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At least 271 records · Page 15

AIMSim : An accessible cheminformatics platform for similarity operations on chemicals datasets

The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Further, most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Environmental vulnerability assessment using Grey Analytic Hierarchy Process based model

Environmental management of an area describes a policy for its systematic and sustainable environmental protection. In the present study, regional environmental vulnerability assessment in Hirakud command area of Odisha, India is envisaged based on Grey Analytic Hierarchy Process method (Grey–AHP) using integrated remote sensing (RS) and geographic information system (GIS) techniques. Grey–AHP combines the advantages of classical analytic hierarchy process (AHP) and grey clustering method for accurate estimation of weight coefficients. It is a new method for environmental vulnerability assessment. Environmental vulnerability index (EVI) uses natural, environmental and human impact related factors, e.g., soil, geology, elevation, slope, rainfall, temperature, wind speed, normalized difference vegetation index, drainage density, crop intensity, agricultural DRASTIC value, population density and road density. EVI map has been classified into four environmental vulnerability zones (EVZs) namely: ‘low’, ‘moderate’ ‘high’, and ‘extreme’ encompassing 17.87%, 44.44%, 27.81% and 9.88% of the study area, respectively. EVI map indicates that the northern part of the study area is more vulnerable from an environmental point of view. EVI map shows close correlation with elevation. Effectiveness of the zone classification is evaluated by using grey clustering method. General effectiveness is in between “better” and “common classes”. This analysis demonstrates the potential applicability of the methodology. - Highlights: • Environmental vulnerability zone identification based on Grey Analytic Hierarchy Process (AHP) • The effectiveness evaluation by means of a grey clustering method with support from AHP • Use of grey approach eliminates the excessive dependency on the experience of experts.

54 ENVIRONMENTAL SCIENCES↗

Emulation and detection of physical faults and cyber-attacks on building energy systems through real-time hardware-in-the-loop experiments

The increasing use of remote or mobile access, integrated wearable technologies, data exchange, and cloud-based data analytics in modern smart buildings is steering the building industry towards open communication technologies. The increased connectivity and accessibility could lead to more cyber-attacks in smart buildings. On the other hand, physical faults (e.g., HVAC -heating, ventilation, and air-conditioning faults) may have similar adverse impacts as those from the cyber-attacks on building energy systems, such as occupant discomfort, energy wastage, and equipment downtime. However, current physical behavior-based anomaly detection methods fail to differentiate between cyber-attacks and physical faults in building energy systems. Moreover, the challenge in collecting real-world threat data with ground truth has led researchers to rely on numerical models with user-defined assumptions, which may not accurately reflect real-world conditions due to the lack of in-situ experimental datasets. To address these challenges and gaps, this paper presents a flexible hardware-in-the-loop (HIL) testbed for generating cyber-attack and physical fault datasets and demonstrating threat detection algorithms in a real building automation system (BAS) environment. This testbed combines hardware (i.e., real BAS with local HVAC controllers and a physical network) with software (i.e., high-fidelity models to represent behaviors of building envelope and HVAC energy systems), enabling emulations of realistic threats. Five HIL experiments, including one baseline without any threats, two with physical faults, and two with cyber-attacks, were conducted to generate datasets containing detailed network traffic and system states. A joint classification framework, incorporating a network analyzer and a physical HVAC fault detector, was proposed to automatically detect cyber-physical abnormalities on BAS at both the network and the physical HVAC levels. The network analyzer comprises a conditional random fields (CRF) based command validator and a statistics-based detection strategy. The fault detector employs a weather and schedule-based pattern matching and feature-based principal component analysis (WPM-FPCA) method. Evaluation of the classification using four metrics from the multi-class confusion matrix revealed an average accuracy of 90.2%, recall of 89.7%, precision of 88.5% and F1-score of 89.2%. Finally, these results demonstrate that the proposed joint classification framework can effectively differentiate between specific types of cyber-attacks (e.g., device reinitialization attack, network Denial-of-Service attack) and physical faults (e.g., air handling unit operational fault, cooling coil valve stuck) in real time for improved building energy management.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Nonlinear behavior in high-frequency aggregate control of thermostatically controlled loads

Coordinated control of electric loads can provide valuable grid services, such as frequency regulation. However, due to the nonlinear characteristics of such load ensembles, it is important to systematically analyze their behavior and establish a thorough understanding of undesirable phenomena that can potentially arise. In this paper, we analyze the frequency response of an aggregate control scheme, with the goal of exploring controller performance limits. We show that rapid switching commands can induce oscillations in the power output due to the inherent lockout mechanism of the underlying devices. Here, we demonstrate that highly detailed aggregate models are required to capture such phenomena. Such models enable deeper understanding of the control boundaries and therefore play an important role in avoiding the introduction of undesirable effects on the grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Enabling co-simulation of tokamak plant models and plasma control systems

A system for connecting the Plasma Control System and a model of the tokamak Plant in closed loop co-simulation for plasma control development has been in routine use at DIII-D for more than 20 years and at other fusion labs that use variants of the DIII-D PCS for approximately the last decade. Here, co-simulation refers to the simultaneous execution of two independent codes with the exchange of data - Plant actuator commands and tokamak diagnostic data - between them during execution. Interest in this type of PCS-Plant simulation technology has also been growing recently at other fusion facilities. In fact, use of such closed loop control simulations is assumed to play an even larger role in the development of both the ITER Plasma Control System (PCS) and the experimental operation of the ITER device, where they will be used to support verification/validation of the PCS and also for ITER pulse schedule development and validation. We describe the key use cases that motivate the co-simulation capability and the features that must be provided by the Plasma Control System to support it. These features could be provided by the PCS itself or by a model of the PCS. If the PCS itself is chosen to provide them, there are requirements imposed on its architecture. If a PCS model is chosen, there are requirements imposed on the initial implementation of this simulation as well as long-term consequences for its continued development and maintenance. We describe these issues for each use case and discuss the relative merits of the two choices. Several examples are given illustrating uses of the co-simulation method to address problems of plasma control during the operation of DIII-D and of other devices that use the DIII-D PCS.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

New features of the ECH control system on DIII-D and impact of power modulation on collector loading

In order to increase the reliability and improve the availability of electron cyclotron heating (ECH) and current drive during a plasma shot, an adaptive gyrotron command generator has been designed and implemented in all gyrotron systems on the DIII-D tokamak. This adaptive real-time generator is able to detect imminent faults, including gyrotron body overcurrent faults that can develop in a few microseconds, block faults, and restart RF generation within 10–30 ms, faster than the DIII-D energy confinement time. The adoption of this adaptive generator has substantially improved the performance of a depressed-collector gyrotron with recurrent body current faults, and has assisted the ECH system to achieve a record reliability of 95% during the last experimental campaign. The impact of power modulation on the collector loading of a depressed-collector gyrotron has been experimentally studied using calorimetry and collector maps taken by a diagnostic developed in-house. While lowering the modulation duty cycle kept the collector power constant as a result of low beam-wave efficiency during the modulation low state, an observed power redistribution inside the collector increased the peak collector power density, which reached levels above the manufacturer power density limit for low duty cycles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Nonlinear, real-time optimization for actuator management in tokamaks

Experiments in DIII-D have been carried out to test a novel actuator management approach in tokamaks. Here, the actuator management scheme is posed as a nonlinear-optimization problem in which the actuator commands are calculated in real time according to the changing control priorities, plasma state, and actuator availability. Such optimization problem is solved using the augmented Lagrangian method, combined with a gradient projection method and a conjugate-gradient iteration algorithm. The algorithmic approach followed in this work does not depend on the particular control objectives or actuators considered, which facilitates its integration with other independently-designed control components within a plasma-control system. In addition, the actuator-management algorithm is able to handle the optimization problem in a computationally efficient manner, making it suitable for real-time implementations. Initial DIII-D results in the steady-state high-q min scenario have demonstrated the capabilities of the actuator manager to perform both simultaneous multiple mission and repurposing sharing, which will be required in ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Preliminary proof-of-concept of real-time divertor heat flux control from infrared cameras with nitrogen injection in the DIII-D tokamak

In future tokamak reactors like ITER and the Fusion Pilot Plant (FPP), real-time feedback control of heat flux to the plasma-facing components (PFC) will be critical for steady-state operation. This work presents the first experimental demonstration of real-time divertor heat flux estimation with infrared thermography and feedback control with impurity seeding on the DIII-D tokamak. The flexible infrastructure of the Plasma Control System (PCS) on DIII-D makes this new capability possible. The PCS software runs on a gateway computer system, and five real-time compute nodes. An array of low latency streaming digitizers from D-TACQ Solutions connects to these real-time computers to collect and process data, and send commands to actuators during plasma discharges. This system handles the signal IO from the tokamak and allows the PCS to utilize the diagnostic data necessary to perform control in real-time. Feedback control on heat flux was accomplished by feeding infrared camera data from the “Infrared TV” (IRTV) camera to a custom-developed User Datagram Protocol (UDP) server. This server transmits infrared data to a newly developed PCS algorithm that estimates the heat flux to PFC. Here, a proportional integral derivative (PID) controller minimizes the error between a heat flux reference and the real-time estimate by injecting nitrogen gas into the divertor.

Algorithm development↗

Performance Evaluation of an Offshore Wave Measurement Buoy in Monochromatic Waves

The accurate measurement of waves underpins marine energy resource characterization, device design, and project development. Datawell wave buoys are widely deployed and have long served as a trusted standard for wave measurements. We quantify the measurement performance, including wave elevation and energy flux estimation, of a Datawell DWR-MkIII buoy using prescribed monochromatic heave motions on a large-amplitude six-degree-of-freedom motion platform at the National Laboratory of the Rockies, assuming the buoy behaves as an ideal wave follower. Commanded motions were validated with an optical motion tracking system while buoy elevation and raw acceleration were recorded. Wave elevations were propagated to wave energy flux estimation using four methods, including one frequency-domain method and three time-domain methods. The Bayesian optimization was applied for design of experiments, and records from three test sites were also applied and evaluated in the present study. Results show two error regions within the nominal period range of 1.6 s to 30 s. For wave periods between 5 s and 25 s, the buoy provides accurate wave height measurements. For short periods less than 5 s, the 1.28 Hz sampling frequency induces sub-Nyquist artifacts that bias elevation and can drive maximum energy flux estimation errors above 100%. For long periods exceeding 25 s, the buoy reported elevation is underpredicted with error depending on period but relatively independent of wave height, with maximum wave height and wave energy flux errors reaching 64% and 87%, respectively. Furthermore, analysis of three field-derived cases shows that frequency-domain estimates at 1.28 Hz agree within 2% of the corresponding 100 Hz estimates, while larger method-dependent differences are observed for the Hilbert method.

16 TIDAL AND WAVE POWER↗

A full-scope, high-fidelity simulator-based hardware-in-the-loop testbed for comprehensive nuclear power plant cybersecurity research

Nuclear power plant (NPP) cybersecurity research often relies on hardware-in-the-loop (HIL) testbeds that integrate real hardware components into simulated environments. These testbeds allow researchers to identify vulnerabilities, evaluate attack impacts, and test security measures in a controlled setting. Furthermore, previous HIL testbeds lacked fidelity to accurately represent real nuclear systems, limiting the scope of cybersecurity analysis. This study presents the creation of a HIL testbed, devised upon a full-scope, high-fidelity NPP simulator, to facilitate realistic and comprehensive cybersecurity research. To demonstrate its capabilities, the control logic for the steam generator water level was migrated from the simulator to an external programmable logic controller. As a practical application of the developed testbed, supply chain attack scenarios were simulated by injecting malicious code into the controller logic, and the effects of manipulating sensor inputs and control commands were observed. While this HIL testbed provides more detailed simulations, enhanced realism, and wider applicability compared to other options utilizing a less complex simulator, it is also more intricate and costly. For this reason, we include a detailed comparison with some alternative architectures to aid fellow researchers and practitioners in the selection of a suitable HIL architecture based on specific research objectives.

47 OTHER INSTRUMENTATION↗

Experimental investigation of air-fuel equivalence ratio effects on advanced dual-fuel ammonia/diesel combustion on a single-cylinder medium-duty diesel engine at high load

Ammonia (NH 3 ) has garnered significant interest as an alternative fuel for meeting international emissions reduction mandates in sectors with high weight and distance requirements, such as shipping. Technical barriers and unanswered questions remain on the combustion strategies that can maximize ammonia utilization and minimize emissions. Prior research studies at the US Department of Energy’s Oak Ridge National Laboratory have shown strong performance with NH 3 under dual-fuel mode using conventional diesel combustion (CDC) manifold air pressure settings. Diesel airflow was initially used to simplify retrofitting (no turbocharger modification), which resulted in air-fuel equivalence ratios (λ) greater than 1.5. To characterize potential improvements in dual-fuel NH 3 combustion performance at richer in-cylinder conditions, a global λ sweep compared the use of early (E-pilot) and late (L-pilot) single diesel injections. The experiments were conducted at 1200 RPM and 12.8 ± 0.2 bar (75 % load), and λ was varied by decreasing the commanded air flow to the engine at greater than 90 % ammonia energy substitution level. A diesel injection timing sweep was conducted for both the injection strategies at fixed λ, and the timing with the lowest engine-out N 2 O emissions was identified. The results indicated an optimal balance between CO 2,eq and thermal efficiency benefits both E-pilot and l-pilot injection strategy cases compared with CDC at a λ of 1.4. In conclusion, the indicated nitrogen-based emissions exhibited a strong correlation to the ratio of CA5–50 and ignition delay for l-pilot, but no apparent trend emerged for the E-pilot injection strategy at the tested boundary conditions.

Ammonia↗

ParNCL and ParGAL: Data-parallel Tools for Postprocessing of Large-scale Earth Science Data

Earth science high-performance applications often require extensive analysis of their output in order to complete the scien- tific goals or produce a visual image or animation. Often this analysis cannot be done in situ because it requires calculating time-series statistics from state sampled over the entire length of the run or analyzing the relationship between similar time series from previous simulations or observations. Many of the tools used for this postprocessing are not themselves high- performance applications, but the new Parallel Gridded Analysis Library (ParGAL) provides high-performance data-parallel versions of several common analysis algorithms for data from a structured or unstructured grid simulation. The library builds on several scalable systems, including the Mesh Oriented DataBase (MOAB), a library for representing mesh data that sup- ports structured, unstructured finite element, and polyhedral grids; the Parallel-NetCDF (PNetCDF) library; and Intrepid, an extensible library for computing operators (such as gradient, curl, and divergence) acting on discretized fields. We have used ParGAL to implement a parallel version of the NCAR Command Language (NCL) a scripting language widely used in the climate community for analysis and visualization. The data-parallel algorithms in ParGAL/ParNCL are both higher performing and more flexible than their serial counterparts.

97 MATHEMATICS AND COMPUTING↗

ParCAT: Parallel Climate Analysis Toolkit

Climate science is employing increasingly complex models and simulations to analyze the past and predict the future of Earth's climate. This growth in complexity is creating a widening gap between the data being produced and the ability to analyze the datasets. Parallel computing tools are necessary to analyze, compare, and interpret the simulation data. The Parallel Climate Analysis Toolkit (ParCAT) provides basic tools to efficiently use parallel computing techniques to make analysis of these datasets manageable. The toolkit provides the ability to compute spatio-temporal means, differences between runs or differences between averages of runs, and histograms of the values in a data set. ParCAT is implemented as a command-line utility written in C. This allows for easy integration in other tools and allows for use in scripts. This also makes it possible to run ParCAT on many platforms – from laptops to supercomputers. ParCAT outputs NetCDF files so it is compatible with existing utilities such as Panoply and UV-CDAT. This paper describes ParCAT and presents results from some example runs on the Titan system at ORNL.

97 MATHEMATICS AND COMPUTING↗

Protocol to detect dilution cycles in chemostat experiments and estimate growth rate slopes with linear modeling with R software chemostat_regression

Chemostat growth chambers measure optical density over time and require manual calculation of growth rates. Here, we present chemostat_regression, R software that enables users to automatically identify chemostat cycles and estimate growth rate using a linear regression approach. We describe steps for creating requisite software environment(s), formatting input data, executing the software via command line/RStudio/R-Shiny, interpreting results, assessing the validity of results, and modifying input parameters.

59 BASIC BIOLOGICAL SCIENCES↗

Rechargeable Zinc Alkaline Anodes for Long-Cycle Energy Storage

Zinc alkaline anodes command significant share of consumer battery markets and are a key technology for the emerging grid-scale battery market. Improved understanding of this electrode is required for long-cycle deployments at kWh and MWh scale due to strict requirements on performance, cost, and safety. For this article, we give a modern literature survey of zinc alkaline anodes with levelized performance metrics and also present an experimental assessment of leading formulations. Long-cycle materials characterization, performance metrics, and failure analysis are reported for over 25 unique anode formulations with up to 1500 cycles and ~1.5 years of shelf life per test. Statistical repeatability of these measurements is made for a baseline design (fewest additives) via 15 duplicates. Baseline design capacity density is 38 mAh per mL of anode volume, and lifetime throughput is 72 Ah per mL of anode volume. We then report identical measurements for anodes with improved material properties via additives and other perturbations, some of which achieve capacity density over 192 mAh per mL of anode volume and lifetime throughput of 190 Ah per mL of anode volume. Novel in operando X-ray microscopy of a cycling zinc paste anode reveals the formation of a nanoscale zinc material that cycles electrochemically and replaces the original anode structure over long-cycle life. Ex situ elemental mapping and other materials characterization suggest that the key physical processes are hydrogen evolution reaction (HER), growth of zinc oxide nanoscale material, concentration deficits of OH – and ZnOH 4 2– , and electrodeposition of Zn growths outside and through separator membranes.

25 ENERGY STORAGE↗

KBKit: A Python Toolkit for Kirkwood–Buff Theory from Molecular Dynamics

Thermodynamic properties of liquid mixtures govern processes that range from drug delivery to energy storage, yet extracting these properties from molecular simulations remains challenging. Kirkwood–Buff (KB) theory offers a rigorous route by linking microscopic pair distribution functions to macroscopic free energies, but practical use of the theory has been hindered by two obstacles: (i) the long simulations needed to obtain well-converged Kirkwood-Buff integrals (KBIs) and (ii) the specialized corrections required to translate finite-size data to the thermodynamic limit. $\texttt{KBKit}$ is an open-source Python package that removes these barriers. It automatically computes KBIs and derived thermodynamic quantities from GROMACS input files, applies state-of-the-art finite-size corrections, and provides built-in diagnostic tools to quantify statistical uncertainty. Written with modern software-engineering practices—continuous integration, extensive unit testing, and thorough documentation—$\texttt{KBKit}$ is both reliable and easy to extend. By condensing complex KBI analysis into a few intuitive commands, $\texttt{KBKit}$ enables researchers to incorporate KB theory into routine simulation workflows and accelerate the discovery of solution-phase thermodynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extending particle tracking capability with Delaunay triangulation

Here, particle tracking, the analysis of individual moving elements in time series of microscopic images, enables burgeoning new applications, but there is need to better resolve conformation and dynamics. Here we describe the advantages of Delaunay triangulation to extend the capabilities of particle tracking in three areas: (1) discriminating irregularly shaped objects, which allows one to track items other than point features; (2) combining time and space to better connect missing frames in trajectories; and (3) identifying shape backbone. To demonstrate the method, specific examples are given, involving analyzing the time-dependent molecular conformations of actin filaments and λ-DNA. The main limitation of this method, shared by all other clustering techniques, is the difficulty to separate objects when they are very close. This can be mitigated by inspecting locally to remove edges that are longer than their neighbors and also edges that link two objects, using methods described here, so that the combination of Delaunay triangulation with edge removal can be robustly applied to processing large data sets. As common software packages, both commercial and open source, can construct Delaunay triangulation on command, the methods described in this paper are both computationally efficient and easy to implement.

36 MATERIALS SCIENCE↗

PR-PR: Cross-Platform Laboratory Automation System

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

Linshiz, G↗