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At least 523 records · Page 29

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

59 BASIC BIOLOGICAL SCIENCES↗

An on-line acoustic fluorocarbon coolant mixture analyzer for the ATLAS silicon tracker

The ATLAS silicon tracker community foresees an upgrade from the present octafluoro-propane (C{sub 3}F{sub 8}) evaporative cooling fluid - to a composite fluid with a probable 10-20% admixture of hexafluoro-ethane (C{sub 2}F{sub 6}). Such a fluid will allow a lower evaporation temperature and will afford the tracker silicon substrates a better safety margin against leakage current-induced thermal runaway caused by cumulative radiation damage as the luminosity profile at the CERN Large Hadron Collider increases. Central to the use of this new fluid is a new custom-developed speed-of-sound instrument for continuous real-time measurement of the C{sub 3}F{sub 8}/C{sub 2}F{sub 6} mixture ratio and flow. An acoustic vapour mixture analyzer/flow meter with new custom electronics allowing ultrasonic frequency transmission through gas mixtures has been developed for this application. Synchronous with the emission of an ultrasound 'chirp' from an acoustic transmitter, a fast readout clock (40 MHz) is started. The clock is stopped on receipt of an above threshold sound pulse at the receiver. Sound is alternately transmitted parallel and anti-parallel with the vapour flow for volume flow measurement from transducers that can serve as acoustic transmitters or receivers. In the development version, continuous real-time measurement of C{sub 3}F{sub 8}/C{sub 2}F{sub 6} flow and calculation of the mixture ratio is performed within a graphical user interface developed in PVSS-II, the Supervisory, Control and Data Acquisition standard chosen for LHC and its experiments at CERN. The described instrument has numerous potential applications - including refrigerant leak detection, the analysis of hydrocarbons, vapour mixtures for semiconductor manufacture and anesthetic gas mixtures. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Real-time online monitoring of radwaste storage: A proof-of-principle test prototype

A prototype array of modular sensors for online monitoring of radioactive waste was developed at INFN-LNS. We implemented a new kind of gamma mini-sensor, based on Silicon Photomultipliers and scintillating fibers, that behaves like a cheap scintillating Geiger-Muller counter. It can be placed in shape of a fine grid around each single waste drum in a repository. After simulating the counting response of thin scintillating fibers to gamma radiation, we verified our simulation results with measurements using radioactive sources. Front-end electronics and an FPGA-based counting system were developed to handle the field data, also implementing data transmission, a graphical user interface and a data storage system. A test of four sensors in a real radwaste storage site was performed with promising results. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Visualization of High Resolution Spatial Mass Spectrometric Data during Acquisition

Mass Spectrometric Imaging (IMS) allows the generation of 2D ion density maps that help visualize molecules present in sections of tissues and cells. The combination of spatial and mass resolution results in large and complex data sets that require powerful and efficient analysis and interpretation. In this paper, a graphical user interface (GUI) that can visualize the large data during data acquisition itself is presented. The program also has the ability to perform processing and analysis of the dataset. The various functions of the GUI including visualization of mass spectra, generation of 2D maps for selected species, manipulation of the heat maps, and peak identification are also presented.

Thomas, Mathew↗

Hy-DAT: A Tool to Address Hydropower Modeling Gaps Using Interdependency, Efficiency Curves, and Unit Dispatch Models

As the power system continues to be flooded with intermittent resources, it becomes more important to accurately assess the role of hydro and its impact on the power grid. While hydropower generation has been studied for decades, dependency of power generation on water availability and constraints in hydro operation are not well represented in power system models used in the planning and operation of large-scale interconnection studies. There are still multiple modeling gaps that need to be addressed; if not, they can lead to inaccurate operation and planning reliability studies, and consequently to unintentional load shedding or even blackouts. As a result, it is very important thathydropower is represented correctly in both steady-state and dynamic power system studies. In this paper, we discuss the development and use of the Hydrological Dispatch and Analysis Tool (Hy-DAT) as an interactive graphical user interface (GUI), that uses a novel methodology to address the hydropower modeling gaps like water availability and inter-dependency using a database, and algorithms, to generate accurate representative models for power system simulation.

Wang, Dewei↗

Fuzzy Linguistic Knowledge Based Behavior Extraction for Building Energy Management Systems

Significant portion of world energy production is consumed by building Heating, Ventilation and Air Conditioning (HVAC) units. Thus along with occupant comfort, energy efficiency is also an important factor in HVAC control. Modern buildings use advanced Multiple Input Multiple Output (MIMO) control schemes to realize these goals. However, since the performance of HVAC units is dependent on many criteria including uncertainties in weather, number of occupants, and thermal state, the performance of current state of the art systems are sub-optimal. Furthermore, because of the large number of sensors in buildings, and the high frequency of data collection, large amount of information is available. Therefore, important behavior of buildings that compromise energy efficiency or occupant comfort is difficult to identify. This paper presents an easy to use and understandable framework for identifying such behavior. The presented framework uses human understandable knowledge-base to extract important behavior of buildings and present it to users via a graphical user interface. The presented framework was tested on a building in the Pacific Northwest and was shown to be able to identify important behavior that relates to energy efficiency and occupant comfort.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Nonrelational Data Warehouse for the Analysis of Field and Laboratory Data From Multiple Heterogeneous Photovoltaic Test Sites

A nonrelational, distributed computing, data warehouse, and analytics environment (Energy-CRADLE) was developed for the analysis of field and laboratory data from multiple heterogeneous photovoltaic (PV) test sites. This data informatics and analytics infrastructure was designed to process diverse formats of PV performance data and climatic telemetry time-series data collected from a PV outdoor test network, i.e., the Solar Durability and Lifetime Extension global SunFarm network, as well as point-in-time laboratory spectral and image measurements of PV material samples. Using Hadoop/HBase for the distributed data warehouse, Energy-CRADLE does not have a predefined data table schema, which enables ingestion of data in diverse and changing formats. For easy data ingestion and data retrieval, Energy-CRADLE utilizes Hadoop streaming to enable Python MapReduce and provides a graphical user interface, i.e., py-CRADLE. By developing the Hadoop distributed computing platform and the HBase NoSQL database schema for solar energy, Energy-CRADLE exemplifies an integrated, scalable, secure, and user-friendly data informatics and analytics system for PV researchers. Furthermore, an example of Energy-CRADLE enabled scalable, data-driven, analytics is presented, where machine learning is used for anomaly detection across 2.2 million real-world current-voltage (I–V) curves of PV modules in three distinct Koppen–Geiger climatic zones.

14 SOLAR ENERGY↗

Spatial-Temporal PV Hosting Capacity Estimation and Evaluation

Evaluating Photovoltaic Hosting Capacity (PVHC) is an essential step in the process of integrating solar energy into power grids, particularly when focusing on the distribution network (DN) as the primary integration target. PVHC needs to be investigated, especially in cases where the grids are unbalanced, and their operational conditions vary spatially and temporally. This motivation prompted us to propose a scalable model tailored to this application. In this paper, we applied linearization to the alternating current optimal power flow (AC-OPF) and solar inverters, transforming the original problem into a mixed-integer linear programming (MILP) problem. Additionally, we accounted for the battery energy storage system (BESS) as a time-coupling factor for calculating PVHC. We then compared the PVHC results between the IEEE-13 bus and SMART-DS San Francisco (SFO) cases and discussed the extent to which BESS can enhance the PVHC of a DN. Furthermore, we designed a web-based graphical visualization for the SFO case, enabling user interaction with raw data and simulation results on a map through a graphical user interface (GUI). In summary, our results and findings provide valuable insights for future three-phase unbalanced AC-OPF PVHC practices and their visualization.

AC-optimal power flow↗

Hardware-in-the-Loop Testing of Wide-Area Damping Controller for Field Implementation in Large-scale Power Grid

In our previous work, an adaptive measurement-driven wide-area damping controller (WADC) for suppressing inter-area oscillations has been proposed and a hardware prototype was developed and validated through hardware-in-the-loop tests. As a continuation of the work, this paper introduces a WADC software prototype to handle the realistic challenges for field implementation in the control room of the power grid. The WADC software is developed and operated as an openPDC adapter with a graphical user interface (GUI) to monitor the WADC inputs and output, the communication delays and other variables. The software prototype has been fully tested through an enhanced hardware-in-the-loop (HIL) test setup. Its performance is verified under various realistic communication uncertainties, such as random time delays and data losses, with different communication protocols. The experiment results have proven the WADC software can deliver sufficient damping to suppress the targeted oscillation mode in handling various communication uncertainties for future field deployment.

Jia, Xinlan↗

WE-Validate: An Open-Source Framework For Wind Power Validation

Grid operators rely on historical weather time series at existing and planned wind power plants to make informed decisions when planning for a future power grid with very high penetration of renewable power. While synthetic wind power time series have been developed based on historical weather models, their validation with actual power production data remains complex due to variations in modeling practices and methodologies. This paper introduces the WE-Validate framework, originally designed for wind speed validation and now enhanced for wind power validation with a graphical user interface to support users with minimal programming experience. Validation of wind power with WE-Validate is based on robust metrics consisting of RMSE, centered RMSE, average bias, average percent bias, mean absolute error, mean absolute percent error, cross correlation, and calculation of ramping magnitude, rate, and duration. This paper showcases WE-Validate with validation of synthetically derived power for a wind plant in Washington state for one month in 2018. Validation of the synthetic power from two comparison data sets compared with observations shows both comparison series have strong correlation with observed across weekly and monthly aggregations while suffering from persistent negative bias. The suite of metrics within WE-Validate facilitates immediate insight into the utility of the comparison data sets through compression across multiple axes. This user-friendly, open-source tool can be extended beyond wind power, making it a valuable resource for system planners and operators in different domains.

Moncheur de Rieudotte, Malcolm P.↗

Extremum Seeking-Based Control System for Particle Accelerator Beam Loss Minimization

Particle accelerators throughout the world vary widely in terms of age and availability of advanced noninvasive diagnostics that provide varying levels of detail about the accelerated beams. Additionally, beam loss measurements and current monitors are ubiquitous in the accelerator community, they are noninvasive, and they are some of the most important metrics in terms of preventing damage or irradiation of beam pipes and equipment for high-energy machines. However, beam loss and current measurements are difficult to use for feedback tuning because of a lack of a known analytic relationship between scalar loss measurements throughout an accelerator and the hundreds of thousands of parameters that influence the beam and time variation of the beam source itself. In this work, we present a model-independent extremum seeking (ES) controller, which has been implemented for automated tuning and optimization of the Los Alamos Neutron Science Center (LANSCE) linear ion accelerator based only on scalar quantities, such as beam loss or flux measurements. We demonstrate the approach on various accelerator subsystems, including groups of radio frequency (RF) accelerating cavities, quadrupole magnets, bending magnets, and steering magnets. This tool is now available as a use graphical user interface (GUI) in the LANSCE control room, allowing beam physicists to choose arbitrary groups of parameters and beam loss or current monitors for adaptive tuning.

43 PARTICLE ACCELERATORS↗

FEgen (v.1): Field Emission Distribution Generator Freeware Based on Fowler–Nordheim Equation

This work presents an open-source code, FEgen, that generates initial field emission distributions based on the time-dependent Fowler–Nordheim equation. Current in-demand and open-source beam tracking software—such as ASTRA, IMPACT-T, and GPT—do not contain native distribution generator functions suitable for field emitted electron tracking and phase space analysis. Furthermore, the intuitive graphical user interface of FEgen generates input files shown to be fully compatible with both ASTRA and GPT. Here, detailed application examples demonstrating a subset of FEgen’s capabilities are given by creating a customized emitter pattern with application to transverse beam shaping and longitudinal beam dynamic experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Planning tools for modulated electron radiotherapy

Purpose: To develop tools to plan modulated electron radiotherapy (MERT) and to compare the MERT plans to conventional or intensity modulated radiotherapy (IMRT) treatment plans. Methods: Monte Carlo dose calculations of electron fields shaped with the inherent photon multileaf collimators (MLCs) were investigated in this study. Treatment plans for four postmastectomy breast cancer patients were generated using MERT. The distances from the patient skin surfaces to the distal planning target volume surfaces were computed along the beam axis direction to determine the physical depth. Electron beam energies were selected to provide target coverage at these depths and energy bins were generated. A custom built MERT treatment planning graphical user interface (MERTgui) was used to shape the electron bins into deliverable electron segments. Monte Carlo dose distribution simulations were performed using the MLC-defined segments generated from the MERTgui. A custom built superposition gui was used to combine doses for each segment using relative weights and final MERT treatment plans were compared to the conventional or IMRT treatment plans. In addition, a demonstration of combined MERT and IMRT treatment plans was performed. Results: The MERT treatment plans provided acceptable target organ coverage in all cases. Relative to 3D conventional or IMRT treatment plans, the MERT plans predicted lower heart doses in all cases; average of the heart D{sub 20} of all plans was reduced from 14.1 to 3.3 Gy. The contralateral breast and contralateral lung doses decreased substantially with MERT planning compared to IMRT (on average, contralateral breast heart D{sub 20} was reduced from 8.7 to 0.7 Gy and contralateral lung D{sub 20} was reduced from 8.4 to 1.2 Gy with MERT). Ipsilateral lung D{sub 20} was lower with MERT than with the conventional plans (44.6 vs 29.2 Gy with MERT), but greater when compared against IMRT treatment plans (25.4 vs 28.9 Gy with MERT). A MERT and IMRT combination plan was generated to benefit from the complementary advantages of MERT and IMRT, resulting in satisfactory target coverage and reduced organ at risk doses. Conclusions: MERT tools can facilitate treatment planning and provide plans for treatment of shallow targets such as the postmastectomy chest wall.

61 RADIATION PROTECTION AND DOSIMETRY↗

Technical Note: DIRART- A software suite for deformable image registration and adaptive radiotherapy research

Purpose: Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). Methods: DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. Results: DIRART provides a set of image processing/registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. Conclusions: By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research.

60 APPLIED LIFE SCIENCES↗

SU-D-9A-03: STAMP: Simulator for Texture Analysis in MRI/PET

Purpose: To develop a convenient simulation platform to facilitate PET/MR image analysis with the prospect of gaining a better understanding of the influence of acquisition parameters on PET/MRI textural features. The simulation platform is demonstrated by showing textural variations of a representative case study using different image acquisition parameters. Methods: The simulation platform is composed of MRI simulators JEMRIS and SIMRI to achieve simulations of customized MRI sequences on sample tumor models. The PET simulator GATE is used to get 2D and 3D Monte Carlo acquisitions of voxelized PET sources using a phantom geometry and a customized scanner architecture. The platform incorporates a series of graphical user interfaces written in Matlab. Two GUIs are used to facilitate communication with the simulation executables installed on a computer cluster. A third GUI is used to collect and display the clinical and simulated images, as well as fused PET/MRI images, and perform computation of textural features.To illustrate the capabilities of this platform, one FDG-PET and T1-weighted (T1w) digitized tumor models were generated from clinical images of a soft-tissue sarcoma patient. Numerically simulated MR images were produced using 3 different echo times (TE) and 5 different repetition times (TR). PET 2D images were simulated using an OSEM algorithm with 1 to 32 iterations and a post-reconstruction Gaussian filter of 0, 2, 4 or 6 mm width. Results: STAMP was successfully used to produce numerically simulated FDG-PET and MRI images, and to calculate their corresponding textures. Three typical textures (GLCM-Contrast, GLSZM-ZSV and NGTDM-Coarseness) were found to vary by a range of 45% on average compared to reference scanning conditions in the case of FDG-PET, and by a range of 40% in the case of T1w MRI. Conclusion: We have successfully developed a Matlab-based simulation platform to facilitate PET/MRI texture image analysis for outcome prediction.

60 APPLIED LIFE SCIENCES↗

SU-E-T-194: From Dicom-RT to Radiobiological Dose Metrics in 5 Minutes

Purpose: To develop a flexible and standalone framework for batch calculation of radiobiological dose metrics from Dicom-RT. Methods: Software has been developed which allows (1) The calculation of DVH data from DICOM dose and structure files (DVHgenerator), (2) Calculation of a wide range of radiobiological metrics from this data (CompPlanGui). Both these tools are run via graphical user interface (GUI), making them fast and simple. Part 1 is a new tool which has not previously been published, whilst part 2 is a GUI overlay for the previously published software ‘Comp-Plan’ (Holloway et. al., Medical Dosimetry, 2012), previously reliant on command line interface. The time taken for an experienced user to evaluate a test case of 6 plans with and without CompPlanGUI was quantified. Results: The DVH-generator has been found to be faster, more robust and require far less physical memory then using alternative software solutions for the same purpose. The Comp Plan GUI significantly reduces the amount of time required to set up a base directory, eliminates code crashes arising from typographical errors, and renders the code far more accessible to non-expert users. It took an experienced user of the code around 3 minutes to set up a base directory of 6 plans compared around 8 minutes without, indicating that using CompPlanGUI reduced setup time by over 50%. Conclusion: A standalone GUI based framework has developed which allows for the batch calculation of radiobiological dose metrics directly from Dicom-RT files. As with the original code, this work will be made freely available on request, as well as via matlab file exchange.

07 ISOTOPE AND RADIATION SOURCES↗

SU-F-18C-01: Minimum Detectability Analysis for Comprehensive Sized Based Optimization of Image Quality and Radiation Dose Across CT Protocols

Purpose: This work involved a comprehensive modeling of task-based performance of CT across a wide range of protocols. The approach was used for optimization and consistency of dose and image quality within a large multi-vendor clinical facility. Methods: 150 adult protocols from the Duke University Medical Center were grouped into sub-protocols with similar acquisition characteristics. A size based image quality phantom (Duke Mercury Phantom) was imaged using these sub-protocols for a range of clinically relevant doses on two CT manufacturer platforms (Siemens, GE). The images were analyzed to extract task-based image quality metrics such as the Task Transfer Function (TTF), Noise Power Spectrum, and Az based on designer nodule task functions. The data were analyzed in terms of the detectability of a lesion size/contrast as a function of dose, patient size, and protocol. A graphical user interface (GUI) was developed to predict image quality and dose to achieve a minimum level of detectability. Results: Image quality trends with variations in dose, patient size, and lesion contrast/size were evaluated and calculated data behaved as predicted. The GUI proved effective to predict the Az values representing radiologist confidence for a targeted lesion, patient size, and dose. As an example, an abdomen pelvis exam for the GE scanner, with a task size/contrast of 5-mm/50-HU, and an Az of 0.9 requires a dose of 4.0, 8.9, and 16.9 mGy for patient diameters of 25, 30, and 35 cm, respectively. For a constant patient diameter of 30 cm, the minimum detected lesion size at those dose levels would be 8.4, 5, and 3.9 mm, respectively. Conclusion: The designed CT protocol optimization platform can be used to evaluate minimum detectability across dose levels and patient diameters. The method can be used to improve individual protocols as well as to improve protocol consistency across CT scanners.

60 APPLIED LIFE SCIENCES↗

TH-A-19A-01: An Open Source Software for Proton Treatment Planning in Heterogeneous Medium

Purpose: Due to its success in Radiation Oncology during the last decade, interest in proton therapy is on the rise. Unfortunately, despite the global enthusiasm in the field, there is presently no free, multiplatform and customizable Treatment Planning System (TPS) providing proton dose distributions in heterogenous medium. This restricts substantially the progress of clinical research for groups without access to a commercial Proton TPS. The latest implementation of our pencil beam dose calculation algorithm for proton beams within the 3D Slicer open-source environment fulfills all the conditions described above. Methods: The core dose calculation algorithm is based on the Hong algorithm (1), which was upgraded with the Kanematsu theory describing the evolution of the lateral scattering of proton beamlets in heterogeneous medium. This algorithm deals with both mono-energetic beams and Spread Out Bragg Peak (SOBP). In order to be user-friendly, we provide a graphical user interface implemented with the Qt libraries, and visualization with the 3D Slicer medical image analysis software. Two different pencil beam algorithms were developed, and the clinical proton beam line at our facility was modeled. Results: The dose distributions provided by our algorithms were compared to dose distributions coming from both commercialized XiO TPS and literature (dose measurements, GEANT4 and MCNPx) and turned out to be in a good agreement, with maximum dose discrepancies of 5% in homogeneous phantoms and 10% in heterogeneous phantoms. The algorithm of SOBP creation from an optimized weigthing of mono-energetic beams results in flat SOBP. Conclusion: We hope that our efforts in implementing this new, open-source proton TPS will help the research groups to have a free access to a useful, reliable proton dose calculation software.(1) L. Hong et al., A pencil beam algorithm for proton dose calculations, Phys. Med. Biol. 41 (1996) 1305–1330. This project is paid for by NCI/MGH Federal share as a research grant.

62 RADIOLOGY AND NUCLEAR MEDICINE↗