) is presented for this purpose. The first technique, relative sinuosity, is presented as a measure of the complexity or detail of a polyline network in comparison to a reference network. We term the second technique longitudinal root mean squared error (LRMSE) and present it as a means for quantitatively assessing the horizontal variance between two polyline data sets representing digitized (reference) and derived stream and river networks. Both relative sinuosity and LRMSE are shown to be suitable measures of horizontal stream network accuracy for assessing quality and variation in linear features. Both techniques have been used in two recent investigations involving extracting of hydrographic features from LiDAR elevation data. One confirmed that, with the greatly increased resolution of LiDAR data, smaller cell sizes yielded better stream network delineations, based on sinuosity and LRMSE, when using LiDAR-derived DEMs. The other demonstrated a new method of delineating stream channels directly from LiDAR point clouds, without the intermediate step of deriving a DEM, showing that the direct delineation from LiDAR point clouds yielded an excellent and much better match, as indicated by the LRMSE.

58 GEOSCIENCES↗

DOE OSTI2024

Bifacial Vertical Testbed and Ground Irradiance Data in Golden, Colorado

This data was collected for Tonita et al., “Vertical bifacial photovoltaic system model validation: study with field data, various orientations, and latitudes,” for validation of optical models for vertically-oriented photovoltaics under high albedo. Ground irradiance data for vertical PV arrays modeling in agrivoltaics is also provided. The dataset is provided for further use or study as open source. For any questions on the dataset, email silvana.ovaitt@nlr.gov.

14 SOLAR ENERGY↗

DOE OSTI2016

Confirming a pyrolitic lower mantle using self-consistent pressure scales and new constraints on CaSiO 3 perovskite

In this study, we have examined the lower mantle composition and mineralogy by modeling the density ( ρ ), bulk sound velocity ( V Φ ), and dln ρ /dln V Φ profiles of candidate lower mantle minerals using literature and new experimental equation of state (EoS) results. Additionally, for CaSiO 3 perovskite, complimentary synchrotron X-ray diffraction measurements in a laser-heated diamond anvil cell were conducted up to 156 GPa between 1200 K and 2600 K to provide more reliable constraints on the thermal EoS parameters. These new experimental results as well as literature P-V-T data sets are systematically analyzed using an internally self-consistent pressure scale. We have modeled ρ , V Φ , and dln ρ /dln V Φ profiles of the lower mantle with representative pyrolitic and chondritic compositional models in which the effect of Fe spin transition in ferropericlase is also taken into account. Our modeling results show that a pyrolitic lower mantle with an aggregate mineralogy of 75 vol % bridgmanite, 17 vol % ferropericlase, and 8 vol % CaSiO 3 perovskite produces ρ and V Φ profiles in better agreement with preliminary reference Earth model than a lower mantle with a chondritic composition. The modeled ρ , V Φ , and dln ρ /dln V Φ are mainly affected by the relative ratio of bridgmanite and ferropericlase but are not sensitive to the variation of the CaSiO 3 perovskite content. In addition, the spin crossover of Fe in ferropericlase can greatly raise the value of dln ρ /dln V Φ in the middle lower mantle, which is useful in detecting the presence of ferropericlase in the region. Based on these new mineral physical constraints and radial seismic structure, our study suggests the lower mantle is pyrolitic, which is chemically indistinguishable from the upper mantle.

58 GEOSCIENCES↗

DOE OSTI2025

Energy Infrastructure Futures: A Multiscale Evaluation of Projected Power Plant Siting Across the Western Interconnection

Energy Infrastructure Futures: A Multiscale Evaluation of Projected Power Plant Siting Across the Western Interconnection Description This dataset contains input and output data for the manuscript Mongird, K. et al. (under review) titled "Energy Infrastructure Futures: A Multiscale Evaluation of Projected Power Plant Siting Across the Western Interconnection". Input data corresponds to gridded spatial siting attributes that are necessary to conduct a random forest machine learning analysis of siting feature importance. Output data includes SHAP feature analysis outputs, and classification report values. For data on power plant siting results referred to in the manuscript, please refer to the CERF: IM3 Projected Western US Power Plant Locations data download page. The downloadable data includes values for eight different future scenarios for the Western US. The scenarios include combinations of two Shared Socioeconomic Pathways (SSP3 and SSP5) with four high-resolution climate projections specific to the United States (see, https://tgw-data.msdlive.org/). These climate projections include "hotter" and "cooler" variants for two Representative Concentration Pathways (RCP4.5 and RCP8.5). The resulting eight simulations are: rcp45cooler_ssp3 rcp45cooler_ssp5 rcp45hotter_ssp3 rcp45hotter_ssp5 rcp85cooler_ssp3 rcp85cooler_ssp5 rcp85hotter_ssp3 rcp85hotter_ssp5 Technical Information The dataset includes two sets of data files: (1) CERF gridded siting parameters and (2) Feature analysis outputs and classification reports. All downloadable data is in csv file format. Files with x/y coordinate information use the Albers Equal Area Conic projection (ESRI:102003). 1. CERF Gridded Siting Parameters This directory provides a balanced sample of gridded CERF siting parameters data for eight different scenarios for the Western US through 2055, seven different technologies, and eight timesteps. This data serves as input to the feature analysis. It contains the following parameters. region_name - name of region (i.e., state) sited - binary value representing whether the grid cell received a siting of that technology type (1=True) rcp - binary value representing scenario resource concentration pathway (0 = RCP4.5, 1 = RCP8.5) ssp - binary value representing scenario shared socioeconomic pathway (0 = SSP3, 1 = SSP5) climate - binary value representing cooler (0) or hotter (1) GCM forcing tech_name - generation technology name sited_year - year that values correspond to transmission_cost - cost of transmission interconnection pipeline_cost - cost of natural gas pipeline interconnection interconnection_cost - total interconnection cost (sum of transmission cost and gas pipeline cost) lmp - associated locational marginal value ($/MWh) associated with the grid cell, timestep, scenario, and technology xcoord - x-coordinate of location ycoord - y-coordinate of location 2a. Feature Analysis Output The dataset includes the feature analysis shap output for locational marginal price and interconnection cost. It contains the following parameters. technology - generator technology name scenario - name of scenario feature - name of feature, either locational_marginal_price or interconnection_cost value - the mean of absolute value of SHAP values for given feature 2b. Feature Analysis Classification Report This download includes the classification report associated with each random forest model. The dataset contains the following parameters. technology - generation technology name scenario - name of scenario test - one of precision (the proportion of predicted positives that are actually correct), recall (the proportion of actual positives that were correctly identified), f1-score (the harmonic mean of precision and recall) 0.0 - value of test for classification of 0 (grid cell not chosen for siting) 1.0 - value of test for classification of 1 (grid cell chosen for siting) accuracy - accuracy of model (i.e., fraction of all predictions that were right) macro avg - Simple average of test values for all classes weighted avg - Weighted average of test values for all classes, weighted based on Acknowledgment IM3 is a multi-institutional effort led by Pacific Northwest National Laboratory and supported by the U.S. Department of Energy's Office of Science as part of research in MultiSector Dynamics, Earth and Environmental Systems Modeling Program. License This data is made available under a CCBY4 License Disclaimer This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. PACIFIC NORTHWEST NATIONAL LABORATORYoperated byBATTELLEfor theUNITED STATES DEPARTMENT OF ENERGYunder Contract DE-AC05-76RL01830

Mongird, Kendall [Pacific Northwest National Labor↗

DOE OSTI2014

Adsorption Properties of p -Methyl Red Monomeric-to-Pentameric Dye Aggregates on Anatase (101) Titania Surfaces: First-Principles Calculations of Dye/TiO 2 Photoanode Interfaces for Dye-Sensitized Solar Cells

The optical and electronic properties of dye aggregates of p-methyl red on a TiO2 anatase (101) surface were modeled as a function of aggregation order (monomer to pentameric dye) via first principles calculations. A progressive red-shifting and intensity increase toward the visible region in UV/vis absorption spectra is observed from monomeric-to-tetrameric dyes, with each molecule in a given aggregate binding to one of the four possible TiO2 (101) adsorption sites. The pentamer exhibits a blue-shifted peak wave- length in the UV/vis absorption spectra and less absorption intensity in the visible region in comparison; a corresponding manifestation of H-aggregation occurs since one of these five molecules cannot occupy an adsorption site. This finding is consistent with experiment. Calculated density of states (DOS) and partial DOS spectra reveal similar dye…TiO2 nanocomposite conduction band characteristics but different valence band features. Associated molecular orbital distributions reveal dye-to-TiO2 interfacial charge transfer in all five differing aggregate orders; meanwhile, the level of intramolecular charge transfer in the dye becomes progressively localized around its azo- and electron-donating groups, up to the tetrameric dye/TiO2 species. Dye adsorption energies and dye coverage levels are calculated and compared with experiment. Overall, the findings of this case study serve to aid the molecular design of azo dyes towards better performing DSSC devices wherein they are incorporated. In addition, they provide a helpful example reference for understanding the effects of dye aggregation on the adsorbate…TiO2 interfacial optical and electronic properties.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Theory Aided Design of Active and Durable Nanoscale Cathode Catalysts (Final Report)

One of the greatest technological hurdles to deployment of fuel cells relates to the sluggish activity, low durability and the high cost of the catalysts that are currently employed. For automotive PEM fuel cells to become commercially viable, the Pt-specific power density would need to be reduced to less than 0.2gPt/kW (at cell voltages >0.65 V). This would require the Pt loadings to be less than 0.15 mg Pt /cm 2 MEA within the membrane electrode assembly. This could be achieved by enhancing the catalytic activity at the cathode, thus lowering its overpotential. Various different Pt-alloys have shown 2-4 times enhanced activities over Pt alone but still suffer some of the same durability issues as that of the pure Pt. There is a general loss of active Pt due to dissolution and sintering. While there have been a number of elegant fundamental experimental and theoretical studies on ideal single crystal Pt and Pt alloy surfaces which have helped to elucidate the factors that control the activity, there have been very few fundamental studies focused on the stability, reactivity and durability of well-defined Pt nanoparticles. We carried out ab initio density functional theory together with a novel double reference method that we developed to simulate constant potential electrochemical systems in order to model the electrocatalytic reduction of oxygen over model Pt alloy surfaces and nanoparticles. These simulations were used to probe the factors that control the electrocatalytic activity, guide the potential selection of new materials and test their stability under reaction conditions. Ab initio calculations were used to determine the reaction energies and activation barriers for a comprehensive array of different elementary adsorption, desorption, surface reaction and diffusion steps over Pt and Pt alloys involved in the electroreduction of oxygen as a function of surface coverage, the electrochemical potential and temperature. The calculations were used to simulate the potential dependent adsorption and surface reaction energies along with activation barriers in order to determine the kinetics for different surface structures and structural features (step edge and corner sites) to provide the necessary input for kinetic Monte Carlo simulations to follow the rates of reaction. More coarse-grained simulated annealing methods were used to help establish the lowest energy structures and morphologies for different Pt and Pt-alloy nanoparticles that form. The results from the DFT calculations were used to establish an ab initio-derived kinetic database that was used in both 2D and 3D kinetic Monte Carlo simulations that were used to follow the electrocatalytic performance over different particle sizes, shapes and compositions. The ab initio calculations together with the kinetic Monte Carlo simulations were used to complete the following objectives: 1) Determine the controlling elementary reaction pathways and intrinsic kinetics involved in ORR and their potential dependent behavior; 2) Establish the influence of the extrinsic reaction environment including surface structure, alloy composition and spatial arrangement and the humidity on ORR kinetics; 3) Elucidate the effects of particle size and morphology as well as the atomic structure and composition of nanoparticles of Pt, Pt 3 Co, Pt 3 Ni, Pt 3 Fe and other Pt-alloys on the electrocatalytic activity and reaction selectivity; 5) Construct surface Pourbaix phase diagrams for different Pt and Pt-alloys in order to map out the most stable surface phases for different material compositions and reaction conditions; 6) Elucidate the mechanisms that control dissolution and re-deposition of Pt.

08 HYDROGEN↗

DOE OSTI2025

Modeling neutral defects in III-V ternary alloys with a special quasirandom structure: Analysis of As- and III-site point defects in InGaAs

While first-principles density functional theory modeling has become a vital tool to investigate defect properties in semiconductors, the lack of crystalline periodicity in pseudobinary random composition alloys, such as In 1−𝑥 ⁢Ga 𝑥 ⁢As, complicates such analyses. We present a simulation strategy to systematically take into account the variability in the local defect environment in order to predict statistical properties of neutral intrinsic defects in In 1−𝑥⁢ Ga 𝑥 ⁢As. We use a comprehensive sampling from a modest-sized 64-atom special quasirandom structure (SQS) to define a statistically representative set of defects, and use a 512-atom hypercell, a 2 × 2 × 2 supercell of SQS supercells, to achieve cell-size convergence. We articulate an equivalent site principle and describe how it constrains atomic chemical reference energies in computation of defect formation energies in pseudobinary alloys. A simple protocol for estimating reference energies for the Ga and In atoms sharing the III site succeeds in obtaining the equivalence of defects at Ga-sites and In sites in the SQS supercell, (<30 meV differences in average formation energies). For III-site defects, such as the As antisite As III , the statistical variability in formation energies is modest, ≈ 0.1–0.2 eV. The variability in formation energy at As-site defects, such as the As vacancy 𝑣 As , can be much larger, >1 eV. The As antisite is shown to be a low-energy defect and the most likely to be present in as-grown materials, just as in GaAs. All other defects are higher-energy defects unlikely to be important in native material, but potentially important in radiation-damaged material. With a strong variability in defect energies, especially on the As-site, explicit consideration of statistical variability due to compositional randomness will be imperative for meaningful and quantitative comparisons to experiment.

Density functional theory↗

DOE OSTI2021

Sensitivity Analysis of MFiX-PIC Parameters Using Nodeworks, PSUADE, and DAKOTA

The study presented in this report was aimed to demonstrate UQ analysis performed not only with Nodeworks, but also two other well-established UQ software tools from the U.S. DOE’s National Laboratories (PSUADE from Lawrence Livermore National Laboratory and DAKOTA from Sandia National Laboratory). It is important to emphasize that the motivation of this study was not to determine the best UQ software, but to verify if the global sensitivity analyses from the end-to-end workflow in Nodeworks are consistent with the results of other two UQ software. The components of Nodeworks from Python’s ecosystem have been tested as standalone libraries. However, an assessment study for the complete workflow targeting a specific UQ analysis has not been performed for Nodeworks. Hence, this study is expected to serve as an equivalent of solution verification for Nodeworks using other established UQ tools as reference solution. For this purpose, three distinct flow configurations (i.e., settling bed, bubbling fluidized, and circulating fluidized bed) have been used as representative multiphase flow problems of interest. The results of the systematic simulation campaigns performed in an earlier study using the particle-in-cell (PIC) approach in the Multiphase Flow with Interphase eXchanges (MFIX) suite of solvers (i.e., MFiX-PIC) was utilized. The same set of tabulated results was provided as input to the different UQ software for global sensitivity analysis. Results for the three cases indicate that based on the Sobol’ Sensitivity Indices method the order of importance ranking determined by Nodeworks for the Sobol’ Total Sensitivity Indices is consistent with PSUADE and DAKOTA in each case for the five model parameters considered. The input files for Nodeworks for the three cases are also shared through NETL’s Gitlab repository for the reader interested in reproducibility and further analysis (See Section 1.2).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Subject-specific multi-scale modeling of the fate of inhaled aerosols

Determining the fate of inhaled aerosols in the respiratory system is essential in assessing the potential toxicity of inhaled airborne materials, responses to airborne pathogens, or in improving inhaled drug delivery. The availability of high-resolution clinical lung imaging and advances in the reconstruction of lung airways from CT images have led to the development of subject-specific in-silico 3D models of aerosol dosimetry, often referred to as computational fluid-particle-dynamics (CFPD) models. As CFPD models require extensive computing resources, they are typically confined to the upper and large airways. These models can be combined with lower-dimensional models to form multiscale models that predict the transport and deposition of inhaled aerosols in the entire respiratory tract. Understanding where aerosols deposit is only the first of potentially several key events necessary to predict an outcome, being a detrimental health effect or a therapeutic response. To that end, multiscale approaches that combine CFPD with physiologically-based pharmacokinetics (PBPK) models have been developed to evaluate the absorption, distribution, metabolism, and excretion (ADME) of toxic or medicinal chemicals in one or more compartments of the human body. CFPD models can also be combined with host cell dynamics (HCD) models to assess regional immune system responses. Here, this paper reviews the state of the art of these different multiscale approaches and discusses the potential role of personalized or subject-specific modeling in respiratory health.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Memristive behavior in a junctionless flash memory cell

We report charge storage based memristive operation of a junctionless thin film flash memory cell when it is operated as a two terminal device by grounding the gate. Unlike memristors based on nanoionics, the presented device mode, which we refer to as the flashristor mode, potentially allows greater control over the memristive properties, allowing rational design. The mode is demonstrated using a depletion type n-channel ZnO transistor grown by atomic layer deposition (ALD), with HfO{sub 2} as the tunnel dielectric, Al{sub 2}O{sub 3} as the control dielectric, and non-stoichiometric silicon nitride as the charge storage layer. The device exhibits the pinched hysteresis of a memristor and in the unoptimized device, R{sub off}/R{sub on} ratios of about 3 are presented with low operating voltages below 5 V. A simplified model predicts R{sub off}/R{sub on} ratios can be improved significantly by adjusting the native threshold voltage of the devices. The repeatability of the resistive switching is excellent and devices exhibit 10{sup 6 }s retention time, which can, in principle, be improved by engineering the gate stack and storage layer properties. The flashristor mode can find use in analog information processing applications, such as neuromorphic computing, where well-behaving and highly repeatable memristive properties are desirable.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Theoretical Multinary Perovskite Oxides Dataset

Perovskite oxides (ternary chemical formula ABO3) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, the AA'BB'O6 compositions were generated in the a-b+a- Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with DFT using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔHf) and decomposition enthalpies (ΔHd) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated AA'BB'O6 perovskite structures using MP-compatible DFT calculations

Bare, Zachary↗

DOE OSTI2018

Accurate Measurement of the Optical Constants for Organic and Organophosphorous Liquid Layers and Drops

We present accurate measurements for the determination of the optical constants for a series of organic liquids, including organophosphorous compounds. Bulk liquids are rarely encountered in the environment, but more commonly are present as droplets of liquids or thin layers on various substrates. Providing reference spectra to account for the plethora of morphological conditions that may be encountered under different scenarios is a challenge. An alternative approach is to provide the complex optical constants, n and k, which can be used to model the optical phenomena in media and at interfaces, minimizing the need for a vast number of laboratory measurements. In this work, we present improved protocols for measuring the optical constants for a series of liquids that span the range from 7800 to 400 cm-1. The broad spectral range means that one needs to account for both the strong and weak spectral features that are encountered, all of which can be useful for detection, depending on the scenario. To span this dynamic range, both long and short cells are required for accurate measurements. The protocols are presented along with experimental and modeling results for thin layers of silicone oil on aluminum.

optical constants↗

DOE OSTI2016

Appalachian Basin Play Fairway Analysis Thermal Risk Factor and Quality Analyses

*This submission revises the analysis and products for Thermal Quality Analysis for the northern half of the Appalachian Basin (https://gdr.openei.org/submissions/638)* This submission is one of five major parts of a Low Temperature Geothermal Play Fairway Analysis. Phase 1 of the project identified potential Geothermal Play Fairways within the Appalachian basin of Pennsylvania, West Virginia and New York. This submission includes a subset of the necessary shapefiles, rasters, datasets, code, and references to code repositories that were used to create the thermal resource and risk factor maps as part of the project. This subset is those contents that were improved upon during calendar year 2016. Figures are provided as examples of some shapefiles and rasters. See also: Final Report: Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (https://gdr.openei.org/submissions/899). The 2015 data submission should be visited to obtain: 1) the regional standardized 1 square km grid used in the project as points (cell centers), polygons, and as a raster, 2) the raw well data for the state well temperature databases, 3) the COSUNA section shapefile and formation thermal conductivities by state as *.xlsx files, 4) the sediment thickness map and 30 m Digital Elevation Model for the Appalachian Basin as GeoTIFF raster files, 5) the BHT correction sections shapefile and drilling fluid databases as *.csv files, 6) the unbuffered interpolation regions as shapefiles, 7) several 50 km buffered interpolation regions as shapefiles, 8) several gridded interpolation regions as raster files, 9) an R script for organizing the thermal data and running the local spatial outlier analysis, 10) shapefiles and rasters for the prediction, uncertainty, and cross validation of the temperature at 1.5 km, 2.5 km, and 3.5 km depth, 11) shapefiles and rasters for the prediction, uncertainty, and cross validation depth to 100 degrees C, 12) an ArcGIS toolbox for thermal risk factor models, 13) an ArcGIS model for extracting results specific to each county of interest, 14) thermal resource cross section plots, 15) the geothermal Play Fairways.

15 GEOTHERMAL ENERGY↗

DOE OSTI2020

Sensitivity Analysis and Effective Parametrization of PEM Fuel Cell Models

The cost of proton-exchange-membrane fuel cells (PEMFCs) remains a major hurdle in large-scale commercialization of this technology. To improve their performance and reduce cost, novel materials and electrode designs are continuously envisioned, e.g., non-PGM catalyst layers, ultra-thin Pt/Pt-Ni based catalyst layers, structured ionomer arrays or NSTF catalyst layers.1 Understanding the impact of these improvement strategies can be extremely time and cost intensive due to complex physical phenomena and large design space. We have previously developed a PEMFC modeling framework2 which has been a time and cost effective tool for understanding and optimizing the complex multi-physics phenomena within PEMFCs; however, several of the cell parameters used in the modeling have large spread in measured data.3 Furthermore, several transport parameters such as water adsorption kinetics have not been accurately measured and the approximations are spread over several orders of magnitude. These uncertainties cause problems in ascertaining accuracy of the modeling approach and they reduce the predictive power of the numerical models. The aim of this work is to identify the sensitivity of PEFC numerical model outputs to various input parameters. The previously in-house developed MEA modeling framework2 is used for PEMFC modeling. The sensitivity of the model outputs with respect to inputs parameters is obtained by analyzing the condition numbers for different output-input pairs at varying operating conditions. An example of the sensitivity analysis is shown in Figure 1. The condition numbers are obtained for the entire possible range of input parameters at varying operating conditions to identify the most crucial parameters of the PEMFC model. Based on our preliminary analysis, parameters related to kinetics (exchange current density and ECSA) and heat/water management in electrodes and ionomer (ionomer fraction, thermal conductivity) are most crucial. One of the major goals of this work is to identify the most crucial set of parameters towards which the model shows maximum sensitivity. This will guide future experimentalists to measure these properties with higher accuracy. Furthermore, the sensitivity analysis will also enable us to optimize the PEMFC performance by selectively targeting the most sensitive parameters and thereby making the largest impact. Acknowledgements The work is funded under the Fuel Cell Performance and Durability Consortium (FC-PAD), by the Fuel Cell Technologies Office (FCTO), Office of Energy Efficiency and Renewable Energy (EERE), of the U.S. Department of Energy under contract number DE-AC02-05CH11231. The authors would like to thank Nathan Craig at Robert Bosch LLC for his valuable input in designing the sensitivity analysis. The authors would also like to thank Giovanna Bucci and Matthias Hanauer at Robert Bosch for their valuable inputs and discussion. References P. K. Sinha, W. Gu, A. Kongkanand and E. Thompson, J. Electrochem. Soc., 158, B831 (2011). L. M. Pant, M. R. Gerhardt, N. Macauley, R. Mukundan, R. L. Borup and A. Z. Weber, Electrochim. Acta, 326, 134963 (2019). R. Vetter and J. O. Schumacher, ArXiv181110091 Phys. (2018). Figure 1

Pant, Lalit↗

DOE OSTI2024

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗