An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

Saber Jelokhani-Niaraki,Zarrin Minuchehr,Mohammad Reza Nassiri,Mojtaba Tahmoorespur 한국유전체학회 2015 Genomics & informatics Vol.13 No.1

During recent years, there has been exponential growth in biological information. With the emergence of large datasets inbiology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integratedgeographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linearreferencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where userscan define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Ourapplication adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharingamong biology domains, applications, and experts. The application was developed in two steps. In the first step, the genomeannotated data were prepared and stored in a MySQL database. The second step involved the connection of the database toboth ArcGIS and Protégé as the GIS engine and ontology platform, respectively. We have designed this application specificallyto manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerfulcapabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

A NOVEL APPROACH TO FIND OPTIMIZED NEUTRON ENERGY GROUP STRUCTURE IN MOX THERMAL LATTICES USING SWARM INTELLIGENCE

Akbari, M.,Khoshahval, F.,Minuchehr, A.,Zolfaghari, A. Korean Nuclear Society 2013 Nuclear Engineering and Technology Vol.45 No.7

Energy group structure has a significant effect on the results of multigroup transport calculations. It is known that $UO_2-PuO_2$ (MOX) is a recently developed fuel which consumes recycled plutonium. For such fuel which contains various resonant nuclides, the selection of energy group structure is more crucial comparing to the $UO_2$ fuels. In this paper, in order to improve the accuracy of the integral results in MOX thermal lattices calculated by WIMSD-5B code, a swarm intelligence method is employed to optimize the energy group structure of WIMS library. In this process, the NJOY code system is used to generate the 69 group cross sections of WIMS code for the specified energy structure. In addition, the multiplication factor and spectral indices are compared against the results of continuous energy MCNP-4C code for evaluating the energy group structure. Calculations performed in four different types of $H_2O$ moderated $UO_2-PuO_2$ (MOX) lattices show that the optimized energy structure obtains more accurate results in comparison with the WIMS original structure.

A Novel Approach to Find Optimized Neutron Energy Group Structure in MOX Thermal Lattices using Swarm Intelligence

M. AKBARI,F. Khoshahval,A. Minuchehr,A. Zolfaghari 한국원자력학회 2013 Nuclear Engineering and Technology Vol.45 No.7

Energy group structure has a significant effect on the results of multigroup transport calculations. It is known thatUO2–PuO2 (MOX) is a recently developed fuel which consumes recycled plutonium. For such fuel which contains variousresonant nuclides, the selection of energy group structure is more crucial comparing to the UO2 fuels. In this paper, in order toimprove the accuracy of the integral results in MOX thermal lattices calculated by WIMSD-5B code, a swarm intelligencemethod is employed to optimize the energy group structure of WIMS library. In this process, the NJOY code system is used togenerate the 69 group cross sections of WIMS code for the specified energy structure. In addition, the multiplication factor andspectral indices are compared against the results of continuous energy MCNP-4C code for evaluating the energy groupstructure. Calculations performed in four different types of H2O moderated UO2–PuO2 (MOX) lattices show that the optimizedenergy structure obtains more accurate results in comparison with the WIMS original structure.

Reactor core analysis through the SP₃-ACMFD approach. Part I: Static solution

Mirzaee, Morteza Khosravi,Zolfaghari, A.,Minuchehr, A. Korean Nuclear Society 2020 Nuclear Engineering and Technology Vol.52 No.2

The present work proposes a solution to the static Boltzmann transport equation approximated by the simplified P₃ (SP₃) on angular, and the analytic coarse mesh finite difference (ACMFD) for spatial variables. Multi-group SP₃-ACMFD equations in 3D rectangular geometry are solved using the GMRES solution technique. As the core time dependent analysis necessitates the solution of an eigenvalue problem for an initial condition, this work is hence devoted to development and verification of the proposed static SP₃-ACMFD solver. A 3D multi-group static diffusion solver is also developed as a byproduct of this work to assess the improvement achieved using the SP₃ technique. Static results are then compared against transport benchmarks to assess the proximity of SP₃-ACMFD solutions to their full transport peers. Results prove that the approach can be considered as an acceptable interim approximation with outputs superior to the diffusion method, close to the transport results, and with the computational costs less than the full transport approach. The work would be further generalized to time dependent solutions in Part II.

Reactor core analysis through the SP₃-ACMFD approach Part II: Transient solution

Mirzaee, Morteza Khosravi,Zolfaghari, A.,Minuchehr, A. Korean Nuclear Society 2020 Nuclear Engineering and Technology Vol.52 No.2

In this part, an implicit time dependent solution is presented for the Boltzmann transport equation discretized by the analytic coarse mesh finite difference method (ACMFD) over the spatial domain as well as the simplified P₃ (SP₃) for the angular variable. In the first part of this work we proposed a SP₃-ACMFD approach to solve the static eigenvalue equations which provide the initial conditions for temp dependent equations. Having solved the 3D multi-group SP₃-ACMFD static equations, an implicit approach is resorted to ensure stability of time steps. An exponential behavior is assumed in transverse integrated equations to establish a relationship between flux moments and currents. Also, analytic integration is benefited for the time-dependent solution of precursor concentration equations. Finally, a multi-channel one-phase thermal hydraulic model is coupled to the proposed methodology. Transient equations are then solved at each step using the GMRES technique. To show the sufficiency of proposed transient SP₃-ACMFD approximation for a full core analysis, a comparison is made using transport peers as the reference. To further demonstrate superiority, results are compared with a 3D multi-group transient diffusion solver developed as a byproduct of this work. Outcomes confirm that the idea can be considered as an economic interim approach which is superior to the diffusion approximation, and comparable with transport in results.

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

Jelokhani-Niaraki, Saber,Tahmoorespur, Mojtaba,Minuchehr, Zarrin,Nassiri, Mohammad Reza Korea Genome Organization 2015 Genomics & informatics Vol.13 No.1

During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and $Prot{\acute{e}}g{\acute{e}}$ as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.

Electromagnetism Mechanism for Enhancing the Refueling Cycle Length of a WWER-1000

Navid Poursalehi,Mostafa Nejati-Zadeh,Abdolhamid Minuchehr 한국원자력학회 2017 Nuclear Engineering and Technology Vol.49 No.1

Increasing the operation cycle length can be an important goal in the fuel reload design of a nuclear reactor core. In this research paper, a new optimization approach, electromagnetism mechanism (EM), is applied to the fuel arrangement design of the Bushehr WWER- 1000 core. For this purpose, a neutronic solver has been developed for calculating the required parameters during the reload cycle of the reactor. In this package, two modules have been linked, including PARCS v2.7 and WIMS-5B codes, integrated in a solver for using in the fuel arrangement optimization operation. The first results of the prepared package, along with the cycle for the original pattern of Bushehr WWER-1000, are compared and verified according to the Final Safety Analysis Report and then the results of exploited EM linked with Purdue Advanced Reactor Core Simulator (PARCS) and Winfrith Improved Multigroup Scheme (WIMS) codes are reported for the loading pattern optimization. Totally, the numerical results of our loading pattern optimization indicate the power of the EM for this problem and also show the effective improvement of desired parameters for the gained semi-optimized core pattern in comparison to the designer scheme.