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At least 199 records · Page 11

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Regridding uncertainty for statistical downscaling of solar radiation

Abstract. Initial steps in statistical downscaling involve being able to compare observed data from regional climate models (RCMs). This prediction requires (1) regridding RCM outputs from their native grids and at differing spatial resolutions to a common grid in order to be comparable to observed data and (2) bias correcting RCM data, for example via quantile mapping, for future modeling and analysis. The uncertainty associated with (1) is not always considered for downstream operations in (2). This work examines this uncertainty, which is not often made available to the user of a regridded data product. This analysis is applied to RCM solar radiation data from the NA-CORDEX (North American Coordinated Regional Climate Downscaling Experiment) data archive and observed data from the National Solar Radiation Database housed at the National Renewable Energy Lab. A case study of the mentioned methods over California is presented.

14 SOLAR ENERGY↗

NASA GLDAS Evapotranspiration Data and Climatology

Evapotranspiration (ET) is the water lost to the atmosphere by evaporation and transpiration. ET is a shared component in the energy and water budget, therefore, a critical variable for global energy and water cycle and climate change studies. However, direct ET measurements and data acquisition are difficult and expensive, especially at the global level. Therefore, modeling is one common alternative for estimating ET. With the goal to generate optimal fields of land surface states and fluxes, the Global Land Data Assimilation System (GLDAS) has been generating quality-controlled, spatially and temporally consistent, terrestrial hydrologic data, including ET and other variables that affect evaporation and transpiration, such as temperature, precipitation, humidity, wind, soil moisture, heat flux, and solar radiation. This poster presents the long-term ET climatology (mean and monthly), derived from the 61-year GLDAS-2 monthly 1.0 deg x 1.0 deg. NOAH model Experiment-1 data, and describes the basic characteristics of spatial and seasonal variations of the climatology. The time series of GLDAS-2 precipitation and radiation, and ET are also discussed to show the improvement of GLDAS-2 forcing data and model output over those from GLDAS-1.

Rui, Hualan↗

Development of a Annual Air Handling Unit Fault Dataset for FDD Tools: Lessons Learned and Considerations for FDD Developers

As energy management and information systems (e.g., automated fault detection and diagnostics [AFDD] tools) become more prevalent in the commercial building stock, it is important to determine the effectiveness of these technologies by benchmarking their performance. The authors have been working to develop the largest publicly available dataset of HVAC fault data for performance benchmarking applications, covering the most common HVAC systems and designs including chiller plants, rooftop packaged units, dual duct air handling units and single duct air handling units. This study covers the development, modeling, and validation of a synthetic fault dataset for a single duct air handling unit (AHU), one of the most common HVAC configurations found in the commercial building stock. Despite this being a common system, real-world time series data are scarce and usually do not span a wide range of weather conditions. Due to this limitation, a detailed AHU model was employed to carry out annual simulations of numerous common sensor and mechanical faults, which were then validated by comparing their effects on system performance to expected symptoms. We summarize the nature of each fault and their impacts under different weather and operation conditions. Finally, we highlight considerations for FDD developers that may want to use this dataset to assess their algorithms’ performance and their improvement over time.

Casillas, Armando↗

The shock physics of giant impacts: Key requirements for the equations of state

We discuss major challenges in modeling giant impacts between planetary bodies, focusing on the equations of state (EOS). During the giant impact stage of planet formation, rocky planets are melted and partially vaporized. However, most EOS models fail to reproduce experimental constraints on the thermodynamic properties of the major minerals over the required phase space. Here, we present an updated version of the widely-used ANEOS model that includes a user-defined heat capacity limit in the thermal free energy term. Our revised model for forsterite (Mg 2 SiO 4 ), a common proxy for the mantles of rocky planets, provides a better fit to material data over most of the phase space of giant impacts. We discuss the limitations of this model and the Tillotson equation of state, a commonly used alternative model.

79 ASTRONOMY AND ASTROPHYSICS↗

Erosional dynamics, flexural isostasy, and long-lived escarpments: A numerical modeling study

Erosional escarpments common features of high-elevation rifted continets. Fission track data suffest that these escarpments form by base level lowering and/or marginal uplift during rifting, followed by lateral retreat of an erosion front across tens to hundreds of kioometers. Previous modeling studies have shown that this characteristic pattern of denudation can have a profound impact upon marginal isostatic uplift and the evolution of offshore sedimentary basins. Yet at present there is only a rudimentary understanding of the geomorphic mechanisms capable of driving such prolonged escarpment retreat. In this study we present a nonlinear, two-dimensional landscape evolution model tha tis used to asses the necessary and sufficient conditions for long-term retreat of a rift-generated escarpment. The model represents topography as a grid of cells, with drainage networkds evolving as water flows across the grid in the direction of steepest descent. The model accounts for sediment production by weathering, fluvial sediment transport, bedrock channel erosion, and hillslope sediment transport by diffusive mechanisms and by mass failure. Numerical experiments presented explore the effects of different combinations of erosion processes and of dynamic coupling between denudation and flexural isostatic uplift. Model results suggest that the necessary and sufficient conditions for long-term escarpment retreat are (1) incising bedrock channels in which the erosion rate increases with increasing drainage area, so that the channels steepen and propagate headward; (2) a low rate of sediment production relative to sediment transport efficiency, which promotes relief-generating processes over diffusive ones; (3) high continental elevation, which allows greater freedom for fluvial dissection; and (4) any process, including flexural isostatic uplift, that helps to maintain a drainage divide near an escarpment crest. Flexural isostatic uplift also facilitates escarpment, thereby increasing channel gradients and accelerating erosion which in turn generates additional isostatic uplift. Of all the above conditions, high continental elevation is common ot most rift margin escarpments and may ultimately be the most important factor.

Tucker, Gregory E.↗

CrossLink: Meshing a 3D part from a STEP file [Slides]

This example shows how to use CrossLink to create a mesh for a 3D geometry part read in from a STEP file. A STEP file (Standard for the Exchange of Product data) is a common file format used for 3D modelling that can be written out from a CAD program (e.g., Creo Parametric). Being able to read and mesh STEP file geometries is essential for meshing parts from engineering models. Creating the mesh typically involves: (1) Importing the geometry; (2) Creating geometry groups; (3) Assigning curves and surfaces to the geometry groups; (4) Building a topology; (5) Applying geometric and mesh constraints; and (6) Generating the final mesh. Current issues with this process in CrossLink include: (1) The GUI does not display trimmed surfaces; (2) The user must manually create and assign geometry groups; and (3) The user must be aware of duplicate curves and surfaces from the CAD model.

97 MATHEMATICS AND COMPUTING↗

Mechanistic studies of polymeric samples exposed aboard STS 8

The early Shuttle flights and the attendant opportunity to deploy material samples to the near-Earth space environment, along well-defined trajectories and accompanied by detailed characterization of these samples prior to and following the flight exposure, have brought to light several novel phenomena associated with interaction of these materials with the space environment. JPL, in coordination with other NASA Centers, has carried out a research program to study the degradation and oxidation processes caused by interaction of these materials with atomic oxygen at an energy of 5 eV. In addition, energetic atomic oxygen is believed to be responsible for the shuttle glow first observed during the flight of STS-3. The shuttle glow phenomenon has been extensively studied and modeled because of its long-range potential impact on optical communication schemes and its more immediate impact on the Space Telescope. This report summarizes the results of certian material degradation and erosion experiments carried out aboard STS-8 between August 30, 1983 and September 5, 1983. Based on these data, a generic degradation model has been developed for common structural polymers.

Liang, Ranty H.↗

Advanced Technology Lifecycle Analysis System (ATLAS) Technology Tool Box (TTB)

The Advanced Technology Lifecycle Analysis System (ATLAS) is a decision support tool designed to aid program managers and strategic planners in determining how to invest technology research and development dollars. It is an Excel-based modeling package that allows a user to build complex space architectures and evaluate the impact of various technology choices. ATLAS contains system models, cost and operations models, a campaign timeline and a centralized technology database. Technology data for all system models is drawn from a common database, the ATLAS Technology Tool Box (TTB). The TTB provides a comprehensive, architecture-independent technology database that is keyed to current and future timeframes.

Doyle, Monica↗

Vector-Ordering Filter Procedure for Data Reduction

The vector-ordering filter (VOF) technique involves a procedure for sampling a large population of data vectors to select a subset of data vectors that fully characterize the state space of the large population. The VOF technique enables a large reduction of the volume of data that must be handled in the automated monitoring system and method discussed in the two immediately preceding articles. In so doing, the VOF technique enables the development of data-driven mathematical models of a monitored asset from sets of data that would otherwise exceed the memory capacities of conventional engineering computers. Data-driven mathematical models have been shown to offer high fidelity for purposes of control and monitoring of assets. In practice, a collection of asset-operating observations is acquired with the intention that the collection contain observations characteristic of the full dynamic range of operation of the asset. Often, such a collection contains an extremely large number of observations, many of which are redundant. The VOF technique fills the need for a means to extract, from the original collection of observational data, a reduced data matrix that excludes redundant data while maintaining the full statistical character and dynamic range of the original data. The reduced data matrix can then be used as the input data for development of a mathematical model of the monitored asset, or as training data for a neural-network substitute for an explicit mathematical model of the asset. Alternatively, the reduced data matrix can, itself, be used directly as a mathematical model of the monitored asset, as is commonly done in multivariate state-estimation techniques. The original data are collected from the asset over a range of operating states and are put in matrix form. Each column vector in the original data matrix represents the signal values acquired at a particular operational state of the asset. Thus, the number of columns of the original data matrix equals the number of observed states and the number of rows in this matrix equals the number of signals acquired at each observation. In the VOF technique, one extracts the reduced data matrix from the original data matrix through the selection of a representative subset of the column (state) vectors.

Bickford, Randall L.↗

Data Driven Model Development for the SuperSonic SemiSpan Transport (S(sup 4)T)

In this report, we will investigate two common approaches to model development for robust control synthesis in the aerospace community; namely, reduced order aeroservoelastic modelling based on structural finite-element and computational fluid dynamics based aerodynamic models, and a data-driven system identification procedure. It is shown via analysis of experimental SuperSonic SemiSpan Transport (S4T) wind-tunnel data that by using a system identification approach it is possible to estimate a model at a fixed Mach, which is parsimonious and robust across varying dynamic pressures.

Kukreja, Sunil L.↗

Flow-based likelihoods for non-Gaussian inference

We investigate the use of data-driven likelihoods to bypass a key assumption made in many scientific analyses, which is that the true likelihood of the data is Gaussian. In particular, we suggest using the optimization targets of flow-based generative models, a class of models that can capture complex distributions by transforming a simple base distribution through layers of nonlinearities. We call these flow-based likelihoods (FBL). We analyze the accuracy and precision of the reconstructed likelihoods on mock Gaussian data, and show that simply gauging the quality of samples drawn from the trained model is not a sufficient indicator that the true likelihood has been learned. We nevertheless demonstrate that the likelihood can be reconstructed to a precision equal to that of sampling error due to a finite sample size. We then apply FBLs to mock weak lensing convergence power spectra, a cosmological observable that is significantly non-Gaussian (NG). We find that the FBL captures the NG signatures in the data extremely well, while other commonly used data-driven likelihoods, such as Gaussian mixture models and independent component analysis, fail to do so. This suggests that works that have found small posterior shifts in NG data with data-driven likelihoods such as these could be underestimating the impact of non-Gaussianity in parameter constraints. By introducing a suite of tests that can capture different levels of NG in the data, we show that the success or failure of traditional data-driven likelihoods can be tied back to the structure of the NG in the data. Here, unlike other methods, the flexibility of the FBL makes it successful at tackling different types of NG simultaneously. Because of this, and consequently their likely applicability across datasets and domains, we encourage their use for inference when sufficient mock data are available for training.

79 ASTRONOMY AND ASTROPHYSICS↗

Constraining long‐term model predictions for woody growth using tropical tree rings

The strength and persistence of the tropical carbon sink hinges on the long-term responses of woody growth to climatic variations and increasing CO 2 . However, the sensitivity of tropical woody growth to these environmental changes is poorly understood, leading to large uncertainties in growth predictions. Here, we used tree ring records from a Southeast Asian tropical forest to constrain ED2.2-hydro, a terrestrial biosphere model with explicit vegetation demography. Specifically, we assessed individual-level woody growth responses to historical climate variability and increases in atmospheric CO 2 (C a ). When forced with historical C a , ED2.2-hydro reproduced the magnitude of increases in intercellular CO 2 concentration (a major determinant of photosynthesis) estimated from tree ring carbon isotope records. In contrast, simulated growth trends were considerably larger than those obtained from tree rings, suggesting that woody biomass production efficiency (WBPE = woody biomass production:gross primary productivity) was overestimated by the model. The estimated WBPE decline under increasing C a based on model-data discrepancy was comparable to or stronger than (depending on tree species and size) the observed WBPE changes from a multi-year mature-forest CO 2 fertilization experiment. In addition, we found that ED2.2-hydro generally overestimated climatic sensitivity of woody growth, especially for late-successional plant functional types. The model-data discrepancy in growth sensitivity to climate was likely caused by underestimating WBPE in hot and dry years due to commonly used model assumptions on carbon use efficiency and allocation. To our knowledge, this is the first study to constrain model predictions of individual tree-level growth sensitivity to C a and climate against tropical tree-ring data. Our results suggest that improving model processes related to WBPE is crucial to obtain better predictions of tropical forest responses to droughts and increasing C a . Finally, more accurate parameterization of WBPE will likely reduce the stimulation of woody growth by C a rise predicted by biosphere models.

54 ENVIRONMENTAL SCIENCES↗

Common Information Model for Electromagnetic Transients (CIM for EMT): CRADA 533 [Abstract only}

The control and protection functions of inverter-based resources (IBR) have raised concerns with bulk system reliability. Most of the current interest lies with solar photovoltaic generation but increasing amounts of storage would pose the same risks. Newer North American Electric Reliability Corporation (NERC) guidelines call for electromagnetic transient (EMT) studies of IBR and recommend that transmission operators collect distributed energy resource (DER) data to support such modeling. IEEE Standard P2800.1 is defining tests for model parameterization, so good model data should become available from inverter vendors. (EMT studies also apply to large power transformer reliability, and transformer vendors can provide EMT models.) Utilities don’t currently have the rest of the bulk system represented for EMT studies at large scale. An International Electrotechnical Commission (IEC) standard Common Information Model (CIM) provides a way of supporting these detailed models from physical asset data, e.g., conductors, towers, transformer data sheets, control block diagrams, while avoiding software vendor lock-in. CIM-for-EMT, with proposed schema extensions and open-source converters, provides a way to exchange EMT data between organizations and tools. This project leverages Office of Electricity (OE) funding of CIM-for-EMT code base through the GridAPPS-DTM project, and of GridPACKTM (parallelized transmission solver), for interoperability testing in CIM-for-EMT. The project also leverages partner PGSTech investments in EMTP® interoperability with CIM.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Bay Area Regional Energy: Network Integrated Commercial Retrofits (BRICR) Project. Final Report

The BRICR project applied large-scale building energy modeling concepts with the aim of reducing the cost of energy efficiency targeting, design, and project development, and measurement of energy savings for energy efficiency programs implemented by local governments that serve small and medium commercial buildings (SMB). The project leveraged the services and resources of existing local government energy programs serving disadvantaged and hard-to-reach SMB customers. In contrast to programs run by utilities, local government programs generally do not have direct access to energy billing records for an entire class of customers in a geographic area, which prior research demonstrated useful for large-scale building energy model baseline development and calibration. , However, local governments are rich in public records that offer important clues about physical attributes and uses that, along with behavior, determine energy use. Relying only on public records, BRICR demonstrated development of credible baseline energy models for 3,792 office, retail, and hotel buildings. Publicly disclosed annual energy use data from a local energy benchmarking program and anonymized data from the Building Performance Database, the nation’s largest dataset about energy-related characteristics of buildings, were utilized to validate and calibrate energy models via an innovative method comparing distributions of energy intensity by fuel type for portfolios of buildings of similar size, vintage, and use. Portfolio calibration does not provide certainty that an energy model fits an individual building; the method is useful when billing data is not accessible – a common situation for researchers, energy service providers and ESCOs, local governments, and any party other than a utility. A software component was developed, the BRICR gem, which automates simulation when relevant data is added or edited by the user to a file saved in the standardized BuildingSync XML schema for energy audit data. The component was demonstrated as a simplified means to generate a mass of energy models corresponding to public records containing basic attributes such as building scale, location, use, year built, and aspect ratio in combination with building energy code prototype data corresponding to use and vintage. The component was also demonstrated as a simplified means to automate energy simulation when attributes are revised; the intention was to enable iterative improvement of the baseline model and energy savings estimates for common energy conservation measures as users revise relevant attributes based on their observations. In the context of institutional change and uncertainty for the participating local government energy programs, 13 whole building retrofits were completed. Impacts were measured by applying the CalTRACK2.0 methods to standardize measurement of normalized metered energy consumption. The GRIDMeter methods of stratified sampling and individual load shape analysis were applied to adjust for impacts of the effect of COVID-19 on retrofitted buildings in the context of all local buildings of similar size and use. Excluding impacts of the pandemic, retrofitted buildings demonstrated between 1.6% and 25.1% reduction in energy use. The project contributed use cases and feedback that helped inform evolution of the software tools and data formats that were combined for the first time in the BRICR project.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

NASA Earth Observing System Data and Information System (EOSDIS): A U.S. Network of Data Centers Serving Earth Science Data: A Network Member of ICSU WDS

NASA's Earth Observing System Data and Information System (EOSDIS) has been in operation since August 1994, and serving a diverse user community around the world with Earth science data from satellites, aircraft, field campaigns and research investigations. The ESDIS Project, responsible for EOSDIS is a Network Member of the International Council for Sciences (ICSU) World Data System (WDS). Nine of the 12 Distributed Active Archive Centers (DAACs), which are part of EOSDIS, are Regular Members of the ICSUWDS. This poster presents the EOSDIS mission objectives, key characteristics of the DAACs that make them world class Earth science data centers, successes, challenges and best practices of EOSDIS focusing on the years 2014-2016, and illustrates some highlights of accomplishments of EOSDIS. The highlights include: high customer satisfaction, growing archive and distribution volumes, exponential growth in number of products distributed to users around the world, unified metadata model and common metadata repository, flexibility provided to uses by supporting data transformations to suit their applications, near-real-time capabilities to support various operational and research applications, and full resolution image browse capabilities to help users select data of interest. The poster also illustrates how the ESDIS Project is actively involved in several US and international data system organizations.

Earth Science↗