Accurate sodium bisulfite sequencing in plants.

DNA cytosine methylation is a conserved epigenetic modification frequently correlating with transcriptional silencing in a wide variety of eukaryotic organisms. Sodium bisulfite treatment of DNA converts unmethylated cytosine to uracil, while 5-methylated cytosine is protected. We describe techniques that ensure reliable sequencing data following sodium bisulfite conversion and to avoid common pitfalls such as amplification of unconverted DNA and inclusion of sibling clones.

HTGR fuel element depletion benchmark: Stage three results

Recently, a new numerical benchmark exercise for High Temperature Gas Cooled Reactor (HTGR) fuel depletion was defined. The purpose of this benchmark is to provide a comparison basis for different codes and methods applied to the burnup analysis of HTGRs. The benchmark specifications include three different models: (1) an infinite lattice of tristructural isotropic (TRISO) fuel particles, (2) an infinite lattice of fuel pebbles, and (3) a prismatic fuel including fuel and coolant channels. In this paper, we present the results of the third stage of the benchmark obtained with MCNP based depletion code BGCore and deterministic lattice code HELIOS 1.9. The depletion calculations were performed for three-dimensional model of prismatic fuel with explicitly described TRISO particles as well as for two-dimensional model, in which double heterogeneity of the TRISO particles was eliminated using reactivity equivalent physical transformation (RPT). Generally, good agreement in the results of the calculations obtained using different methods and codes was observed.

Comparison among MCNP-based depletion codes applied to burnup calculations of pebble-bed HTR lattices

The double-heterogeneity characterising pebble-bed high temperature reactors (HTRs) makes Monte Carlo based calculation tools the most suitable for detailed core analyses. These codes can be successfully used to predict the isotopic evolution during irradiation of the fuel of this kind of cores. At the moment, there are many computational systems based on MCNP that are available for performing depletion calculation. All these systems use MCNP to supply problem dependent fluxes and/or microscopic cross sections to the depletion module. This latter then calculates the isotopic evolution of the fuel resolving Bateman's equations. In this paper, a comparative analysis of three different MCNP-based depletion codes is performed: Montburns2.0, MCNPX2.6.0 and BGCore. Monteburns code can be considered as the reference code for HTR calculations, since it has been already verified during HTR-N and HTR-N1 EU project. All calculations have been performed on a reference model representing an infinite lattice of thorium-plutonium fuelled pebbles. The evolution of k-inf as a function of burnup has been compared, as well as the inventory of the important actinides. The k-inf comparison among the codes shows a good agreement during the entire burnup history with the maximum difference lower than 1%. The actinide inventory prediction agrees well. However significant discrepancy in Am and Cm concentrations calculated by MCNPX as compared to those of Monteburns and BGCore has been observed. This is mainly due to different Am-241 (n,γ) branching ratio utilized by the codes. The important advantage of BGCore is its significantly lower execution time required to perform considered depletion calculations. While providing reasonably accurate results BGCore runs depletion problem about two times faster than Monteburns and two to five times faster than MCNPX. © 2009 Elsevier B.V. All rights reserved.

HTGR fuel element depletion benchmark: Stage one results

In this paper, we reported the results of the first stage of HTGR fuel element depletion benchmark obtained with BGCore and HELIOS depletion codes. The results of the k-inf are generally in good agreement. However, significant deviation in concentrations of several nuclides between MCNP based and HELIOS codes was observed.

Implementation of multi-group cross-section methodology in BGCore MC-depletion code

BGCore is a software package for comprehensive computer simulation of nuclear reactor systems and their fuel cycles. The BGCore interfaces Monte Carlo particles transport code MCNP4C with a SARAF module - an independently developed code for calculating in-core fuel composition and spent fuel emissions following discharge. In BGCore system, depletion coupling methodology is based on the multi-group approach that significantly reduces computation time and allows tracking of large number of nuclides during calculations. In this study, burnup calculation capabilities of BGCore system were validated against well established and verified, computer codes for thermal and fast spectrum lattices. Very good agreement in k eigenvalue and nuclide densities prediction was observed for all cases under consideration. In addition, decay heat prediction capabilities of the BGCore system were benchmarked against the most recent edition of ANS Standard methodology for UO2 fuel decay power prediction in LWRs. It was found that the difference between ANS standard data and that predicted by the BGCore does not exceed 5%.

Efficient generation of one-group cross sections for coupled Monte Carlo depletion calculations

Coupled Monte Carlo depletion systems provide a versatile and an accurate tool for analyzing advanced thermal and fast reactor designs for a variety of fuel compositions and geometries. The main drawback of Monte Carlo-based systems is a long calculation time imposing significant restrictions on the complexity and amount of design-oriented calculations. This paper presents an alternative approach to interfacing the Monte Carlo and depletion modules aimed at addressing this problem. The main idea is to calculate the one-group cross sections for all relevant isotopes required by the depletion module in a separate module external to Monte Carlo calculations. Thus, the Monte Carlo module will produce the criticality and neutron spectrum only, without tallying of the individual isotope reaction rates. The onegroup cross section for all isotopes will be generated in a separate module by collapsing a universal multigroup (MG) cross-section library using the Monte Carlo calculated flux. Here, the term "universal" means that a single MG cross-section set will be applicable for all reactor systems and is independent of reactor characteristics such as a neutron spectrum; fuel composition; and fuel cell, assembly, and core geometries. This approach was originally proposed by Haeck et al. and implemented in the ALEPH code. Implementation of the proposed approach to Monte Carlo burnup interfacing was carried out through the BGCORE system. One-group cross sections generated by the BGCORE system were compared with those tallied directly by the MCNP code. Analysis of this comparison was carried out and led to the conclusion that in order to achieve the accuracy required for a reliable core and fuel cycle analysis, accounting for the background cross section (σ0) in the unresolved resonance energy region is essential. An extension of the one-group cross-section generation model was implemented and tested by tabulating and interpolating by a simplified σ0 model. A significant improvement of the one-group cross-section accuracy was demonstrated.

Optimization of efficiency-loss figure of merit in carrier-depletion silicon Mach-Zehnder optical modulator.

In this paper we study the optimization of interleaved Mach-Zehnder silicon carrier depletion electro-optic modulator. Following the simulation results we demonstrate a phase shifter with the lowest figure of merit (modulation efficiency multiplied by the loss per unit length) 6.7 V-dB. This result was achieved by reducing the junction width to 200 nm along the phase-shifter and optimizing the doping levels of the PN junction for operation in nearly fully depleted mode. The demonstrated low FOM is the result of both low V(π)L of ~0.78 Vcm (at reverse bias of 1V), and low free carrier loss (~6.6 dB/cm for zero bias). Our simulation results indicate that additional improvement in performance may be achieved by further reducing the junction width followed by increasing the doping levels.