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At least 37 records · Page 2

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

AlphaFold has recently become an important tool in providing models for experimental structure determination by X-ray crystallography and cryo-EM. Large parts of the predicted models typically approach the accuracy of experimentally determined structures, although there are frequently local errors and errors in the relative orientations of domains. Importantly, residues in the model of a protein predicted by AlphaFold are tagged with a predicted local distance difference test score, informing users about which regions of the structure are predicted with less confidence. AlphaFold also produces a predicted aligned error matrix indicating its confidence in the relative positions of each pair of residues in the predicted model. The phenix.process_predicted_model tool downweights or removes low-confidence residues and can break a model into confidently predicted domains in preparation for molecular replacement or cryo-EM docking. These confidence metrics are further used in ISOLDE to weight torsion and atom–atom distance restraints, allowing the complete AlphaFold model to be interactively rearranged to match the docked fragments and reducing the need for the rebuilding of connecting regions.

59 BASIC BIOLOGICAL SCIENCES↗

Patterns, drivers, and a predictive model of dam removal cost in the United States

Given the burgeoning dam removal movement and the large number of dams approaching obsolescence in the United States, cost estimating data and tools are needed for dam removal prioritization, planning, and execution. We used the list of removed dams compiled by American Rivers to search for publicly available reported costs for dam removal projects. Total cost information could include component costs related to project planning, dam deconstruction, monitoring, and several categories of mitigation activities. We compiled reported costs from 455 unique sources for 668 dams removed in the United States from 1965 to 2020. The dam removals occurred within 571 unique projects involving 1–18 dams. When adjusted for inflation into 2020 USD, cost of these projects totaled $\$1.522$ billion, with per-dam costs ranging from $\$1$ thousand (k) to $\$268.8$ million (M). The median cost for dam removals was $\$157$k, $\$823$k, and $\$6.2$M for dams that were< 5 m, between 5–10 m, and > 10 m in height, respectively. Geographic differences in total costs showed that northern states in general, and the Pacific Northwest in particular, spent the most on dam removal. The Midwest and the Northeast spent proportionally more on removal of dams less than 5 m in height, whereas the Northwest and Southwest spent the most on larger dam removals > 10 m tall. We used stochastic gradient boosting with quantile regression to model dam removal cost against potential predictor variables including dam characteristics (dam height and material), hydrography (average annual discharge and drainage area), project complexity (inferred from construction and sediment management, mitigation, and post-removal cost drivers), and geographic region. Dam height, annual average discharge at the dam site, and project complexity were the predominant drivers of removal cost. The final model had an R 2 of 57% and when applied to a test dataset model predictions had a root mean squared error of $\$5.09$M and a mean absolute error of $\$1.45$M, indicating its potential utility to predict estimated costs of dam removal. We developed a R shiny application for estimating dam removal costs using customized model inputs for exploratory analyses and potential dam removal planning.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Predictive Modeling of Electrodeposition in a Single Pore Flow-Through Electrode: From Electronucleation to Coating Thickness Uniformity

The emergence of advanced manufacturing methods capable of producing porous three-dimensional structures has expanded the design space for next-generation functional components. The ability to fabricate ordered 3D foams for use in electrocatalysis reactors has increased the need for controlled deposition of catalytic metals onto porous support materials, such as carbon. However, there is a lack of clear design guidelines for electrodeposition onto 3D substrates, due to the geometric complexity and multi-scale nature of the problem. Furthermore, electro-nucleation phenomena are often overlooked in macro-scale models of current distribution during deposition. Here, a graphite flow-through electrode (FTE) is used as a model system for copper deposition within a single pore. Potential distributions and electro-nucleation phenomena are coupled in a continuum level model by incorporating nucleation size and density as a function of overpotential, determined experimentally using in situ atomic force microscopy (AFM). The model predictions are validated by measuring the coating uniformity in the pore using micro-computed X-ray tomography (μCT). A scaling analysis comprising dimensionless parameters such as the Wagner number is presented. The simplified scaling relationship framework can guide the electrodeposition process and electrode design to optimize plating of porous substrates under fluid flow conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Field Performance of Commercial Building Load Flexibility Using Model Predictive Control

Model Predictive Control (MPC) applied to buildings is starting to see some commercial adoption by companies. However, it is hard to estimate if relative energy cost savings are enough to justify the cost of MPC implementation with few reported demonstrations. In small commercial and residential buildings, a one size-fits-all solution can help reduce implementation costs, while in very large buildings or districts the potential energy cost savings magnitude can cover more tailored solutions. This estimation becomes harder for medium to large commercial buildings, where a one-size-fits-all solution cannot be adopted and potential energy cost savings might not be sufficient to cover a tailored solution. Therefore, value propositions in addition to energy efficiency alone can make MPC technology more attractive through additional energy cost savings. One such value proposition is load shifting in response to dynamic electricity prices. On this aspect, MPC is a key technology to unlock building thermal mass for energy flexibility in response to electric grid conditions. This study shows the experimental results of MPC control of an office building in Berkeley, where different dynamic electricity price profiles were used in the MPC objective function to shift the building load and to calculate hypothetical electricity costs. Results show potential 50% cost savings with respect to the existing controller with the dynamic price scenario.

Zanetti, Ettore↗

Milestone 1.2.13: Preliminary Measurements of Radiolytic Nitric Acid Formation to Support Predictive Model Validation

Predictive computational models have been developed to support the technical basis for extended dry storage of aluminum-clad spent nuclear fuel (ASNF) in helium-backfilled cannisters. To date, these models have been optimized on a variety of irradiation experiments designed to elucidate the radiation-induced formation of molecular hydrogen gas, a radiolysis product that is potentially problematic for the safe storage of ASNF. However, the yield of nitric acid (HNO3) has not been determined, despite conservative predictions of its formation (300–4000 ppm) in 1% residual air environments irradiated in contact with ASNF. HNO3, another problematic radiolysis product, can lead to enhanced corrosion and potentially compromise storage canister integrity. Thus, to support the validation of predictive computer models, we report the measurement and quantification of HNO3 from the gamma irradiation of aluminum alloy coupons in humid air.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Can reanalysis products outperform mesoscale numerical weather prediction models in modeling the wind resource in simple terrain?

Mesoscale numerical weather prediction (NWP) models are generally considered more accurate than reanalysis products in characterizing the wind resource at heights of interest for wind energy, given their finer spatial resolution and more comprehensive physics. However, advancements in the latest ERA-5 reanalysis product motivate an assessment on whether ERA-5 can model wind speeds as well as a state-of-the-art NWP model – the Weather Research and Forecasting (WRF) Model. We consider this research question for both simple terrain and offshore applications. Specifically, we compare wind profiles from ERA-5 and the preliminary WRF runs of the Wind Integration National Dataset (WIND) Toolkit Long-term Ensemble Dataset (WTK-LED) to those observed by lidars at a site in Oklahoma, United States, and in a United States Atlantic offshore wind energy area. We find that ERA-5 shows a significant negative bias (~-1ms-1) at both locations, with a larger bias at the land-based site. WTK-LED-predicted wind speed profiles show a limited negative bias (~-0.5ms-1) offshore and a slight positive bias (~+0.5ms-1) at the land-based site. On the other hand, we find that ERA-5 outperforms WTK-LED in terms of the centered root-mean-square error (cRMSE) and correlation coefficient, for both the land-based and offshore cases, in all atmospheric stability conditions. We find that WTK-LED's higher cRMSE is caused by its tendency to overpredict the amplitude of the wind speed diurnal cycle. At the land-based site, this is partially caused by wind plant wake effects not being accurately captured by WTK-LED.

17 WIND ENERGY↗

Self-Consistent Implementation of a Zero-Equation Transport Model Into a Predictive Model for a Hall Effect Thruster

The performance of an axisymmetric multi-fluid Hall thruster code that incorporates a self-consistent, data-driven closure model for the anomalous electron transport is investigated. Five different operating conditions of the H9 magnetically shielded Hall thruster are simulated with the Jet Propulsion Laboratory’s Hall2De. In order to capture the inherent uncertainty associated with the closure model, O(100) simulations are run for each condition, each of using a coefficient set sampled randomly from a probability distribution. The results of these simulations provide probabilistic predictions of thruster performance quantities including thrust, and discharge current, as well as several component efficiencies and centerline plasma properties. The model is found to yield converged solutions at all conditions, with large 10 kHzrange oscillations and performance trends with voltage and flow rate similar to experiment. The model under-predicts the thrust by 15-25% and over-predicts the discharge current by 20% on average compared to experiments at the same discharge voltage and mass flow rate. This performance discrepancy is due to lower beam utilization, mass utilization, and divergence efficiency than experiment, resulting from high Hall parameters in the acceleration region, which lead to a protracted ion acceleration region. The physical processes underlying this result are discussed in the context of future data-driven modeling efforts.

Jorns, Benjamin A.↗

A Multirange Vehicle Speed Prediction With Application to Model Predictive Control-Based Integrated Power and Thermal Management of Connected Hybrid Electric Vehicles

Abstract Connectivity and automated driving technologies have opened up new research directions in the energy management of vehicles which exploit look-ahead preview and enhance the situational awareness. Despite this advancement, the vehicle speed preview that can be obtained from vehicle-to-vehicle/infrastructure (V2V/I) communications is often limited to a relatively short time-horizon. The vehicular energy systems, specifically those of the electrified vehicles, consist of multiple interacting power and thermal subsystems that respond over different time-scales. Consequently, their optimal energy management can greatly benefit from long-term speed prediction beyond that available through V2V/I communications. Accurately extending the look-ahead preview, on the other hand, is fundamentally challenging due to the dynamic nature of the traffic environment. To address this challenge, we propose a data-driven multirange vehicle speed prediction strategy for arterial corridors with signalized intersections, providing the vehicle speed preview for three different ranges, i.e., short-, medium-, and long-range. The short-range preview is obtained by V2V/I communications. The medium-range preview is realized using a neural network (NN), while the long-range preview is predicted based on a Bayesian network (BN). The predictions are updated in real-time based on the current state of traffic and incorporated into a multihorizon model predictive control (MH-MPC) for integrated power and thermal management (iPTM) of connected vehicles. The results of design and evaluation of the performance of the proposed data-informed MH-MPC for iPTM of connected hybrid electric vehicles (HEVs) using traffic data for real-world city driving are reported.

Automation & Control Systems↗

Characterization of Precipitation-Strengthening Heat-Resistant Austenitic Stainless Steels for Life-Prediction Modeling

In this study, the role of minor alloying additions in 347H stainless steels (UNS34709, ASTM A240/240M) on creep-rupture properties at 650-750°C and microstructure evolution during isothermal exposure at 750°C has been investigated, aiming to provide the experimental dataset as boundary conditions of physics-based modeling for material/component life prediction. Four different 347H heats containing various amounts of boron and nitrogen additions were prepared and evaluated. The combined additions of B and N are found to stabilize the strengthening secondary M23C6 carbides and retarding the transition from M23C6 to sigma phase precipitates during thermal exposure. The observed kinetics of microstructure evolution reasonably explains the improvement of creep-rupture properties of 347H stainless steels with the B and N additions.

Yamamoto, Yukinori↗

Analysis of predicted mean vote-based model predictive control for residential HVAC systems

Model Predictive Control (MPC) is an advanced process control method that has attracted much attention in building heating, ventilation, and air conditioning (HVAC) systems. Here, this paper analyzes the optimal precooling performance in residential buildings using MPC with two different comfort indices, namely, temperature and predicted mean vote (PMV). It first formulates, for each comfort index, an optimization problem that accounts for different factors, such as weather, home thermal condition, prediction horizon, time-of use (TOU) utility rate, and rated cooling capacity. The problem is then solved, resulting in an MPC strategy that determines the HVAC on/off control signal and minimizes energy cost over a receding time horizon while maintaining thermal comfort. The energy performance difference between temperature-based and PMV-based MPC strategies is subsequently investigated, especially in light of the interior wall surface temperature and under different combinations of the factors. Extensive simulation results demonstrated that the proposed MPC strategies are adaptive and their performances depend primarily on weather, home thermal condition, and prediction horizon, while the impact of TOU utility rate and rated cooling capacity is relatively small. Because the PMV-based MPC strategy can take advantage of the lower interior wall surface temperature due to precooling, it resulted in 8–45% cost savings for the scenarios investigated and an average increase of 0.042–0.113 in the absolute value of the PMV index compared to the temperature-based MPC strategy.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Life prediction model comparisons

Predictive failure models for nickel cadmium batteries are discussed. Emphasis is given to the McDermott model, the Lander model, and the JPL failure model.

Schulmam, I. M.↗

Understanding the Impact of Unobservable Variables on the Performance of Predictive Models: The Need for Feature Space Partitioning and Fusion

When developing predictive models over a dataset, the model is globally optimized across the entire feature space to learn a decision boundary. However, when unobservable variables—which cannot be measured or estimated—interact with the observable variables, this can negatively impact the optimization applied to the decision boundary since the data samples introduced by unobservable variables may have little to no association with the applied global optimization. This, consequently, penalizes the entire decision boundary and model performance. This paper examines some of the detrimental effects of unobservable variables, particularly their role in creating new modes in the distribution of observable variables and reducing the separability of class distributions. Such challenges result in skewed or warped decision boundaries and decreased accuracy of model predictions, particularly for interpretable models like logistic regression and decision trees. Through two illustrative case examples, we highlight the need to address the challenges imposed by unobservable variables. We propose a strategy to mitigate these challenges by creating local regions within the feature space through partitioning. This enables the optimization of local models within the regions to overcome the impact of unobservability in different feature space localities. Research into a more sophisticated partitioning strategy and where the partition should be relative to the sample of interest is left as future work. Through the analysis of the impact of unobservability and the development of a partitioning method, we demonstrate the clear need for a partitioning strategy that integrates knowledge from multiple local models to estimate risk factors using information fusion. Thus, we establish the foundation and motivation for using partitioning and information fusion to overcome the effects of unobservability in predictive models. Formal fusion methods, such as Dempster-Shafer theory, can better leverage the information from local regions to improve the performance of interpretable predictive models in the presence of unobservable variables.

Time Series Data↗

Estimates of Southern Hemispheric Gravity Wave Momentum Fluxes across Observations, Reanalyses, and Kilometer-Scale Numerical Weather Prediction Model

Abstract Gravity waves (GWs) are among the key drivers of the meridional overturning circulation in the mesosphere and upper stratosphere. Their representation in climate models suffers from insufficient resolution and limited observational constraints on their parameterizations. This obscures assessments of middle atmospheric circulation changes in a changing climate. This study presents a comprehensive analysis of stratospheric GW activity above and downstream of the Andes from 1 to 15 August 2019, with special focus on GW representation ranging from an unprecedented kilometer-scale global forecast model (1.4 km ECMWF IFS), ground-based Rayleigh lidar (CORAL) observations, modern reanalysis (ERA5), to a coarse-resolution climate model (EMAC). Resolved vertical flux of zonal GW momentum (GWMF) is found to be stronger by a factor of at least 2–2.5 in IFS compared to ERA5. Compared to resolved GWMF in IFS, parameterizations in ERA5 and EMAC continue to inaccurately generate excessive GWMF poleward of 60°S, yielding prominent differences between resolved and parameterized GWMFs. A like-to-like validation of GW profiles in IFS and ERA5 reveals similar wave structures. Still, even at ∼1 km resolution, the resolved waves in IFS are weaker than those observed by lidar. Further, GWMF estimates across datasets reveal that temperature-based proxies, based on midfrequency approximations for linear GWs, overestimate GWMF due to simplifications and uncertainties in GW wavelength estimation from data. Overall, the analysis provides GWMF benchmarks for parameterization validation and calls for three-dimensional GW parameterizations, better upper-boundary treatment, and vertical resolution increases commensurate with increases in horizontal resolution in models, for a more realistic GW analysis. Significance Statement Gravity wave–induced momentum forcing forms a key component of the middle atmospheric circulation. However, complete knowledge of gravity waves, their atmospheric effects, and their long-term trends are obscured due to limited global observations, and the inability of current climate models to fully resolve them. This study combines a kilometer-scale forecast model, modern reanalysis, and a coarse-resolution climate model to first compare the resolved and parameterized momentum fluxes by gravity waves generated over the Andes, and then evaluate the fluxes using a state-of-the-art ground-based Rayleigh lidar. Our analysis reveals shortcomings in current model parameterizations of gravity waves in the middle atmosphere and highlights the sensitivity of the estimated flux to the formulation used.

Meteorology & Atmospheric Sciences↗

A Spatiotemporal Prediction Model for Regional Scheduling of Shared Bicycles Based on the INLA Method

Dock-less bicycle-sharing programs have been widely accepted as an efficient mode to benefit health and reduce congestions. And modeling and prediction has always been a core proposition in the field of transportation. Most of the existing demand prediction models for shared bikes take regions as research objects; therefore, a POI-based method can be a beneficial complement to existing research, including zone-level, OD-level, and station-level techniques. Point of interest (POI) is the location description of spatial entities, which can reflect the cycling route characteristics for both commuting and noncommuting trips to a certain extent, and is also the main generating point and attraction point of shared-bike travel flow. In this study, we make an effort to model a POI-level cycling demand with a Bayesian hierarchical method. The proposed model combines the integrated nested Laplace approximation (INLA) and random partial differential equation (SPDE) to cope with the huge computation in the modeling process. In particular, we have adopted the dock-less bicycle-sharing rental records of Mobike as a case study to validate our method; the study area was one of the fastest growing urban districts in Shanghai in August 2016. The operation results show that the method can help better understand, measure, and characterize spatiotemporal patterns of bike-share ridership at the POI level and quantify the impact of the spatiotemporal effect on bicycle-sharing use.

Yu, Zhuoran↗

Station Keeping with an Autonomous Underwater Glider Using a Predictive Model of Ocean Currents

We investigate the use of an autonomous underwater glider as a platform for a virtual mooring. Our approach uses a simple vehicle motion model, a predictive model of ocean currents, and a greedy search algorithm in order to simulate possible actions available to the vehicle and select an action to minimize the distance from the target point. Results from a 19 day experiment in October 2016 near Monterey Bay are presented where we test our control algorithm as well as investigate the effect of a glider’s dive profile on its ability to act as a virtual mooring.

Chien, Steve↗

Prediction modeling of physiological responses and human performance in the heat with application to space operations

This institute has developed a comprehensive USARIEM heat strain model for predicting physiological responses and soldier performance in the heat which has been programmed for use by hand-held calculators, personal computers, and incorporated into the development of a heat strain decision aid. This model deals directly with five major inputs: the clothing worn, the physical work intensity, the state of heat acclimation, the ambient environment (air temperature, relative humidity, wind speed, and solar load), and the accepted heat casualty level. In addition to predicting rectal temperature, heart rate, and sweat loss given the above inputs, our model predicts the expected physical work/rest cycle, the maximum safe physical work time, the estimated recovery time from maximal physical work, and the drinking water requirements associated with each of these situations. This model provides heat injury risk management guidance based on thermal strain predictions from the user specified environmental conditions, soldier characteristics, clothing worn, and the physical work intensity. If heat transfer values for space operations' clothing are known, NASA can use this prediction model to help avoid undue heat strain in astronauts during space flight.

Pandolf, Kent B.↗

Model Predictive Control-Based Dual-Mode Operation of an Energy-Stored Quasi-Z-Source Photovoltaic Power System

The energy-stored quasi-Z-source inverter (ES-qZSI) has attracted much attention for photovoltaic (PV) power generations, due to its capability to stabilize the PV power fluctuations with simple structure and other advantages of Z-source inverter. The improved dual-mode (DM) ES-qZSI is able to support all-weather operation even at night or cloudy days when PV power is extremely low. However, the traditional proportional–integral (PI) based control suffers from complicated controller design and poor dynamic response during mode transition, due to two sets of PI control required for the daytime and night operation modes. In order to overcome that, here in this article, we propose a model predictive control strategy for the DM-ES-qZSI PV power system. The system predictive models in both day and night operating modes are derived. The control strategy is disclosed to ensure high performance of the system, through calling the predictive models and defined cost functions of the two modes within a single control loop. Simulation and experiment are carried out to verify the effectiveness of the proposed control strategy.

14 SOLAR ENERGY↗