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At least 109 records · Page 6

From lab to table: Expanding gastronomic possibilities with fermentation using the edible fungus Neurospora intermedia

Fermentation is a powerful tool for enhancing flavor, improving sustainability, and expanding creative possibilities in the kitchen. However, most fermentations done in gastronomic contexts are restricted to a small set of readily available microbial species. Expanding beyond this limited biological diversity holds promise to unlock new gastronomic innovation. Here, we explore novel culinary applications of Neurospora intermedia, an edible fungus traditionally used in Java, Indonesia to produce the fermented food oncom. Our work demonstrates that N. intermedia can be readily used in the production of oncom-like meat alternatives with non-traditional substrates, as well as in the production of enzymes for starch-to-sugar conversion. As an example, we harness secreted N. intermedia starch-degrading enzymes to produce an amazake that has a distinct volatile aroma composition compared to traditional amazake produced with Aspergillus oryzae. In addition to providing texture and flavor, N. intermedia can be used to add an orange color to dishes due to the development of brightly colored spores and aerial mycelia. This property, along with its secreted enzymes, was utilized to create a dish for fine-dining restaurant Alchemist in Copenhagen, Denmark. Overall, the novel foods produced in this study were rated favorably in consumer trials, indicating a broad sensory appeal of N. intermedia across different culinary applications and cultural contexts. The protocols and approaches presented in this study represent a new addition to the chef's toolbox that hold promise to expand gastronomic possibilities with fermentation in restaurants and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

Heuristic algorithms for design of integrated monitoring of geologic carbon storage sites

Designs for Risk Evaluation and Management (DREAM) is a tool developed under the National Risk Assessment Partnership (NRAP) to enhance geologic carbon storage safety and efficiency. Using potential leakage scenarios generated externally by the users preferred history-matching approach, DREAM constructs ideal combinations of sensor locations in the right place at the right time to detect as many leaks as possible, detect them as early as possible, and minimize cost. This user-friendly tool, developed in Java, features a window-based GUI for input and a 3D visualization tool for viewing the domain space and optimized monitoring plans. DREAM's latest version accommodates real-world usage by allowing for joint optimization of wellbore point sensor placements and surface geophysics survey geometries, and by using more efficient multi-objective optimization algorithms. We show an example where, these two improvements combined allow us to support containment assurance and go from detecting 80–90 % of the potential CO 2 leakage to +99.7 %, a step-change improvement that can make the deciding difference in whether a site is suitable for geologic carbon storage. Though developed for geologic carbon storage, this tool would be equally applicable in many surface or offshore environmental monitoring projects.

58 GEOSCIENCES↗

Initiation of the Lusi mudflow disaster

The Lusi mudflow is a unique disaster. Mud suddenly erupted in an urban area in Java, Indonesia, in May 2006. Nine years of continuous eruption have displaced 39,700 people and cost over US$2.7 billion in damages and disaster management. Intense debate has focused on whether the eruption was naturally triggered by the Yogyakarta earthquake, which occurred two days prior to the eruption and 260 km away or was the result of gas drilling operations in the nearby Banjar Panji-1 (BJP-1) well. Here we use subsurface gas measurements from the well before and immediately after the Yogyakarta earthquake to demonstrate that an earthquake trigger is unlikely.

58 GEOSCIENCES↗

Perovskite- and Dye-Sensitized Solar-Cell Device Databases Auto-generated Using ChemDataExtractor

The number of scientific publications reporting cutting-edge third-generation photovoltaic devices is increasing rapidly, owing to the pressing need to develop renewable-energy technologies that address the climate-change crisis. Consequently, the field could benefit from a central repository where photovoltaic-performance metrics, such as the power-conversion efficiency (η) are recorded. We present two automatically generated databases that contain photovoltaic properties and device material data for dye-sensitized solar cells (DSCs) and perovskite solar cells (PSCs), totalling 660,881 data entries representing 57,678 photovoltaic devices. The databases were generated by applying the text-mining toolkit ChemDataExtractor on a corpus of 25,720 articles. A multi-faceted evaluation, incorporating manual and automatic methods, was applied to ensure that the data contained therein were of the highest quality, with precision metrics ranging from 73.1% to 95.8%. The DSC database contains 475,045 entries representing 41,680 devices, and the PSC database contains 185,836 entries representing 15,818 devices. The databases are available in MongoDB and JSON formats, which can be queried in Python, R, Java and MATLAB for data-driven photovoltaic materials discovery.

14 SOLAR ENERGY↗

Auto-generated materials database of Curie and Néel temperatures via semi-supervised relationship extraction

article presents an auto-generated database of 39,822 records containing chemical compounds and their associated Curie and Néel magnetic phase transition temperatures. The database was produced using natural language processing and semi-supervised quaternary relationship extraction, applied to a corpus of 68,078 chemistry and physics articles. Evaluation of the database shows an estimated overall precision of 73%. Therein, records processed with the text-mining toolkit, ChemDataExtractor, were assisted by a modified Snowball algorithm, whose original binary relationship extraction capabilities were extended to quaternary relationship extraction. Consequently, its machine learning component can now train with ≤500 seeds, rather than the 4,000 originally used. Data processed with the modified Snowball algorithm affords 82% precision. Database records are available in MongoDB, CSV and JSON formats which can easily be read using Python, R, Java and MatLab. As a result, this makes the database easy to query for tackling big-data materials science initiatives and provides a basis for magnetic materials discovery.

36 MATERIALS SCIENCE↗

Operational experience with the new CMS DAQ-Expert

The data acquisition (DAQ) system of the Compact Muon Solenoid (CMS) at CERN reads out the detector at the level-1 trigger accept rate of 100 kHz, assembles events with a bandwidth of 200 GB/s, provides these events to the high level-trigger running on a farm of about 30k cores and records the accepted events. Comprising custom-built and cutting edge commercial hardware and several 1000 instances of software applications, the DAQ system is complex in itself and failures cannot be completely excluded. Moreover, problems in the readout of the detectors,in the first level trigger system or in the high level trigger may provoke anomalous behaviour of the DAQ systemwhich sometimes cannot easily be differentiated from a problem in the DAQ system itself. In order to achieve high data taking efficiency with operators from the entire collaboration and without relying too heavily on the on-call experts, an expert system, the DAQ-Expert, has been developed that can pinpoint the source of most failures and give advice to the shift crew on how to recover in the quickest way. The DAQ-Expert constantly analyzes monitoring data from the DAQ system and the high level trigger by making use of logic modules written in Java that encapsulate the expert knowledge about potential operational problems. The results of the reasoning are presented to the operator in a web-based dashboard, may trigger sound alerts in the control room and are archived for post-mortem analysis - presented in a web-based timeline browser. We present the design of the DAQ-Expert and report on the operational experience since 2017, when it was first put into production.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Performance of the Belle II Conditions Database

The Belle II experiment at KEK observed its first collisions in the summer of 2018. Processing the large amounts of data that will be produced requires conditions data to be readily available to systems worldwide in a fast and efficient manner that is straightforward for both the user and maintainer. This was accomplished by relying on industry-standard tools and methods: the conditions database is built as an HTTP REST service using tools such as Swagger for the API interface development, Payara for the Java EE application server, and Squid for the caching proxy. This article presents the design of the Belle II conditions database production environment as well as details about the capabilities and performance during both Monte Carlo campaigns and data reprocessing.

Wood, Lynn S.↗

New approach of determinations of earthquake moment magnitude using near earthquake source duration and maximum displacement amplitude of high frequency energy radiation

The new approach method to determine the magnitude by using amplitude displacement relationship (A), epicenter distance ({Delta}) and duration of high frequency radiation (t) has been investigated for Tasikmalaya earthquake, on September 2, 2009, and their aftershock. Moment magnitude scale commonly used seismic surface waves with the teleseismic range of the period is greater than 200 seconds or a moment magnitude of the P wave using teleseismic seismogram data and the range of 10-60 seconds. In this research techniques have been developed a new approach to determine the displacement amplitude and duration of high frequency radiation using near earthquake. Determination of the duration of high frequency using half of period of P waves on the seismograms displacement. This is due tothe very complex rupture process in the near earthquake. Seismic data of the P wave mixing with other wave (S wave) before the duration runs out, so it is difficult to separate or determined the final of P-wave. Application of the 68 earthquakes recorded by station of CISI, Garut West Java, the following relationship is obtained: Mw = 0.78 log (A) + 0.83 log {Delta}+ 0.69 log (t) + 6.46 with: A (m), d (km) and t (second). Moment magnitude of this new approach is quite reliable, time processing faster so useful for early warning.

58 GEOSCIENCES↗

AtomicJ: An open source software for analysis of force curves

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

42 ENGINEERING↗

Preliminary results of teleseismic double-difference relocation of earthquakes around Indonesian archipelago region

Indonesian archipelago region is located in active tectonic setting and high seismicity zone. During the last decade, Indonesian was experienced with destructive major earthquakes causing damage and victims. The information of precise earthquake location parameters are very important in partular for earthquake early warning to the society and for advance seismic studies. In this study, we attempted to improve hypocenter location compiled by BMKG for time periods of April, 2009 up to June, 2014 for about 22,000 earthquake events around Indonesian region. For the firts time, we applied teleseismic double-difference relocation algorithm (teletomoDD) to improve hypocenter region in Indonesia region combining regional and teleseismic stations. Hypocenter relocation was performed utilizing local, regional, and teleseismic P-wave arrival time data. Our relocation result show that travel-time RMS errors were greatly reduced compared to the BMKG catalog. Seismicity at shallower depth (less than 50 km) shows significantly improvement especially in depth, and refined shallow geological structures, e.g. trench and major strike slip faults. Clustered seismicity is also detected beneath volcanic region, and probably related volcano activities and also major faults nearby. In the Sunda arc region, seismicity at shallower depth centered at two major distributions parallel to the trench strike direction, i.e. around fore-arc and in mainland that related to major fault, e.g. the Sumatran fault, and volcanic fronts. Below Central Java region, relocated hypocenter result showed double seismic zone pattern. A seismic gap is detected around the Sunda-Banda transition zone where transition between oceanic subduction to continental crust collision of Australian plate occurs. In Eastern Indonesia region, shallow earthquakes are observed related to major strike slip faults, e.g. Sorong and Palu-Koro fault, volcanism, and shallow part of subduction and collision zones. We also compare our result in the Sunda Arc region with slab1.0 model and our relocated seismicity shows good agreement with the previous slab geometry. Horizontal position shift of relocated events are mostly perpendicular to the trench directions.

58 GEOSCIENCES↗

Modeling of two-storey precast school building using Ruaumoko 2D program

The long-distant earthquake loading from Sumatra and Java Island had caused some slight damages to precast and reinforced concrete buildings in West Malaysia such as cracks on wall panels, columns and beams. Subsequently, the safety of existing precast concrete building is needed to be analyzed because these buildings were designed using BS 8110 which did not include the seismic loading in the design. Thus, this paper emphasizes on the seismic performance and dynamic behavior of precast school building constructed in Malaysia under three selected past earthquakes excitations ; El Centro 1940 North-South, El Centro East-West components and San Fernando 1971 using RUAUMOKO 2D program. This program is fully utilized by using prototype precast school model and dynamic non-linear time history analysis. From the results, it can be concluded that two-storey precast school building has experienced severe damage and partial collapse especially at beam-column joint under San Fernando and El Centro North-South Earthquake as its exceeds the allowable inter-storey drift and displacement as specified in Eurocode 8. The San Fernando earthquake has produced a massive destruction to the precast building under viscous damping, ξ = 5% and this building has generated maximum building displacement of 435mm, maximum building drift of 0.68% and maximum bending moment at 8458kNm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Extension of Alvis compiler front-end

Alvis is a formal modelling language that enables possibility of verification of distributed concurrent systems. An Alvis model semantics finds expression in an LTS graph (labelled transition system). Execution of any language statement is expressed as a transition between formally defined states of such a model. An LTS graph is generated using a middle-stage Haskell representation of an Alvis model. Moreover, Haskell is used as a part of the Alvis language and is used to define parameters’ types and operations on them. Thanks to the compiler’s modular construction many aspects of compilation of an Alvis model may be modified. Providing new plugins for Alvis Compiler that support languages like Java or C makes possible using these languages as a part of Alvis instead of Haskell. The paper presents the compiler internal model and describes how the default specification language can be altered by new plugins.

97 MATHEMATICS AND COMPUTING↗

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

UNF-ST&DARDS Unified Database and the Automatic Document Generator

The U.S. Department of Energy, Office of Nuclear Energy is sponsoring development of a database to store information related to spent nuclear fuel (SNF) in support of its Spent Fuel and Waste Disposition efforts. This database, referred to as the Unified Database (UDB), is part of a larger engineering analysis tool, the Used Nuclear Fuel Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS). The UDB provides a comprehensive, controlled source of SNF information, including dry cask attributes, assembly data, economic attributes, transportation infrastructure attributes, potential future facility attributes, and federal government radioactive waste attributes. There are a number of existing and envisioned data reports that can be expected to use data stored within the UDB; however, previously, there was not a streamlined method to couple the database to such data reports. Therefore, to streamline the creation of these reports, two methods were developed to generate documents from information in the database automatically. The first method used Java and LaTeX for automatically generating the report, and the second method used the Python programming language along with Sphinx, a Python documentation generator. There are some advantages and disadvantages to both approaches, but both methods produced equally high-quality, automatically generated reports that were directly coupled to the database. Finally, this study describes data currently available in the UDB; explains the two different methods for automatically generating reports from these data; and shows examples of inline text, figures, and tables automatically generated using both approaches.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Used Nuclear Fuel Management Using the Next Generation System Analysis Model

The U.S. Department of Energy (DOE) is leading the National effort to manage the back end of the nuclear fuel cycle, encompassing the safe transportation, storage/staging, and/or eventual disposal of used nuclear fuel (UNF) and high-level radioactive waste. The Next Generation System Analysis Model (NGSAM) is DOE’s discrete-event, agent-based simulation tool designed to model the full life cycle of UNF from reactor discharge to final disposal. NGSAM supports the DOE Office of Spent Fuel and High-Level Waste Disposition by enabling a detailed, scenario-based analysis of logistics, infrastructure, and shipping strategies. NGSAM replaces legacy models with a modern, flexible platform built on Repast Simphony and enhanced by the Process Analysis Tool. NGSAM simulates the movement and interaction of individual fuel assemblies with system components such as canisters, casks, railcars, and facilities. The model integrates with the Java Transportation Operations Model to plan and execute transportation scenarios, supporting both constrained and unconstrained resource allocation. Key features include customizable allocation and acceptance algorithms, detailed facility-level operations, and a Quick Edit tool for rapid scenario adjustments. NGSAM supports multimodal transportation modeling (e.g. rail, road, barge) and provides comprehensive cost, schedule, and infrastructure data. NGSAM utilizes data from sources such as DOE’s STANDARDS UNF database and DOE’s Stakeholder Tool for Assessing Radioactive Transportation, while also allowing user-defined inputs for scenario customization. NGSAM enables stakeholders to evaluate complex UNF management strategies, assess system performance under varying assumptions, and inform decision making for future infrastructure investments. Its modular architecture and integration with other Integrated Waste Management System tools make it a critical asset for planning the safe and efficient disposition of the Nation’s growing UNF inventory.

Craig, Brian [Argonne National Laboratory (ANL)]↗

Serpent and MCNP Calculations of the Energy Deposition in the Transformational Challenge Reactor

This paper focuses on the calculation of the energy deposition in the Transformational Challenge Reactor by two major Monte Carlo codes: Serpent and MCNP. The first software computation relies on Kinetic Energy Released per unit Mass (KERMA) factors while the second one relies on Q-values. The results from these two independent computation methodologies are in very good agreement; however, Serpent runs much faster than MCNP (for the same computational model) and allows for a detailed energy deposition distribution from a 1-mm-side square mesh with a relative statistical error between 0.5% and 1%. This detailed energy deposition is suitable for multiphysics analyses aimed at design optimizations. In order to calculate the energy deposition, Serpent needs enhanced ACE files (distributed by the software developers). Unlike other Monte Carlo software that uses inputs based on Python or Java languages, the Serpent input syntax is very similar to that of MCNP; a Python script can convert a MCNP input to a Serpent input in seconds. For simulations not requiring the calculation of the energy deposition, Serpent can also read nuclear data from MCNP ACE files, which eventually improves the comparison of the results of the two codes.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Enhancing Monte Carlo Workflows for Nuclear Reactor Analysis with Metamodel-Driven Modeling

Monte Carlo codes are essential components of many reactor physics simulation workflows as high-fidelity continuous-energy neutron transport solvers. Among Monte Carlo radiation transport codes, MCNP is particularly notable due to its diverse simulation capabilities, large user base, and long validation history. Despite being a powerful simulation tool, MCNP provides limited capabilities to allow automated execution, model transformation, or support for user-defined logic and abstractions that limit its compatibility with modern workflows. Here, to better integrate MCNP into a modern scientific workflow, we have developed an intuitive yet full-featured MCNP Application Program Interface (API) in Python, named MCNPy, which provides a specialized set of classes for MCNP input development. Moreover, to guarantee that our reading, writing, and modeling capabilities remain self-consistent (and to render the huge scope of the MCNP API manageable), we have adopted a strategy of model-driven software development in which a generalized model of the MCNP input format has been created. From this generalized model, or “metamodel,” problem-specific implementations such as an engine for input validation or a codebase for programmatic operations may be automatically generated. Since MCNPy primarily acts as a Python front-end to the underlying Java API that directly interfaces with the metamodel, it is intrinsically linked to the metamodel and thus remains maintainable. With MCNPy, users can programmatically read, write, and modify any syntactically valid MCNP input file regardless of its origin. These capabilities allow users to automate complicated tasks like design optimization and model translation for nuclear systems. As examples, this work demonstrates the use of MCNPy to find the critical radius of a plutonium sphere and to translate a 9000+ line MCNP input file into a corresponding OpenMC model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

CostMAP: an open-source software package for developing cost surfaces using a multi-scale search kernel

Cost surfaces are a crucial aspect of route optimization and least cost path (LCP) calculations and are used in awide range of disciplines including computer science, landscape ecology, and energy-infrastructure modeling. Linear features introduce akey weakness to traditional routing calculations along cost surfaces because they cannot identify whether moving from acell to its adjacent neighbors constitutes crossing alinear barrier (increased cost) or following acorridor (reduced cost). Following and avoiding linear features can drastically change predicted routes. We introduce an approach to address this adjacency issue using asearch kernel that determines these critical barriers and corridors. We have built this method into anew Java-based open-source software package– CostMAP (cost surface multi-layer aggregation program)– which calculates cost surfaces and cost networks using the search kernel. CostMAP allows users to input multiple GIS data layers and to set weights and rules for developing aweighted-cost network. We compare CostMAP performance with traditional cost surface approaches and show significant performance gains– both following corridors and avoiding barriers– by modeling the movement of alarge terrestrial animal– the Baird’s Tapir (Tapirus bairdii)– in amovement ecology framework and by modeling pipeline routing for carbon capture and storage (CCS).

58 GEOSCIENCES↗