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At least 1,513 records · Page 84

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Abstract Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis , here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗

International database of reference gamma spectra for nuclear safeguards applications

Nuclear safeguards missions use gamma spectroscopy as a non-destructive measurement technique for examining nuclear materials. Despite advances in the development of detection equipment as well as software codes, one of the concerns is the lack of well-documented spectra needed to test and validate isotopic analysis codes for their applicability. To address this need, this work introduces IDB, an international database of the reference gamma spectra of uranium, plutonium and mixed oxide nuclear material samples. IDB provides access to well-characterized sets of gamma spectra described by rich metadata, including information on the sample, measurement configuration and detector specifications. These spectra are accessible in different formats, also compatible with analysis code standards, thus promoting their sustainability and maintenance.

None, Dipti [International Atomic Energy Agency (I↗

Demonstration of low-mode shape control in indirect-drive double shell implosions at the NIF

Double shell inertial confinement fusion is a concept for achieving robust thermonuclear burn that uses dense metal shells to compress deuterium-tritium (DT) fuel to fusion conditions. Double shell implosions are typically indirectly driven and involve a target that consists of a low-Z ablator, a foam layer, and a high-Z pusher surrounding the DT fuel. The goal of the campaign is to achieve a volumetric burn as radiation losses from the DT fuel are trapped by the opaque high-Z shell. The overall performance of double shell implosions relies on the efficient collisional transfer of kinetic energy between layers. The efficiency of this transfer (and therefore the overall performance of a given implosion) is degraded by the presence of low-mode asymmetries. P2 asymmetries are often observed in spatially resolved 2D radiographs of nominal double shell implosions. This work discusses three such experiments: one with an oblate P2 asymmetry, one with a prolate P2 asymmetry, and one with an approximate spherical symmetry. After performing a shape analysis of the oblate and prolate implosions to quantify asymmetries, these experimental results were compared with the results of hydrodynamic simulations for the two experiments. Differences between the experiment and simulation were then used to design an approximately spherical implosion by altering the incident laser cone fraction. Radiographs from the experiment that implemented the modified cone fraction show evidence of an implosion that is approximately spherical until bang time. This design is intended to serve as a point design for future studies that will seek to optimize various aspects of the double shell target.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

X-ray-line coincidence photopumping in a potassium-chlorine mixed plasma

Exploiting the multiple long pulse capability and suite of x-ray diagnostics of the Orion laser, we have set out to explore line coincidence photopuming—the enhancement in population of an atomic level brought on by resonant absorption of x rays from a different emitting ion. Unlike previous work, the two ions are in the same plasma and so the experiment is an x-ray analog of the well-known Bowen resonance fluorescence mechanism that operates in astrophysical situations in the optical region. Herein, our measurements have shown enhanced fluorescence in a chlorine plasma, attributable to line coincident photopumping from co-mixed potassium ions. To detect this relatively low signal-to-noise phenomenon, the data from multiple shots are combined, and the statistical method of bootstrapping is used to assign a confidence value to the measured enhancement, resulting in an estimate of the enhancement of 39 ± 18 16 % compared to the null case, where no pumping occurs. The experimental results have been compared to coupled radiation-transport and radiation hydrodynamics simulations using the CRETIN code together with the NYM radiation hydrodynamics model and agreement has been found, with the simulations also predicting modest enhancement.

74 ATOMIC AND MOLECULAR PHYSICS↗

Improving performance of inverse Compton sources through laser chirping

We present a new method for computation of radiation spectra in the non-linear regime of operation of inverse Compton sources characterized by high laser intensities. The resulting simulations agree well with the experiments. Increasing the laser intensity changes the longitudinal velocity of the electrons during their collision, leading to considerable non-linear broadening in the scattered radiation spectra. The effects of such ponderomotive broadening are so deleterious that most inverse Compton sources either remain at low laser intensities or pay a steep price to operate at a small fraction of the physically possible peak spectral output. This ponderomotive broadening can be reduced by a suitable frequency modulation (also referred to as "chirping", which is not necessarily linear) of the incident laser pulse, thereby drastically increasing the peak spectral density. This frequency modulation, included in the new code as an optional functionality, is used in simulations to motivate the experimental implementation of this transformative technique.

Terzić, B.↗

An IIPG-based finite element framework in MOOSE for modeling fiber reinforced composite failure governed by extrinsic cohesive laws

Fiber reinforced composites (FRC) are widely applied to many important engineering structures such as silicon carbide ceramic matrix composite (SiC CMC) of nuclear fuel claddings. Many material and structure failures are initiated at the interface between two distinctive materials, such as the debonding of interfaces of matrix/fiber of composites or bulk matrix/inclusion in metals at micro-scales. Accurate and robust modeling of these interface failures is critical to the development of novel material and structure with improved functionality. This paper presents a discontinuous Galerkin (DG) finite element method based on the Incomplete Interior Penalty scheme and its implementation in MOOSE for modeling material interface behaviors. The proposed method naturally accommodates important extrinsic cohesive zone material models and is capable of modeling the failures of material interfaces across which material properties are highly distinctive. We demonstrate a good performance of the proposed method using single fiber and multiple fiber debonding problems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

User Guidelines and Best Practices for CASL VUQ Analysis Using Dakota.

Sandia's Dakota software (available at http://dakota.sandia.gov) supports science and engineering transformation through advanced exploration of simulations. Specifically, it manages and analyzes ensembles of simulations to provide broader and deeper perspective for analysts and decision makers. This enables them to enhance understanding of risk, improve products, and assess simulation credibility. This manual offers Consortium for Advanced Simulation of Light Water Reactors (LWRs) (CASL) partners a guide to conducting Dakota-based VUQ studies for CASL problems. It motivates various classes of Dakota methods and includes examples of their use on representative application problems. On reading, a CASL analyst should understand why and how to apply Dakota to a simulation problem.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

RELAP-7 Closure Correlations

The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). The code is based on the INL’s modern scientific software development framework, MOOSE (Multi-Physics Object Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5’s and TRACE’s capabilities and extends their analysis capabilities for all reactor system simulation scenarios. The RELAP-7 code utilizes the well-posed 7-equation two-phase flow model for compressible two-phase flow. Closure models used in the TRACE code has been reviewed and selected to reflect the progress made during the past decades and provide a basis for the colure correlations implemented in the RELAP-7 code. This document provides a summary on the closure correlations that are currently implemented in the RELAP-7 code. The closure correlations include sub-grid models that describe interactions between the fluids and the flow channel, and interactions between the two phases.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Report on an Assessment of the Application of EPP Results from the Strain Limit Evaluation Procedure to the Prediction of Cyclic Life Based on the SMT Methodology

The goal of the proposed integrated Elastic Perfectly-Plastic (EPP) and Simplified Model Test (SMT) methodology is to incorporate an SMT data based approach for creep-fatigue damage evaluation into the EPP methodology to avoid the separate evaluation of creep and fatigue damage and eliminate the requirement for stress classification in current methods; thus greatly simplifying evaluation of elevated temperature cyclic service. This methodology should minimize over-conservatism while properly accounting for localized defects and stress risers. To support the implementation of the proposed methodology and to verify the applicability of the code rules, analytical studies and evaluation of thermomechanical test results continued in FY17. This report presents the results of those studies. An EPP strain limits methodology assessment was based on recent two-bar thermal ratcheting test results on 316H stainless steel in the temperature range of 405 to 7050C. Strain range predictions from the EPP evaluation of the two-bar tests were also evaluated and compared with the experimental results. The role of sustained primary loading on cyclic life was assessed using the results of pressurized SMT data from tests on Alloy 617 at 9500C. A viscoplastic material model was used in an analytic simulation of two-bar tests to compare with EPP strain limits assessments using isochronous stress strain curves that are consistent with the viscoplastic material model. A finite element model of a prior 304H stainless steel Oak Ridge National Laboratory (ORNL) nozzle-to-sphere test was developed and used for an EPP strain limits and creep-fatigue code case damage evaluations. A theoretical treatment of a recurring issue with convergence criteria for plastic shakedown illustrated the role of computer machine precision in EPP calculations.

36 MATERIALS SCIENCE↗

DOSECALCX, A Bremsstrahlung Radiation Dose Code for Electron Beam Targets

The Dual-Axis Radiographic Hydrodynamic Test (DARHT) Facility is a two-axis, linear induction electron accelerator designed to produce Bremsstrahlung radiation for imaging hydrodynamic physics within rapidly compressed targets. The radiation dose code DOSECALC, used to obtain approximate results for experiments, was modified to include new materials and renamed DOSECALCX. Calculations were compared with results from the MCNP code. Photon spectra was found to agree visibly and quantitatively while angular dose data was only comparable within an order of magnitude.

43 PARTICLE ACCELERATORS↗

EMPHASIS™/Nevada Unstructured FEM Implementaiton Version 2.1.3. Description, verification, and validation

EMPHASIS™/NEVADA is the SIERRA/NEVADA toolkit implementation of portions of the EMPHASIS TM code suite. The purpose of the toolkit implementation is to facilitate coupling to other physics drivers such as radiation transport as well as to better manage code design, implementation, complexity, and important verification and validation processes. This document describes the theory and implementation of the unstructured finite- element method solver, associated algorithms, and selected verification and validation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

HPC for Optimizing Process Parameters to Control Material Evolution in Seamless Induction Hardening of Wind Turbine Main Shaft Bearings

Work proposed in this project focused on understanding the effect of martensitic transformation in the steel on the potential for cracking during seamless induction hardening (SIH) as a function of process conditions to allow the process to optimally scale up. Large-scale, three-dimensional phase-field simulations of martensitic transformation were performed using MEUMAPPS-SS (Microstructure Evolution Using Massively Parallel Phase-field Simulations – Solid State) code developed at Oak Ridge National Laboratory. The simulations were guided by location-specific thermal history generated by experimental measurements of time-temperature history generated at The Timken Company. The simulations were able to capture the morphological evolution of the martensite variants in an Fe-1.0C-1.5Cr steel based on the Nishiyama-Wasserman (NW) orientation relationship. The simulations were also able to quantify the stress-state at the interface between impinging martensite variants. The simulations indicated that the magnitude of the various stress and strain components were dependent on the sizes of the impinging plates with a reduction in these quantities with reduced plate size in agreement with experimental findings. The results obtained from the simulations will be used to guide the optimization of the alloy thermal conditions to eliminate quench cracking during SIH of bearing steels.

99 GENERAL AND MISCELLANEOUS↗

HPC for optimizing process parameters to control material evolution in seamless induction hardening of wind turbine main shaft bearings

Work proposed in this project focused on understanding the effect of martensitic transformation in the steel on the potential for cracking during seamless induction hardening (SIH) as a function of process conditions to allow the process to optimally scale up. Large-scale, three-dimensional phase-field simulations of martensitic transformation were performed using MEUMAPPS-SS (Microstructure Evolution Using Massively Parallel Phase-field Simulations – Solid State) code developed at Oak Ridge National Laboratory. The simulations were guided by location-specific thermal history generated by experimental measurements of time-temperature history generated at The Timken Company. The simulations were able to capture the morphological evolution of the martensite variants in an Fe-1.0C-1.5Cr steel based on the Nishiyama-Wasserman (NW) orientation relationship. The simulations were also able to quantify the stress-state at the interface between impinging martensite variants. The simulations indicated that the magnitude of the various stress and strain components were dependent on the sizes of the impinging plates with a reduction in these quantities with reduced plate size in agreement with experimental findings. The results obtained from the simulations will be used to guide the optimization of the alloy thermal conditions to eliminate quench cracking during SIH of bearing steels.

17 WIND ENERGY↗

Massively parallel modeling and inversion of electrical resistivity tomography data using PFLOTRAN

Abstract. Electrical resistivity tomography (ERT) is a broadly accepted geophysical method for subsurface investigations. Interpretation of field ERT data usually requires the application of computationally intensive forward modeling and inversion algorithms. For large-scale ERT data, the efficiency of these algorithms depends on the robustness, accuracy, and scalability on high-performance computing resources. In this regard, we present a robust and highly scalable implementation of forward modeling and inversion algorithms for ERT data. The implementation is publicly available and developed within the framework of PFLOTRAN, an open-source, state-of-the-art massively parallel subsurface flow and transport simulation code. The forward modeling is based on a finite-volume discretization of the governing differential equations, and the inversion uses a Gauss–Newton optimization scheme. To evaluate the accuracy of the forward modeling, two examples are first presented by considering layered (1D) and 3D earth conductivity models. The computed numerical results show good agreement with the analytical solutions for the layered earth model and results from a well-established code for the 3D model. Inversion of ERT data, simulated for a 3D model, is then performed to demonstrate the inversion capability by recovering the conductivity of the model. To demonstrate the parallel performance of PFLOTRAN's ERT process model and inversion capabilities, large-scale scalability tests are performed by using up to 131 072 processes on a leadership class supercomputer. These tests are performed for the two most computationally intensive steps of the ERT inversion: forward modeling and Jacobian computation. For the forward modeling, we consider models with up to 122 ×106 degrees of freedom (DOFs) in the resulting system of linear equations and demonstrate that the code exhibits almost linear scalability on up to 10 000 DOFs per process. On the other hand, the code shows superlinear scalability for the Jacobian computation, mainly because all computations are fairly evenly distributed over each process with no parallel communication.

58 GEOSCIENCES↗

Monte Carlo/CFD Coupling for Accurate Modeling of the Delayed Neutron Precursors and Compressibility Effects in Molten Salt Reactors

Multiphysics reactor analysis has become one of the leading activities of most nuclear engineering research groups. Coupled neutronics and thermal/hydraulics (T/H) simulations have traditionally been performed by adopting deterministic transport tools and reactor system T/H codes. The main reason for avoiding higher fidelity numerical methods like continuous-energy Monte Carlo analysis has been the high computational cost of coupled, full-scale simulations. Nowadays, high fidelity multiphysics simulations represent a hot research topic, with several applications involving advanced nuclear systems. Liquid fuel Molten Salt Reactors (MSRs) feature peculiar physical phenomena that are not present in solid fuel reactors. Some of these phenomena are not correctly resolved by legacy reactor physics tools, and require specific treatments. This work focuses in particular on the analysis of the effect of the delayed neutron precursors drift and the impact of liquid fluid thermal expansion and compressibility in postulated criticality excursion transients in fast-spectrum MSRs. A new modeling tool based on a Monte Carlo approach for neutronics (Serpent code) coupled to a Computational Fluid Dynamic (CFD) analysis (OpenFOAM) was developed to obtain accurate modeling and simulation of these phenomena. The development of the Serpent Monte Carlo code [1] at VTT in the past few years has made this code particularly attractive for performing multiphysics studies. The availability of a flexible multiphysics interface, on-the-fly Doppler broadening and density-based collision rejection, and Delta-tracking, proved of paramount importance for the computationally efficient performance of coupled Monte Carlo/CFD calculations [2]. OpenFOAM is a C++ multiphysics toolkit featured by automatic matrix construction and solution capabilities for scalar and vector partial differential equations (PDEs), adopting several possible differencing and interpolation schemes, based on the Finite-Volume method. The ease of implementing the constitutive equations of different physical phenomena makes OpenFOAM particularly suitable for the modeling of complex coupled phenomena. In the past, several research activities proposed the adoption of both Serpent and OpenFOAM for the modeling and simulation of MSRs and the associated fuel cycles. In this work, these tools have been internally coupled for the steady-state and transient analysis of fast-spectrum systems, accounting for the effect of delayed neutron precursors transport and the salt thermal expansion and compressibility.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Neutronic analysis of a PWR-type SMR core using duplex ThO{sub 2}-UO{sub 2} in TRISO fuel particles

Currently, studies on small modular reactors (SMRs) present an important development due to the potential they represent in terms of safety, operational flexibility, economy, and non-energy applications. Furthermore, there is increasing interest in studying the use of thorium as fuel, as an effective way to solve problems such as the shortage of uranium reserves, reduction of nuclear waste and nuclear proliferation. Also, the use of thorium combined with highly enriched uranium TRISO particles has been studied, showing proper performance. In this work, the concept of ThO{sub 2}-UO{sub 2} duplex fuel is used, for the core configuration of a PWR type SMR that uses TRISO fuel, designed to achieve extended fuel cycles. Three distribution cases of ThO{sub 2} and UO{sub 2} in TRISO particles inside the fuel rods are compared. First, particles composed by a homogeneous mixture of ThO{sub 2} and UO{sub 2} are distributed inside of fuel elements. Second, the fuel zone of the fuel elements is divided into two radially, an internal one where the TRISO particles composed of ThO{sub 2} are distributed and the external one where the TRISO particles composed of UO{sub 2} are distributed. The third case is like the previous one, except that the particles that contain UO{sub 2} are distributed in the inner zone and those that contain ThO{sub 2} in the outer zone of the fuel elements. The comparison of the cases is carried out in terms of cycle main isotopes' mass transmutation, power distribution and temperature reactivity coefficients. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Development of Thermal Scattering Law and Cross Sections of Hydrogen in Paraffin Wax

Paraffin wax is frequently used as a neutron moderator and shielding material. The main component of paraffin wax is straight-chain alkanes (n-alkanes). The deposition of paraffin wax is primarily attributed to the crystallization of n-alkanes. It is important to gain a deeper understanding of the mechanisms underlying the behavior of paraffin wax, which would impact the thermal scattering Law (TSL) and cross sections and affect the analysis of neutronic and critical systems. In this work, a classical molecular dynamics (CMD) simulation model was used in LAMMPS to create the TSL and cross sections at room temperature and pressure. To generate the required velocity autocorrelation functions (VACF), previously published data were used to validate the approach and models by comparing them with key model parameters. The phonon density of state (DOS) was calculated using Fourier transformation of the normalized VACF. This DOS was used as the primary input to estimate the TSL (S($a$, $β$)) and cross sections of hydrogen in paraffin wax. The TSL and cross sections of hydrogen were estimated using the Full Law Analysis Scattering System Hub (FLASSH) code. The cross section of hydrogen in paraffin wax is consistent with other hydrocarbon materials such as polyethylene with deviations due to structure in the lowest energy region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Software management for the NO ν A Experiment

The NO$\nu$A software (NO$\nu$ASoft) is written in C++, and built on the Fermilab Computing Division's art framework that uses ROOT analysis software. NO$\nu$ASoft makes use of more than 50 external software packages, is developed by more than 50 developers and is used by more than 100 physicists from over 30 universities and laboratories in 3 continents. The software builds are handled by Fermilab's custom version of Software Release Tools (SRT), a UNIX based software management system for large, collaborative projects that is used by several experiments at Fermilab. The system provides software version control with SVN configured in a client-server mode and is based on the code originally developed by the BaBar collaboration. In this paper, we present efforts towards distributing the NO$\nu$A software via the CernVM File System distributed file system. Here, we will also describe our recent work to use a CMake build system and Jenkins, the open source continuous integration system, for NOASoft.

97 MATHEMATICS AND COMPUTING↗