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Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗

A Machine Learning Approach to Improve Air Traffic Management Initiatives

Collaborating closely with commercial air carriers and related organizations, the Federal Aviation Administration(FAA) regulates air traffic and ensures the safety and efficiency of air operations. Air traffic controllers make strategic decisions, such as delaying, rerouting, or canceling flights, partly based on guidance provided by the FAA’s Air TrafficControl System Command Center (ATCSCC). The guidance includes, among other things, control measures known asTraffic Management Initiatives (TMIs) designed to enhance safety and improve operational efficiency. TMIs play a crucial role in managing the demand and capacity within the U.S. National Airspace System (NAS). Two major TMIs that are routinely used (primarily to mitigate the adverse effects of bad weather) are Ground Delay Programs (GDPs) andGround Stops (GSs). In a GDP, flights destined for airports facing thunderstorm activity experience delays at their origin airports. This proactive approach minimizes the risk of routing aircraft through hazardous weather conditions and also replaces (fuel burning) airborne delays with ground delays. In a GS, a temporary restriction is imposed on the departure or arrival of aircraft at a specific airport or within a designated airspace. Although other TMIs (e.g., miles-in-trail) are also implemented as part of (air) traffic flow management in the NAS, the focus of this work is on GDPs and GSs. Since TMIs, by design, lead to flight delays or cancellations, it is crucial to put in place the right set of parameters(e.g., scope and duration of the GDP). For example, when the end time of a GDP extends beyond what is necessary, it imposes unnecessary delays on departing flights. This situation could occur as a result of inaccurate prediction of the(required) duration of the GDP based on the weather forecast. On the other hand, if a GDP ends prematurely before the underlying capacity constraints are resolved at the destination airport, it may result in airborne holding. The delicate balance lies in matching the termination of the GDP precisely with the resolution of capacity constraints, avoiding both the imposition of unnecessary ground delays and the need for airborne holding due to premature program termination.Failing to specify the right parameters for TMIs also leads to flight delays, creating a significant obstacle in managing the increasing traffic volumes causing increased work load for the controllers. To address this issue, we propose the integration of Machine Learning (ML) models in the traffic flow management(TFM) pipeline. In current operations, decisions are made by human experts based on extensive training, historical patterns, available traffic and weather data. Since we have an abundance of data from past events that tell us the likely impact of various TMIs, by ingesting historical data, properly trained ML models can offer valuable insights and aid human decision-making. With the FAA increasingly exploring advanced analytics, ML emerges as a focal point for enhancing TFM within the National Airspace System (NAS). As a first step, this study aims to provide traffic controllers with decision-making support for the issuance and adjustment of TMIs. Data analytics and machine learning have been previously employed to address some of the challenges associated with TMIs. Numerous studies have concentrated on various facets of TMI issuance, exploring factors influencing TMI parameters, including arrival rate, airport capacity, and delay prediction. For example, using weather forecasts, several statistical methods were used to produce probabilistic capacity profiles which in conjunction with deterministic models provided insights into the GDP planning process [1–4]. The downside of using deterministic models is that they rely on fixed inputs and predetermined rules, which lack the ability to account for the inherent uncertainty and variability present in real-world scenarios. In a separate series of studies, researchers aimed to predict the occurrences of GDPs and GSs. The majority of these studies utilized various supervised learning methods, including Decision Trees, Naive Bayes, Support VectorMachines, and Random Forests to analyze the influence of weather conditions and arrival demand on TMI incidents[5–8]. However, these studies primarily focused on predicting the incidence of TMIs without explicitly addressing the scope of TMIs, including their duration and their geographical coverage. Furthermore, the emphasis of these studies was largely on GDPs, given their higher frequency and longer duration when compared to GSs. A limited number of studies focused on predicting the parameters of TMIs, specifically addressing their duration and extent. In one such study focusing on optimizing the TMI parameters at San Francisco International Airport (SFO),the authors utilized a probabilistic forecast of fog [9]. They simulated various capacity scenarios based on the (fog)burn-off forecasts, selecting GDP parameters that minimized airborne and overall ground delays. However, this approach exclusively emphasizes stratus (fog) burn-off as the primary determinant of GDP and GS, neglecting other influential factors like severe weather events, runway closures, lower capacity than traffic demand, and other important variables. Given the complexity of predicting the TMI and determining its scope, we seek a more holistic approach. We aim to consider all significant factors that could impact TMIs and their parameters. What sets this research apart is the fusion of all data sources relevant to the issuance and adjustment of TMIs and it represents the first comprehensive attempt to optimize TMIs in this manner. Since this comprehensive solution involves various aspects, we break down the problem into smaller components and input all parameters into a unified model called the “TMI Adjuster”. Figure 1 shows the overall framework and the list of datasets used in each model. The objective of the TMI Adjuster module is to deliver reliable, consistent and expedited recommendations for the progression, adjustment, and termination of TMIs. The ML solution entails developing a pipeline capable of predicting the necessity of a TMI (e.g., GS or GDP) along with its various parameters. For example, in the case of a GS, this includes the scope of the GS either in terms of distance from the destination airport or based on pre-defined airspace sectors. Here, scope refers to those regions and departing airports that are subject to the GS. In this paper, we concentrate on the issuance of GSs in the three major airports in the New York area — LaGuardia(LGA), John F. Kennedy International (JFK), and Newark Liberty International (EWR). We fuse traffic, weather and other relevant aviation data from years 2017 to 2019 to train and validate the ML models. In particular, we use the following datasets: •Terminal Aerodrome Forecast (TAF): meteorological forecasts specific to each airport, issued four times a day, covering predefined time periods. •TMI data: includes all GSs and GDPs along with their respective parameters. •Aviation System Performance Metrics (ASPM): includes traffic related data such as aircraft delays, arrival, and departure rates. •Notices to Airmen (NOTAMs): utilized to extract runway closure data and manage interdependencies between terminals in close proximity. •Flight cancellation data •Airspace Flow Programs (AFP): includes information on flight airborne holdings caused by TMIs. The data preprocessing entails transforming ASPM, TMI, AFP, NOTAMs, and weather data into an hourly format and consolidating all datasets by merging them based on date and time as the primary key. The TMI Adjuster framework comprises two parallel models: one dedicated to GS and a second model focused on GDP. As previously mentioned, our specific focus is on the GS model as a multi-classification problem. In this framework, each data point of the GS model input summarizes ten hours of data. Specifically, the data loader for the GS model generates the input and output of the model as follows: at a given time step, the input includes the actual traffic, weather, and TMI data from the two-hour window before the time step, alongside the weather forecast and scheduled traffic for the next 8 hours starting from the time step. Based on this information, the output of the GS model for each time interval consists of three dimensions. The first dimension represents a binary decision on whether there should be a GS in place for the next hour or not. The second dimension is related to the scope of the GS in the United States, and the third dimension is related to the scope of the GS in Canada (i.e., to determine if the GS impacts airports in Canada).One of the challenges with TMI modeling is the sparsity of TMI events, particularly regarding its scope. To address this challenge in the scope of the GS model output, we implement grouping. The GS scope for the US region is defined based on a list of centers that should be included when the GS is in place. With 20 centers in the US, we utilized historical data to group them into 4 categories. In particular, we summarized our historical data in a graph format where nodes represent centers, and link weights are defined based on the co-occurrence of centers in the scope parameter ofTMIs. By identified strongly connected components in this graph, we were able to partition the centers into four groups. We consider two model structures for the GS Model. Firstly, a hierarchical classification model [10], where the human decision-making for a GS is of hierarchical nature. The decision-maker first decides whether there is a need fora GS, and if the answer is yes, determines the scope. A hierarchical classification model organizes the problem into a class hierarchy, typically a tree or a Directed Acyclic Graph (DAG) structure, and considers the dependency of the decision in the previous step to the next component [10]. Here, we employ the local classifier per level approach, which involves training one multi-class classifier for each level of the class hierarchy. The second structure is the independent structure. In this setting, as the name suggests, we do not consider the dependency of the decisions in the different dimensions of the output of the model. Instead, for each dimension, we train a multi-class classifier independently. Table 1 summarizes GS model statistics for training, validation and testing. The table documents the effect of limiting data to the time steps when there was actually a TMI in place or when a TMI had just terminated. This resulted in a more balanced distribution of the GS class(GS positive class)versus “No GS”(GS negative class), which might help the training process. While JFK and LGA follow very similar distributions, with 40% and 42% GS positive class respectively, EWR has proportionally fewer GS incidents at 28%. Our subsequent phase involves evaluating the performance of both hierarchical structure and independent structure using different state-of-the-art multi-class classifier models such as Random Forest, Decision Trees, K-nearest Neighbors, and Logistic Regression and forecast the duration and scope of the GSs.

Farzan Masrour Shalmani↗

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando↗

Field Validation of Thermoelectric Generation System at Holcim Cement Plant in Alpena, Michigan

Executive Summary Project Background The Industrial Technology Validation (ITV) program aims to identify and demonstrate the performance of new, emerging, and underutilized energy-saving technologies in the industrial sector to help inform decisions to help accelerate their commercialization and deployment, as well as to help make industries more competitive. This ITV demonstration evaluated a thermoelectric generation (TEG) technology at a cement plant, aiming to reduce energy demand in the cement industry. A median cement plant consumes 5.73 million British thermal units per ton of clinker production (resulting in 0.838 metric tons of carbon dioxide [CO₂] emissions per ton of clinker) (Boyd and Zhang 2011, EPA 2021), equivalent to approximately 6.9 trillion British thermal units (TBtu) per year in energy consumption at a cement plant producing 3,300 tons of clinker per day.¹ Collaborating with Holcim, Advanced Thermovoltaic Systems (ATS) developed and deployed a pilot-scale thermoelectric power system to efficiently capture and convert waste heat to electricity. The system leverages the Seebeck effect to convert temperature differences on two sides of semiconductor cartridges into electrical power (ScienceDirect, n.d.). This generation is realized with minimal moving parts compared to existing waste-heat-to-generation solutions and allows capture from heat sources with temperatures as low as 150°C. This project aimed to validate a scalable solution applicable for capturing medium-temperature waste heat, including ambient losses from other high-temperature processes, and high-temperature sources less suitable for other waste-heat-to-power solutions. By recovering this otherwise wasted heat, this project intends to validate improvements to overall process efficiency through reduction in purchased electricity, thereby reducing operational costs while enhancing resiliency and competitiveness. Description and Scope This study evaluated the performance of a TEG system from ATS as a solution to convert waste heat into useful power at a Holcim cement plant in Alpena, Michigan. This plant is a fully integrated cement plant that has been operating since 1907. The facility operates continuously (24/7/365) with approximately 250 employees and five long dry kilns, yielding a total production capacity of 7,852 tons of cement per day (EPA 2023). Currently, the Alpena plant uses waste heat boilers to convert waste heat from the exhaust of each kiln into steam, which drives steam turbine generators. The ATS TEG is being evaluated for its potential to supplement the steam turbines by capturing the remaining lower grade heat. This technology is also being considered for other Holcim plants where steam turbines are not a viable option. ATS installed a pilot-scale TEG unit with an array of 582 individual thermoelectric semiconductor cartridges, of which 573 were operational. The cartridges are sandwiched between 48 hot plates and 49 cold plates. Each cartridge is designed to generate 20 watts (W) of gross power at a hot-side temperature of 240°C and cold-side temperature of 20°C. As such, the total gross generation capacity of the installed system is 11.5 kilowatts (kW) at design conditions. The system configuration for the evaluation was designed to prioritize convenience of installation and minimize disruption to production at the site, while ensuring that the heat required can be obtained for evaluating the TEG system at various operational conditions. To accomplish this, a portion of the steam supplied to Alpena’s steam turbine generation system was diverted to be used as the heat source for the TEG system, while water was supplied to the cold side of the system from nearby Lake Huron. This configuration was designed for the evaluation of the pilot-scale system to assess the performance at different conditions. A commercial-scale system will likely vary from the pilot system depending on typical configurations, including both scale and application. Future commercial applications of the ATS system would involve integrating the system into the exhaust from kiln preheaters, clinker coolers, or radiant heat capture from kiln shells for the heat source. For the cold source, a range of cooling solutions can be considered, including a mechanical cooling system, depending on the location and the application. To increase the generation capacity for commercial applications, the technology provider is working toward developing a commercial-scale TEG system, which would combine multiple TEG units (each similar in design to the pilot system) together. The scope of this evaluation includes the pilot-scale TEG system and all impacted equipment including pumps, controllers, and power handling equipment. Study Objectives The evaluation's goal was to assess the potential of the ATS TEG system to generate useful electrical power by capturing waste heat from cement production kilns. The objectives of this study are to evaluate and verify the following claims made by ATS regarding the pilot-scale system installed at the Holcim Alpena plant. The following design parameters and claims are also outlined in Table ES- 1 and Table ES- 2: • Gross Power: The thermoelectric system converts heat into power to create gross power, the total measured power generated by the system. The 573 active cartridge pilot-scale system is expected to generate 11.5 kW of gross power at the designed hot-side temperature of 240°C and cold-side temperature of 20°C. Power production is dependent on the temperature difference between the heat source (ultimately from the waste heat) and cold temperature supply source. • Net Power: The net power is the total usable power provided to the site by the TEG system after deducting parasitic power loads from the gross generated power. Supplementary equipment is required to operate the TEG system including pumps, controllers, and, in certain anticipated applications, mechanical cooling, which introduce parasitic loads to system operation. After deducting the parasitic loads from the gross power generation, ATS anticipates achieving a net power generation of 7.5 kW from the pilot-scale system. • Thermal Efficiency: The thermal efficiency is the percent of the total heat transferred to the TEG system that is converted to gross power. Historically, TEGs have a thermal efficiency of 2%–5% (DOE 2008). Prior industrial-scale TEG systems, such as the E1 TEG offered by Alphabet Energy, operated at an efficiency of 2.5% (Lamonica, 2014). ATS anticipates achieving an average efficiency of 4.8% or higher in converting heat energy to usable electricity. • Cartridge Performance: The TEG system comprises 573 active individual semiconductor cartridges, each of which generates a portion of the total power. Cartridge optimization and selection is an important design consideration for potential future TEG system design performance. Therefore, understanding the distribution of gross power and efficiency within the pilot system is vital to understanding what is achievable. At a design hot-side temperature of 240°C and cold-side temperature of 20°C, ATS anticipates a cartridge performance of 20 W of gross power per cartridge at an efficiency of 4.8% per cartridge. In addition to evaluating the claimed performance of the TEG pilot-scale unit, the study estimated the potential annual impacts of a scaled-up commercial system used to capture kiln waste heat over annual operations. The evaluation estimated the gross and net annual electric generation achievable by capturing heat from the two proposed tap-in points: the kiln exhaust and the clinker cooler exhaust; see Section 2.1 for details. Two use cases were examined: • Holcim Alpena: The Holcim Alpena site consists of long dry kilns with superheater boilers, which differs from the rest of Holcim’s cement plant portfolio and results in lower waste heat temperatures. The study estimates gross and net annual generation using the superheater boiler exhaust and clinker cooler exhaust, based on 2023 operational data. • Typical Installation: Common cement plants have preheater kilns with higher exhaust temperatures than Holcim Alpena across a range of production rates. The study estimates gross and net annual generation using the preheater exhaust and clinker cooler exhaust, with a sensitivity analysis to account for the typical range of preheater exhaust temperatures, clinker cooler exhaust temperatures, and clinker production rates. Methodology The evaluation methodology followed a measurement and verification (M&V) strategy based on the International Performance Measurement and Verification Protocol Option B through comprehensive measurements and analyses of the affected systems. Evaluation data was collected from March 9 to March 11, 2024, the test period of the pilot TEG system. During the test period, in coordination with the ITV team, the ATS team adjusted system operations to capture the range of variability expected for each of the variables pertinent to performance of the system. The methodology consisted of two parts: evaluating the performance of the pilot unit's TEG system and estimating the annual TEG impact in terms of gross and net power based on a given waste heat profile. First, the evaluation of the thermoelectric generation performance of the pilot unit relative to the claims was performed by analyzing the collected test data. Gross power of the pilot TEG system was directly measured. Net power was determined by deducting the measured parasitic power from the gross power. The gross power generation was compared to heat transferred to the system by the working fluid (which was heated by steam generated from the kiln waste heat) to calculate the thermal efficiency achieved by the system. Performance of individual semiconductor cartridges within the pilot array was also assessed in terms of measured gross cartridge power and calculated cartridge thermal efficiency. The second part of the evaluation estimated the annual TEG impacts in terms of gross power and net power (calculated from the difference between gross power and parasitic power). This analysis comprised development of mathematical regression models for gross power and parasitic power, with assessment of each model’s goodness-of-fit characteristics to ensure satisfaction of statistical requirements. The models predicted the gross power generation, the parasitic load based on the temperature difference between the hot working fluid and the cold-side fluid (cold water from Lake Huron) entering the system, the volumetric flow rate of the cold-side fluid at the inlet, and the volumetric flow rate of the hot working fluid at the inlet. The annual impact analysis considered a theoretical commercial-scale system sized to capture the available waste heat at a cement plant, consisting of linked pilot-scale units that receive heat from a theoretical gas-to-working-fluid heat exchanger. To estimate annual impacts at the Alpena plant, the gross power and parasitic power regression models were applied to the arrays in the theoretical commercial-scale system. The heat supplied to the unit was calculated based on the kiln run time, annual production, kiln exhaust waste heat, and clinker cooler waste heat derived from 2023 Holcim Alpena kiln operational data. Net power impacts were calculated by deducting the resulting parasitic power from the estimated gross power. Inputs for the model were generated from a combination of hourly data, assumed design considerations for TEG system scale-up from the pilot-scale unit, and assumptions regarding TEG system operations. This analysis was then used as the basis for estimating annual impacts of typical TEG installation at cement plants, by applying sensitivity analyses to key kiln operational characteristics including kiln preheater exhaust temperatures, cooler clinker exhaust temperatures, and plant daily production rates across a range of expected values. Project Results/Findings Table ES- 2 and Table ES- 2 provide a summary of the operating conditions and evaluation results compared to the stated claims from the technology provider. Key takeaways include: • Gross Power: The peak gross power achieved during the testing period was 10.0 kW, compared to the 11.5 kW expected for 573 active cartridges. The claimed gross power was associated with a target hot side of 240°C; however, the system only received a maximum hot-side mean plate temperature of 212°C during the testing period. • Net Power: The pilot-scale unit exceeded the claims for net power, achieving a peak of 7.7 kW net compared to a claim of 7.5 kW. One factor contributing to the higher achieved net power is the relatively high water pressure available through Lake Huron. The pilot TEG system did not require cold-side pumps during the test, whereas most installations would. This reduced the parasitic loads on the system, ultimately contributing to higher net power relative to the gross power. • Thermal Efficiency: The pilot-scale unit outperformed the claimed efficiency, achieving a peak system efficiency of 5.0% thermal efficiency compared to the stated 4.8%. • Cartridge Performance: To compare cartridge performance against claims, the study focused on the third day of testing, which aimed for conditions closest to the design specifications, with a hot side of 240°C and cold-side exit temperature of 6.4°–30°C. On this day, the mean gross power observed in the cartridges within the TEG array was 18.1 W/cartridge, and the peak performance was 34.7 W/cartridge. The estimated mean cartridge efficiency was 5.2%, and the estimated efficiency at peak gross cartridge power was 10%. The regression models developed for gross power generation and parasitic loads were used to estimate the generation impact for given heat input to the TEG from the working fluid (captured from the waste heat) and from the cold loop (Lake Huron) on an hourly basis for a year of operation. Based on this analysis, installation of a commercial-scale TEG system at the Holcim cement plant in Alpena, Michigan, with a waste heat exchanger of 0.85 effectiveness, would generate up to 391 kW of net power, translating to between 920,000 and 1,800,000 kilowatt-hours (kWh) in net electricity per year. Based on typical grid emissions for Alpena, this would avoid estimated net emissions by 752 metric tons of CO₂ annually.² The sensitivity analysis estimated that typical TEG system installations at cement plants could generate an average of 56–1,040 kW of net power, or between 488,000 and 9,110,000 kWh of net energy. This generation potential is most significantly affected by plant production rates and also influenced by preheater and clinker cooler exhaust temperatures. Applying the national average emission rate, typical commercial-scale installations at Holcim plants are projected to avoid between 182 and 3,401 metric tons of CO₂ annually per site. Table ES- 3 shows a summary of the estimated annual impacts.³ While parasitic loads are significant and vary by application, this analysis assumed the use of heating loop pumps and access to Lake Huron as a cold sink. This setup assumed no need for cooling loop pumps due to the available water pressure at the test site. Applications that require cooling towers or additional equipment are likely to experience higher parasitic loads. Therefore, the study’s estimates are most applicable to scenarios with similar parasitic load configurations—namely, access to a high-pressure cold sink. Applicability to other locations may be limited, as differing conditions could necessitate additional pumps and cooling systems, potentially impacting performance significantly.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗