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A virtual simulator designed for collision prevention in proton therapy

Purpose: In proton therapy, collisions between the patient and nozzle potentially occur because of the large nozzle structure and efforts to minimize the air gap. Thus, software was developed to predict such collisions between the nozzle and patient using treatment virtual simulation. Methods: Three-dimensional (3D) modeling of a gantry inner-floor, nozzle, and robotic-couch was performed using SolidWorks based on the manufacturer’s machine data. To obtain patient body information, a 3D-scanner was utilized right before CT scanning. Using the acquired images, a 3D-image of the patient’s body contour was reconstructed. The accuracy of the image was confirmed against the CT image of a humanoid phantom. The machine components and the virtual patient were combined on the treatment-room coordinate system, resulting in a virtual simulator. The simulator simulated the motion of its components such as rotation and translation of the gantry, nozzle, and couch in real scale. A collision, if any, was examined both in static and dynamic modes. The static mode assessed collisions only at fixed positions of the machine’s components, while the dynamic mode operated any time a component was in motion. A collision was identified if any voxels of two components, e.g., the nozzle and the patient or couch, overlapped when calculating volume locations. The event and collision point were visualized, and collision volumes were reported. Results: All components were successfully assembled, and the motions were accurately controlled. The 3D-shape of the phantom agreed with CT images within a deviation of 2 mm. Collision situations were simulated within minutes, and the results were displayed and reported. Conclusions: The developed software will be useful in improving patient safety and clinical efficiency of proton therapy.

60 APPLIED LIFE SCIENCES↗

PymePix : a python library for SPIDR readout of Timepix3

PymePix is a new Python 3 library that provides control and acquisition for the Timepix3-SPIDR hardware. The rich set of data-structures and intuitive routines reduces time and coding effort to quickly configure, acquire, and visualize data from Timepix3. The highly extensible high-performance data-pipeline allows for alteration of the Timepix3 datastream into a form that is convinient for the user. This library is intended to be easily inserted into a standard scientific software stack as well as to allow for more direct interaction of Timepix3 with interactive flavors of Python. Included with the library are two example programs using PymePix: pymepix-acq is a command line control and acquisition program that can capture UDP packets and decode them into pixels and triggers. The second is pymepixviewer, an online control and data-acquisition program for general use, but with features geared toward mass-spectroscopy and ion imaging.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗

A Parallel Computing Infrastructure for Building Energy Simulation

In order to study grid-interactive efficient buildings, Pacific Northwest National Laboratories (PNNL) needs an infrastructure for urban-scale building energy modeling. Such an infrastructure should be fast, scalable, and easy-to-use. Given a set of data from the Energy Information Administration’s Commercial Building Energy Consumption Survey (CBECS) and tool to translate survey data into simulation inputs, this project aimed to conduct the simulation of the entire dataset in parallel. Before running the simulations, the necessary software was bundled into a container for use on the PNNL supercomputing network. Then, the parallel simulation workflow was designed using GNU Make, a file creation software, and submitted to a supercomputing partition which could run hundreds of simulations simultaneously. The EnergyPlus simulations output hourly electric meter data for each CBECS sample, which represents the electricity consumption of similar commercial buildings across the United States. Analyzing and visualizing the meter data is important to the future of the work, and this project wrote code to make common analysis methods simple, fast, and accessible. Moving forwards, the model will need to be expanded to include data from other sources and its accuracy will need to be improved and eventually validated.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Digital Twin + AI: Control Room of the Future [Slides]

The control room functions as the central brain of the grid, essential for balancing supply and demand and ensuring moment-to-moment grid reliability. Like the human brain, which processes sensory data to make decisions, control room operators analyze operational data from power generation, transmission, and distribution to make informed decisions. Currently, decision-making primarily rests with operators due to hardware and software limitations. However, with technological advancements, Digital Twins and AI are becoming high interest points in the control room's decision-making pilot programs. NREL is developing a comprehensive decision-making platform that integrates Digital Twins, AI, and advanced visualization techniques. As this integration progresses, the role of Digital Twins will evolve from conducting automated simulations to serving as a Trustworthy AI enabler, offering verification and validation of AI-generated response for power systems or providing physics-aware synthetic data of AI pre-training.

24 POWER TRANSMISSION AND DISTRIBUTION↗

ACDC (Automated Campbell Diagram Code) [SWR-26-042]

This application provides a web-based graphical user interface to generating Campbell Diagrams and visualizing mode shapes for OpenFAST turbine models. Determining the aeroelastic stability and dynamic characteristics of wind turbines is a critical step in turbine design and analysis. Historically, extracting natural frequencies and mode shapes from OpenFAST—the industry-standard whole-turbine simulation code—has been a fragmented and tedious process. It required manual model configuration, command-line linearization execution, and complex post-processing via proprietary scripts to handle rotating-frame dynamics. To address these workflow bottlenecks, we present the Automated Campbell Diagram Code (ACDC), an open-source graphical software tool developed by the National Laboratory of the Rockies (NLR) under the DOE-funded Distributed Wind Aeroelastic Modeling (dWAM) project. ACDC streamlines the end-to-end linearization and stability analysis workflow into a single, intuitive cross-platform application. The software guides users through OpenFAST model configuration, definition of operating points, and the automated execution of steady-state trim and linearization simulations. Under the hood, ACDC automates the complex mathematical post-processing steps required for rotating systems, including Multi-Blade Coordinate (MBC) transformations, eigenanalysis, and advanced modal tracking utilizing the Modal Assurance Criterion (MAC) and spectral clustering. Finally, ACDC processes these results to automatically generate Campbell diagrams and features a robust 3D visualization engine to animate full-system mode shapes. By eliminating the reliance on external post-processing environments and manual data manipulation, ACDC significantly accelerates dynamic analysis and lowers the barrier to entry for wind energy researchers and engineers.

Summerville, Brent [National Laboratory of the Roc↗

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

Biomedical applications↗

Opportunistic bone density screening for the abdominal radiologist using colored CT images: a pilot retrospective study

Purpose: The purpose of the study was to develop an accurate and reproducible method for detecting low spinal bone density on abdominal CT images. Methods: For this IRB-approved HIPAA-compliant single-center retrospective study, nonenhanced CT images of the lower abdomen were obtained in 631 African-American participants. Mean attenuation of L3/L4 was associated with quantitative CT bone density (QCT) in a randomly selected training cohort (N = 511), and receiver operating characteristics analysis was used to identify the optimal mean attenuation threshold for differentiating normal from low bone density. Custom image processing software was used to generate grayscale and colored CT images of the midline spine, with green for normal and red for low bone density. Five radiologists independently assessed bone density at L3/L4 in a validation cohort (N = 120) using various methods: QCT, visual assessment of sagittal grayscale images (Grayscale), quantitative measurement of mean attenuation on a midline sagittal image (Attenuation), and visual assessment of a midline sagittal colored image (Color). Accuracy was calculated using the average QCT bone density as a reference standard. Inter-observer agreement was assessed using intraclass correlation coefficient (ICC). Results: The optimal mean attenuation threshold for differentiating normal from low bone density at L3/L4 was 145 Hounsfield Units. The average accuracy of Grayscale, Attenuation, and Color methods was 58, 87, and 91% (p < 0.001), respectively. Inter-observer agreement was poor for Grayscale (ICC: 0.20; 95% CI 0.12, 0.28) and excellent for both Attenuation (ICC: 0.85; 95% CI 0.73, 0.91) and Color methods (ICC: 0.87; 95% CI 0.83, 0.90). Conclusion: Detection of low spinal bone density using colored abdominal CT images was highly accurate and reproducible.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Preface to the Special Issue on TOUGH Symposium 2015

The TOUGH Symposium 2015 was held in Berkeley, California, September 28-30, 2015. The TOUGH family of codes, developed at the Energy Geosciences Division of Lawrence Berkeley National Laboratory (LBNL), is a suite of computer programs for the simulation of multiphase and multicomponent fluid and heat flows in porous and fractured media with applications in many geosciences fields, such as geothermal reservoir engineering, nuclear waste disposal, geological carbon sequestration, oil and gas reservoirs, gas hydrate research, vadose zone hydrology and environmental remediation. Since the first release in the 1980s, many modifications and enhancements have been continuously made to TOUGH and its various descendants (iTOUGH2, TOUGH+, TOUGH-MP, TOUGHREACT, TOUGH+HYDRATE, TMVOC...), at LBNL and elsewhere. Today, these codes are used worldwide in academia, government organizations and private companies in problems involving coupled hydrological, thermal, biogeochemical and geomechanical processes. The Symposia, organized every 2-3 years, bring together developers and users for an open exchange on recent code enhancements and applications. In 2015, the Symposium was attended by one hundred participants, representing thirty-four nationalities. This Special Issue in Computers & Geosciences gathers extended versions of selected Symposium proceedings related to (i) recent enhancements to the TOUGH family of codes and (ii) coupled flow and geomechanics processes modeling. In this special issue, a paper by Jung et al. provides a new base version of TOUGH, TOUGH3. This latest version addresses the computational robustness and efficiency needed for the increasing complexity of the simulated processes and the growing size of model domains. Moreover, it consolidates the serial and parallel versions into a single code, hence, inconsistencies between different versions are less likely to occur, and code maintenance and development become more efficient. Finsterle et al. present a review of the capabilities of iTOUGH2 and illustrate the workflow of an integrated simulation-optimization framework. Liu et al. present an approach to reduce the computational cost of performing Bayesian inverse modeling and demonstrate their approach using a synthetic experiment simulated with TOUGH2. Regarding the mesh generation process, the paper by Doughty presents a generalization of the grid-generation algorithm embedded in TOUGH2 (MESHMAKER) to create one-column grids with fractal dimension, useful for representing flow through fractures or highly heterogeneous media with fractal geometry, and also for inverse methods. Sentís and Gable present a module to interface the open source code Lagrit with TOUGH2, that assists in the processes of mesh generation and model setup, and that can be particularly useful for complex geometries and large models. Bonduà et al. present a pre-processing tool (VORO2MESH) that features a full 3D Voronoi approach for structured and unstructured grids, and an enhanced post-processor (TOUGH2Viewer) for the visualization of 3D Voronoi grids. The literature review shows that coupled fluid flow and geomechanics has gained increasing attention in the last years in many geosciences fields. In this context, several codes of the TOUGH family have been successfully coupled with geomechanics software. The paper by Rutqvist presents a review of some of these TOUGH-based geomechanics models, of which the TOUGH-FLAC simulator – presented for the first time in the TOUGH Symposium 2003 – is well-known worldwide and has been used in a large variety of applications, encompassing the application domains of the TOUGH codes. Blanco-Martín et al. present an extension of TOUGH-FLAC to the finite strain framework, motivated by the existence of large strains associated with rock salt deformation in the context of heat-generating nuclear waste disposal. Following a paper published in the Special Issue of the TOUGH Symposium 2012 in this journal, Kim et al. present the current status of the TOUGH-RSBN simulator for coupled hydro-mechanical modeling of hydraulic fracturing using a discrete fracture network approach, and present some validation and demonstration cases. Rinaldi and Nespoli present TOUGH-SEED, an injection-induced seismicity modeling approach using TOUGH2 and a geomechanics stochastic model, and apply it to the Basel EGS project. Finally, Rinaldi et al. use the PEST protocol implemented in iTOUGH2, combined with TOUGH-FLAC as the forward model, to perform inverse modeling for the In Salah CO2 demonstration site in Algeria. Using pore pressures and InSAR displacements as observations, this approach allows for a multi-physics joint inversion and takes advantage of the inverse capabilities of iTOUGH2 (parameter estimation, sensitivity analysis, uncertainty estimation …), applied to coupled fluid flow and geomechanics. On behalf of the members of the TOUGH Symposium 2015 Organizing Committee, I hope that this collection of papers will provide the readers of Computers & Geosciences with a recent view of the capabilities of the TOUGH family of codes, as well as with current modeling research domains in the geosciences. Last but not least, I would like to express my gratitude to all the reviewers who kindly contributed to this Special Issue, as well as the Journal staff who have made this publication possible.

99 GENERAL AND MISCELLANEOUS↗

Visualizing effective potentials and using the IBM-Q to study quantum field theory models in 0+1 dimensions

This work explores the utility of two novel techniques applied to studying quantum field theory, namely quantum computing and visualizing effective potentials. We studied the ground state properties of the anharmonic oscillator and the Wess-Zumino model using the variational quantum eigensolver algorithm. We performed calculations for three and four qubit systems using IBM’s open source quantum computing simulation software. Using effective potentials, we study a simple dark mat-ter system with a Higgs and dark Higgs like particle interacting through a porthole fermion.

97 MATHEMATICS AND COMPUTING↗

LIQUID

LIQUID is a software tool for identifying lipids in LC-MS/MS-based lipidomics data. It is described in publication LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data (doi: 10.1093/bioinformatics/btx046). LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.

Payne, Sam↗

datasight [SWR-26-045]

This software is an AI-powered data exploration with natural language. datasight connects an AI agent to your database and provides a web UI where you can ask questions in natural language. The agent writes SQL, runs queries, and generates interactive Plotly visualizations. Supports DuckDB, PostgreSQL, SQLite, and Flight SQL databases. Also queries local CSV and Parquet files directly — no database setup required. Supports Anthropic Claude (default), GitHub Models (open source), and Ollama (local) as LLM backends.

Thom, Daniel [National Laboratory of the Rockies (↗

Pre-commercial Demonstration of Direct Non-iterative State Estimator for Operational Use of Synchrophasor Management Systems

The objective of this project was to demonstrate functionality and performance of a Direct Non-iterative State Estimator (DNSE) integrated with NYPA’s Energy Management System (EMS) and with enhanced Real Time Dynamics Monitoring System (RTDMS) synchrophasor platform from Electric Power Group (EPG). DNSE is designed to overcome a major obstacle to operational use of Synchro-Phasor Management Systems (SPMS) by providing to synchrophasor management systems (SPMS) applications a consistent and a complete synchrophasor data foundation in the same way that a traditional EMS State Estimator (SE) provides to EMS applications. Specifically, DNSE is designed to use synchrophasor measurements collected by a central PDC, Supervisory Control and Data Acquisition (SCADA) measurements, and Energy Management System (EMS) network model, to obtain the complete state of the utility’s operating model at rates that are close to the synchrophasor data rates. In this way, the system is comprehensive in that it does not only cover the part of the network that is “visible” via synchrophasors, but also the part that is only “visible” through the SCADA measurements. Visualization needs associated with the use of DNSE results are fulfilled through suitably enhanced Real Time Dynamics Monitoring System (RTDMS), with the enhancements implemented by EPG. This project had the following goals in mind: To advance the deployment of commercial grade DNSE software application that relies on synchrophasor and SCADA data ; Apply DNSE at other utilities, to address a generic and fundamental need for “clean” operational data for synchrophasor applications; Provide means for “live” estimated data access by control system operators; Enhance potential for situational awareness through full system operational model coverage; Sub-second execution rate of the Direct Non-iterative State Estimator, eventually at a near-phasor data rate execution speed, i.e. < 0.1 sec. Anticipated benefits from this projects are: Enhanced reliability and improvements in the economic efficiency of bulk power system planning and operations; Providing “clean” data to other synchrophasor applications; Enhancement of situational awareness by providing the full operational model updated at near synchrophasor rate; A production-grade software tool that incorporate synchrophasor and SCADA data; Provides a basis for development of next generation monitoring and control applications, based on both SCADA and PMU data. Quanta Technology (QT) team worked in collaboration with Electric Power Group (EPG) whose team has enhanced its commercial Real Time Dynamics Monitoring System (RTDMS) to accommodate the requirements posed by DNSE application. EPG also provided its ePDC and Model-less Data Conditioning (PDVC) software for integration with DNSE+. QT developed the system requirements for DNSE; developed system architecture and defined interfaces between internal DNSE components. The core DNSE algorithm with all surrounding interfaces was named DNSE+. Since the DNSE development was done in a simulated system environment, QT used its PMU simulator that was enhanced during this project for development and factory acceptance testing (FAT). SCADA data in this stage was simulated by commercial PSS/e software. The output of DNSE are estimates of System states in C37.118-2 format, sent to RTDMS for further processing and display. As the number of these states is large, it was necessary to expand the C37.111-2 standard to accommodate large data sets. This enhancement was implemented in RTDMS. The demonstration of pre-production DNSE technology was done at NYPA using streaming field data from NYPA PMUs and from its RTUs through their SCADA system. NYPA provided ICCP interface as well as Common Information Model (CIM). The relevance of the DNSE+ application is that it provides state estimation of the power system based on hybrid set of data, consisting of both available PMU data and SCADA measurements. As this is a direct, non-iterative method of calculation of the system states, if does not suffer from convergence issues which is potential problem for conventional state estimators. Also, it can take any available PMU measurements, so it does not need to have a high percentage of PMU coverage needed in the case of Linear State Estimator. As the DNSE calculates synchrophasors of the system states (both phase and absolute value) as sub-second rate, this application can provide a basis for development of next generation of applications based both on SCADA and PMU data.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Innovative Patient Room Lighting System with Integrated Spectrally Adaptive Control

In December of 2013, the U.S. Department of Energy’s SSL R&D Program released a Funding Opportunity Announcement (FOA), that for the first time, contained opportunities for comprehensive application-specific system development. The FOA included opportunities for two applications, one of which was a Patient Room. Philips Lighting Research North America, submitted a proposal for the Patient Room application, and was selected for the complete project award. The award amount was for $497,127, with a Philips Research co-funding commitment 165,709 dollars. The total project value was 662,836 dollars. This project sought to redefine lighting for the patient room application. The goal was to deliver an innovative LED patient suite (patient room and bathroom) lighting system solution that was 40% more energy-efficient than traditional fluorescent incumbent technologies, and would meet all the visual and non-visual needs of patients, caregivers and visitors, and improve the patient experience. State-of-the-art multichannel LED platforms and control technologies that would provide spectral tuning and become part of an intelligent, connected lighting system drove the solution. The project was scoped into four main task areas that included a) System Concept Creation, b) Identification of the Luminaire Portfolio, c) Development of the Connected Lighting Infrastructure, and d) System Performance Validation. Each of the four main tasks were completed and validated extensively over the course the 2 ½ year project. The system concept was created by first developing a lighting design that demonstrated best practices for patient room lighting – illuminance and uniformity for task performance, reduced glare, and convenient controls, in addition to giving patients control over the lighting in their environment. A framework was defined to deliver circadian support via software behaviors. Through that process luminaires were identified from the Philips portfolio that were adaptable – by their form, dimensions, and optical materials – to mix multicolor LED platforms uniformly and deliver target design lumen levels. The Blue Sky luminaire was selected for the patient bed area to give the illusion of skylight while providing white light on the patient bed. Luminaires used existing 2-channel tunable white LED boards, and newly developed 4-channel LED boards. Red-Orange, Blue, Green, and Blue-shifted Yellow LED chips were selected based on spectral characteristics and their ability to produce high quality white light. 4-channel Power over Ethernet (PoE) drivers were developed and firmware written so they would communicate with both 2- and 4-channel boards. These components formed the backbone of the connected lighting infrastructure. Software, flexible and nuanced in its complexity, was written to set behaviors for myriad lighting scenes in the room throughout the 24 hour day – and all could be overridden by manual controls. This included a dynamic tunable white program, three color changing automatic programs that simulated degrees of sunrise to sunset palettes, and an amber night lighting system that offered visual cues for postural stability to minimize the risk of falls. All programs were carefully designed to provide visual comfort for all occupants, support critical task performance for staff, and to support the patient’s 24hr rhythms. A full scale mockup room was constructed in the Philips Cambridge Lab. The lighting system was installed, tested and functionality demonstrated to ensure smooth operation of system components – luminaires, drivers, PoE switches, wall controls, patient remote, and daylight and occupancy sensors. How did the system perform? It met visual criteria, confirmed by calculations, simulations and measurements in the field. It met non-visual criteria, confirmed by setting circadian stimulus (CS) targets and performing calculations using the calculator developed by the Lighting Research Center. Finally, human factors validation studies were conducted to gain insight from real end users in the healthcare profession; surveys were administered, data analyzed, and audio comments captured. The general consensus was positive, with requests to pilot the system in their hospitals. The importance of the research completed under this grant is that it allowed the exploration and development of a unique lighting system, one that would deliver a blend of visual and non-visual criteria in patient room design for today’s healthcare environment. The research investigated the area of multichannel LED technology, multichannel Power over Ethernet (PoE) drivers and their integration with automatic and manual controls as a system – uncovering and meeting challenges along the way. It married visual needs of patients and staff with support for 24 hour rhythms, placing value on the wellbeing of the patient – while successfully saving energy over incumbent technologies. Indications are that the market is ready and willing to invest – multiple healthcare facilities are in line to pilot this system, recognizing its value beyond energy to patient and staff well-being. Its value to the public can best be expressed by a patient support coordinator who, after spending several hours in the room being immersed in the lighting, analyzing all its features, commented: “This re-writes lighting for healthcare”.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Automation of Nanoparticle Synthesis Processes in a Plasma Environment Using LabVIEW

This work presents an automated control system for the synthesis of nanomaterials by plasma-enhanced chemical vapor deposition (PECVD), implemented using the LabVIEW software environment. The main objective of the study is to develop an integrated hardware-software platform that enables sequential control of the key stages of the PECVD process, including vacuum chamber preparation, pressure monitoring, working gas supply, plasma ignition, power matching, cyclic nanomaterial growth, and optical monitoring of nanoparticles in the plasma environment. The use of LabVIEW made it possible to integrate actuator control, experimental parameter acquisition, and realtime process visualization within a single automated system. The automated cycle begins with evacuation of the reaction chamber to a predefined base pressure. Transition to the next stage is permitted only after the specified pressure threshold has been reached, ensuring reproducible initial conditions for each experiment. The program then controls the supply of the working gas through mass flow controllers (MFCs). In this work, two gas-flow control modes were considered: analog control using a 0-5 V voltage signal and digital communication via RS-232 interface. It was shown that the analog approach requires accurate scaling of the control voltage, since applying 5 V corresponds to full-scale opening of the controller and results in the maximum gas flow. In contrast, the RS232 interface enables the gas flow rate to be specified directly in sccm, improving the accuracy, flexibility, and convenience of gas-environment control. After pressure stabilization, LabVIEW initiates RF plasma ignition and executes the RF matching algorithm aimed at minimizing reflected power and improving the stability of the plasma process. A separate software module implements the cyclic nanomaterial growth mode, in which the plasma-on time, plasma duration, and total number of synthesis cycles are predefined. This approach makes it possible to control material accumulation on the substrate and to correlate the process parameters with the morphological characteristics of the resulting nanostructures. The final module of the system is designed for optical monitoring of the nanoparticle cloud density in dusty plasma. For this purpose, the change in the intensity of laser radiation passing through the plasma region is recorded using a photodetector and a Keithley 2401 measuring unit connected to LabVIEW via RS-232 interface. The difference between the initial and modified optical signal intensity is used as a diagnostic parameter characterizing the formation and temporal evolution of nanoparticles. The developed system demonstrates that LabVIEW can be effectively applied not only for the automation of individual instruments, but also for the implementation of a complete digital control cycle for PECVD-based nanomaterial synthesis.

PECVD↗

OpenSAMPL: An Open Source Library for Timing and Synchronization Measurements and Analytics

Today's power grid operators are implementing timing and synchronization solutions that provide resilience to Global Navigation Satellite System (GNSS) vulnerabilities. These vendor-specific solutions often come with additional software applications that are designed to monitor that vendor's synchronization performance data. However, resilient timing architectures often resulting in multi-vendor solutions, including approaches that blend terrestrial clocks with space-based subscription services. In such an environment, collecting, analyzing, and visualizing data from a variety of sources within a single platform was heretofore not possible. To address this need, the US Department of Energy's Center for Alternative Synchronization and Timing (CAST) developed OpenSAMPL, the Open Synchronized Analytics and Monitoring Platform, an open-source Python framework for processing, loading, and observing clock measurement data from distributed devices. OpenSAMPL enables the ingestion of diverse clock-probe sources into a scalable time-series database and applies robust analytics. OpenSAMPL currently supports two vendor data pipelines, and will be extended to more in the near future, enabling seamless monitoring of a variety of timing and synchronization devices in a common environment.

Grant, Josh [ORNL] (ORCID:0000000163475060)↗

Multiscale Solar Water Heating (MSWH) v1.0

The main purpose of the software is to model energy use for individual and community scale solar water heating projects in California. Usage The user provides a climate zone for a project, an occupancy for each household and whether any of the occupants stay at home during the day. The software can then load a set of example California specific hourly domestic hot water end-use load profiles from a database, size and locate the systems. The user can now simulate the hourly system performance over a period of one representative year, visualize and explore the simulation results using time-series plots for temperature profiles, heat and power rates, or look at annual summaries. Similarly the user can model individual household solar water heating projects and base case conventional gas tank water heater systems, such that the results can be compared between the individual, community and base case systems. This functionality is readily available through a Jupyter notebook and a Django web framework, depending on what level of detail the user would like to access. Features - Python module to calculate solar irradiation on a tilted surface - Python module with simplified component models for Converter (solar collectors, electric resistance heater, gas burner, photovoltaic panels, heat pump), Storage (solar thermal tank, heat pump thermal tank, conventional gas tank water heater), and Distribution (distribution and solar pump, piping losses) components - Python module with preconfigured system simulation models for: base case gas tank water heaters, solar thermal water heaters (solar collector feeding a storage tank, with a tankeless gas water heater backup in a new installation cases and a base case gas tank water heater in a retrofit case) and solar electric water heaters (heat pump storage tank with an electric resistance backup) - Database with component performance parameters, California specific weather data and domestic hot water end-use load profiles - Django web framework to configure project, parametrize components and run simulation from a web browser The package contains functional and unit tests and it is structured so that it can be extended with further technologies, applications and locations.

Grahovac, Milica↗

The Neurodata Without Borders ecosystem for neurophysiological data science

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB’s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

59 BASIC BIOLOGICAL SCIENCES↗