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At least 91 records · Page 5

JLIFE: THE JEFFERSON LAB INTERACTIVE FRONT END FOR THE OPTICAL PROPAGATION CODE

We present details on a graphical interface for the open source software program Optical Propagation Code, or OPC. This interface, written in Java, allows a user with no knowledge of OPC to create an optical system, with lenses, mirrors, apertures, etc. and the appropriate drifts between them. The Java code creates the appropriate Perl script that serves as the input for OPC. The mode profile is then output at each optical element. The display can be either an intensity profile along the x axis, or as an isometric 3D plot which can be tilted and rotated. These profiles can be saved. Examples of the input and output will be presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Middleware Automated Deployment Utilities - MRW Suite

The Middleware Automated Deployment Utilities consists the these three components: MAD: Utility designed to automate the deployment of java applications to multiple java application servers. The product contains a front end web utility and backend deployment scripts. MAR: Web front end to maintain and update the components inside database. MWR-Encrypt: Web utility to convert a text string to an encrypted string that is used by the Oracle Weblogic application server. The encryption is done using the built in functions if the Oracle Weblogic product and is mainly used to create an encrypted version of a database password.

Anderson, Mathew↗

Toward tsunami early warning system in Indonesia by using rapid rupture durations estimation

Indonesia has Indonesian Tsunami Early Warning System (Ina-TEWS) since 2008. The Ina-TEWS has used automatic processing on hypocenter; Mwp, Mw (mB) and Mj. If earthquake occurred in Ocean, depth < 70 km and magnitude > 7, then Ina-TEWS announce early warning that the earthquake can generate tsunami. However, the announcement of the Ina-TEWS is still not accuracy. Purposes of this research are to estimate earthquake rupture duration of large Indonesia earthquakes that occurred in Indian Ocean, Java, Timor sea, Banda sea, Arafura sea and Pasific ocean. We analyzed at least 330 vertical seismogram recorded by IRIS-DMC network using a direct procedure for rapid assessment of earthquake tsunami potential using simple measures on P-wave vertical seismograms on the velocity records, and the likelihood that the high-frequency, apparent rupture duration, T{sub dur}. T{sub dur} can be related to the critical parameters rupture length (L), depth (z), and shear modulus ({mu}) while T{sub dur} may be related to wide (W), slip (D), z or {mu}. Our analysis shows that the rupture duration has a stronger influence to generate tsunami than Mw and depth. The rupture duration gives more information on tsunami impact, Mo/{mu}, depth and size than Mw and other currently used discriminants. We show more information which known from the rupture durations. The longer rupture duration, the shallower source of the earthquake. For rupture duration greater than 50 s, the depth less than 50 km, Mw greater than 7, the longer rupture length, because T{sub dur} is proportional L and greater Mo/{mu}. Because Mo/{mu} is proportional L. So, with rupture duration information can be known information of the four parameters. We also suggest that tsunami potential is not directly related to the faulting type of source and for events that have rupture duration greater than 50 s, the earthquakes generated tsunami. With available real-time seismogram data, rapid calculation, rupture duration discriminant can be completed within 4-5 min after an earthquake occurs and thus can aid in effective, accuracy and reliable tsunami early warning for Indonesia region.

58 GEOSCIENCES↗

Preliminary results of local earthquake tomography around Bali, Lombok, and Sumbawa regions

Bali, Sumbawa, and Lombok regions are located in active tectonic influence by Indo-Australia plate subducts beneath Sunda plate in southern part and local back-arc thrust in northern part the region. Some active volcanoes also lie from eastern part of Java, Bali, Lombok and Sumbawa regions. Previous studies have conducted subsurface seismic velocity imaging using regional and global earthquake data around the region. In this study, we used P-arrival time from local earthquake networks compiled by MCGA, Indonesia within time periods of 2009 up to 2013 to determine seismic velocity structure and simultaneously hypocenter adjustment by applying seismic tomography inversion method. For the tomographic inversion procedure, we started from 1-D initial velocity structure. We evaluated the resolution of tomography inversion results through checkerboard test and calculating derivative weigh sum. The preliminary results of tomography inversion show fairly clearly high seismic velocity subducting Indo-Australian and low velocity anomaly around volcano regions. The relocated hypocenters seem to cluster around the local fault system such as back-arc thrust fault in northern part of the region and around local fault in Sumbawa regions. Our local earthquake tomography results demonstrated consistent with previous studies and improved the resolution. For future works, we will determine S-wave velocity structure using S-wave arrival time to enhance our understanding of geological processes and for much better interpretation.

58 GEOSCIENCES↗

Earthquake response of storey building in Jakarta using accelerographs data analysis

As seismotectonic, the Jakarta city will be greatly affected by the earthquake which originated from the subduction zone of the Sunda Strait and south of Java. Some occurrences of earthquakes in these location are often perceived by the occupants in the upper floors of multi-storey buildings in Jakarta but was not perceived by the occupants on the ground floor. The case shows the difference in ground-motion parameters on each floor height. The analysis of the earthquake data recorded by accelerographs on different floors need to be done to know the differences in ground-motion parameters. Data used in this research is accelerograph data installed on several floors in the main building of Meteorology Climatology and Geophysics Agency with a case study of Kebumen earthquake on January 25{sup th} 2014. Parameters analyzed include the Peak Ground Acceleration (PGA), Peak Ground Displacement (PGD), Peak Spectral Acceleration (PSA), Amplification (Ag), and the Effective Duration of earthquake (t{sub e}). Research stages include accelerographs data acquisition in three (3) different floors, conversion and data partition for each component, conversion to units of acceleration, determination of PGA, PGD, PSA, Ag and t{sub e} as well as data analysis. The study shows the value of PGA on the ground floor, 7{sup th} floor and 15{sup th} floors, respectively are 0.016 g, 0.053 g and 0.116 g. PGD on the ground floor, 7{sup th} floor and 15{sup th} floor respectively are 2.15 cm, 2.98 cm and 4.92 cm. PSA on the ground floor, 7{sup th} floor and 15{sup th} floor respectively are 0.067 g, 0.308 g and 0.836 g. Amplification of the peak acceleration value on the ground floor, 7{sup th} floor and 15{sup th} floor to the surface rock are 4.37, 6.07 and 7.30. Effective duration of the earthquake on the ground floor, 7{sup th} floor and 15{sup th} floor respectively are 222.28 s, 202.28 s and 91.58 s. In general, with increasing floor of the building, the value of the peak ground acceleration, peak ground displacement, peak spectral acceleration and amplification growing, contrary to the value of the effective duration of earthquake decreases. The difference in this parameter is strongly influenced by local soil conditions and building construction.

58 GEOSCIENCES↗

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA{sup +}-DS{sup −}). The experimental measures of emf indicate Nernstian behaviour with the CTA{sup +} content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

TEAMER: Crossflow Turbine Fairing Geometry Optimization - Report and CFD Modeling Files

The dataset includes computational fluid dynamics (CFD) models and simulation files for crossflow turbines as well as a detailed project report. The report documents the project undertaken by the Ocean Renewable Power Company (ORPC) to design and optimize a modular fairing for the Modular RivGen Marine Hydrokinetic (MHK) turbine, which enhances the efficient deployment and operation of turbine arrays. The project focused on optimizing the hydrodynamic performance of the fairing using CFD, with an emphasis on two key geometric parameters: the fairing's cross-sectional shape and the spacing between the rotor and the fairing. The analysis aimed to maximize net power output while also assessing discretized loading to evaluate ultimate and fatigue loads on the turbine components. The numerical modeling was conducted using both the commercial CFD software Star-CCM+ and the open-source code openFOAM, with the latter utilizing the actuator line library, turbinesFOAM. This dual-code approach was intended to increase confidence in the results and demonstrate the viability of using open-source tools for high-fidelity marine energy modeling. This dataset includes all necessary files for actuator line simulations in openFOAM, as well as 2D blade-resolved CFD results, along with Python and Java scripts for setting up and post-processing simulations.

16 TIDAL AND WAVE POWER↗

Enabling a systems biology knowledgebase with gaggle and firegoose

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is an open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.

97 MATHEMATICS AND COMPUTING↗

User Guide for the Plotting Software for the Los Alamos National Laboratory Nuclear Weapons Analysis Tools Version 2.0

The Los Alamos National Laboratory Plotting Software for the Nuclear Weapons Analysis Tools is a Java™ application based upon the open source library JFreeChart. The software provides a capability for plotting data on graphs with a rich variety of display options while allowing the viewer interaction via graph manipulation and scaling to best view the data. The graph types include XY plots, Date XY plots, Bar plots and Histogram plots.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Knowledge management information tool analytics with distributed database engine - 15737

The D and D KM-IT is a web-based knowledge management information tool custom built for the deactivation and decommissioning (D and D) user community. The system allows interested users to post information which goes through a custom work flow. To better improve the performance and user experience, the analysis of server logs is being conducted using MongoDB. MongoDB is a document database that provides high performance, high availability, and easy scalability. Objectives: - Feasibility study of Distributed Database Engine, MongoDB for web analytics; - Analyze server logs to evaluate D and D KM-IT module usage; - Generate useful information from the analysis. Method: - The server logs were loaded and stored in MongoDB for analysis; - Analysis and visualization was performed using NodeJS and Java Script library. Results: - It was possible to store log files in MongoDB; - Log files with different time stamps and groups from different servers can be aggregated; - Queries can be written to extract meaningful information from aggregated log files (e.g. users from different countries/organizations). Conclusions: - MongoDB is useful for server log analytics as the analyst can immediately access, analyze, and visualize MongoDB data based on the requirements; - The information can be extracted to develop custom reports; - Optimized queries can be run for fast data access. Path forward: - Custom queries need to be developed to extract information leading to improved user information.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Deep and shallow sources for the Lusi mud eruption revealed by surface deformation

The Lusi mud eruption, in East Java, Indonesia, began in May 2006 and continues to the present. Previous analyses of surface deformation data suggested an exponential decay of the pressure in the mud source but did not constrain the location, geometry, and evolution of the possible source(s) of the erupting mud and fluids. To map the surface deformation, we employ multitemporal interferometric synthetic aperture radar and analyze a well-populated L-band data set acquired by the Advanced Land Observing Satellite (ALOS) between May 2006 and April 2011. We then apply a time-dependent inverse modeling scheme. Volume changes occur in two regions beneath Lusi, at 0.3-2.0km and 3.5-4.75km depth. The cumulative volume change within the shallow source is ~2-3 times larger than that of the deep source. The observation and model suggest that a shallow source plays a key role by supplying the erupting mud, but that additional fluids do ascend from depths >4km on eruptive timescales. Key Points Spatiotemporal map of the surface deformation associated with Lusi mud eruption Time-dependent source model of the Lusi and nearby gas field Revealing the deep and shallow sources of the Lusi and characterizing their relationship.

58 GEOSCIENCES↗

Influence of seismicity on the Lusi mud eruption

Earthquakes trigger the eruption of mud and magmatic volcanoes and affect ongoing eruptive activity. One mechanism that could trigger an eruption is clay liquefaction. In this work we model the propagation of seismic waves beneath the Lusi mud eruption (East Java, Indonesia) using available seismic velocity and density models to assess the effect of subsurface structure on the amplification of incident seismic waves. We find that using an updated subsurface density and velocity structure, there is no significant amplification of incident seismic energy in the Upper Kalibeng Formation, the source of the erupting solids. Thus, the hypothesis that the Lusi eruption was triggered by clay liquefaction appears unlikely to be correct. Independent constraints from gas chemistry as well as analyses of drilling activities at the nearby Banjar-Panji 1 gas exploration well and an analysis of the effects of other earthquakes all favor a drilling trigger.

58 GEOSCIENCES↗

A Parallel Computing Framework for Finding the Supported Solutions to a Biobjective Network Optimization Problem

Abstract Solving multi‐objective combinatorial optimization problems can quickly become computationally challenging when applied to large networks generated from big data. Present‐day first‐rate Mixed Integer Programming (MIP) solvers have parallelism built‐in to take advantage of multicore architectures; but specialized network optimization algorithms that can often solve graph problems more efficiently than a general MIP solver are typically programmed serially. Thus, these network algorithm implementations do not take full advantage of modern multicore computer capabilities. Many parallel computing languages include a fork/join framework into their concurrency packages that allow for simple conversion of recursive serial algorithms to operate in parallel without having to use complicated low‐level message‐passing interfaces. Fork/join is particularly well suited to divide and conquer algorithms such as Non‐Inferior Set Estimation (NISE) method for computing the supported Pareto front of a multi‐objective optimization problem. This work develops a simple general parallel NISE (pNISE) implementation using the Java 7 concurrency tools, and then offers results from a specific implementation of solving a bi‐objective shortest path problem. The results indicate that this method is capable of sizeable speed‐ups on both small‐scale personal computers as well as large‐scale shared memory supercomputers. Finally, other network problems suitable to this method are discussed, including multi‐objective variants of the minimum spanning tree problem, transportation problem, assignment problem, maximum flow problem, and the minimum‐cost flow problem. Copyright © 2015 John Wiley & Sons, Ltd.

Medrano, Fernando Antonio↗

Using Natural Language Processing of Free-Text Radiology Reports to Identify Type 1 Modic Endplate Changes

Electronic medical record (EMR) systems provide easy access to radiology reports and offer great potential to support quality improvement efforts and clinical research. Harnessing the full potential of the EMR requires scalable approaches such as natural language processing (NLP) to convert text into variables used for evaluation or analysis. Our goal was to determine the feasibility of using NLP to identify patients with Type 1 Modic endplate changes using clinical reports of magnetic resonance (MR) imaging examinations of the spine. Identifying patients with Type 1 Modic change who may be eligible for clinical trials is important as these findings may be important targets for intervention. Four annotators identified all reports that contained Type 1 Modic change, using N = 458 randomly selected lumbar spine MR reports. We then implemented a rule-based NLP algorithm in Java using regular expressions. The prevalence of Type 1 Modic change in the annotated dataset was 10%. Results were recall (sensitivity) 35/50 = 0.70 (95% confidence interval (C.I.) 0.52–0.82), specificity 404/408 = 0.99 (0.97–1.0), precision (positive predictive value) 35/39 = 0.90 (0.75–0.97), negative predictive value 404/419 = 0.96 (0.94–0.98), and F1-score 0.79 (0.43–1.0). Our evaluation shows the efficacy of rule-based NLP approach for identifying patients with Type 1 Modic change if the emphasis is on identifying only relevant cases with low concern regarding false negatives. As expected, our results show that specificity is higher than recall. This is due to the inherent difficulty of eliciting all possible keywords given the enormous variability of lumbar spine reporting, which decreases recall, while availability of good negation algorithms improves specificity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

High-performance data format for scientific data storage and analysis

Here, in this article, we present the High-Performance Output (HiPO) data format developed at Jefferson Laboratory for storing and analyzing data from Nuclear Physics experiments. The format was designed to efficiently store large amounts of experimental data, utilizing modern fast compression algorithms. The purpose of this development was to provide organized data in the output, facilitating access to relevant information within the large data files. The HiPO data format has features that are suited for storing raw detector data, reconstruction data, and the final physics analysis data efficiently, eliminating the need to do data conversions through the lifecycle of experimental data. The HiPO data format is implemented in C++ and JAVA, and provides bindings to FORTRAN, Python, and Julia, providing users with the choice of data analysis frameworks to use. In this paper, we will present the general design and functionalities of the HiPO library and compare the performance of the library with more established data formats used in data analysis in High Energy and Nuclear Physics (such as ROOT and Parquete). In columnar data analysis, HiPO surpasses established data formats in performance and can be effectively applied to data analysis in other scientific fields.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cross-boundary collaboration in waste management research: A network analysis

Highlights: • No core scholars stood out from cross-boundary research collaboration networks. • No institution occupied a critical position. • Old-line developed countries stay in the center of research than developing ones. • More research has focused on “hard” technologies than “soft” measures. • CBRC from different perspectives were limited but increasing steadily over time. - Abstract: This paper aims to illustrate the cross-boundary research collaboration (CBRC) landscape of waste management (WM) by various collaboration networks. Through a set of rigorous procedures, a total of 15,396 research papers were extracted from eight subject-related journals published between 1981 and 2016. The authors utilized CiteSpace, a Java programme that helps visualize and dissect patterns in scientific literature, to evaluate the content through individual, institutional, national, and disciplinary perspectives. The evaluations of three former perspectives revealed a steady rise in CBRC within WM over the last thirty-five years, although the overall intensities proved fairly low. Inter-individual collaboration groups were limited to their respective regions and only loosely connected, but as more and more academic institutions and universities engaged in WM research, the number and quality of the collaborations increased. Developed countries, chiefly in North America and Western Europe, comprised the bulk of the WM research, whilst the mounting contributions from developing countries, China in particular, forecasts greater diversity in the future. The analysis also suggested that the intensity of the interdisciplinary collaboration network declined slightly, however, the intensity proved low to begin with. Previous WM research focused more on “hard” technologies than “soft” measures. Future endeavors to encourage CBRC in WM should promote more innovative research to tackle waste challenges globally in a sustainable way.

54 ENVIRONMENTAL SCIENCES↗

SimCCS: An open-source tool for optimizing CO 2 capture, transport, and storage infrastructure

Commercial-scale carbon capture and storage (CCS) technology will involve deploying infrastructure on a massive and costly scale. This effort will require careful and comprehensive planning to ensure that capture locations, storage sites, and the dedicated CO 2 distribution pipelines are selected in a robust and cost-effective manner. Presented in 2009, SimCCS is an optimization model for integrated system design that enables researchers, stakeholders, and policy makers to design CCS infrastructure networks. SimCCS 2.0 is a complete, ground-up redesign that is now a portable software package, useable and shareable by the CCS research, industrial, policy, and public communities. SimCCS 2.0 integrates multiple new capabilities including a refined optimization model, novel candidate network generation techniques, and optional integration with high-performance computing platforms. Accessing user-provided CO 2 source, sink, and transportation data, SimCCS 2.0 creates candidate transportation routes and formalizes an optimization problem that determines the most cost-effective CCS system design. This optimization problem is further solved either through a high-performance computing interface, or through third-party software on a local desktop computing platform. Finally, SimCCS 2.0 employs an open-access geographic information system framework to enable analysis and visualization capabilities. SimCCS 2.0 is written in Java and is publicly available via GitHub to encourage collaboration, modification, and community development.

42 ENGINEERING↗