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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A swapped genetic code prevents viral infections and gene transfer

Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus, potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature. Furthermore, our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Modeling Warm Dense Matter Experiments using the 3D ALE-AMR Code and the Move Toward Exascale Computing

The Neutralized Drift Compression Experiment II (NDCX II) is an induction accelerator planned for initial commissioning in 2012. The final design calls for a 3 MeV, Li+ ion beam, delivered in a bunch with characteristic pulse duration of 1 ns, and transverse dimension of order 1 mm. The NDCX II will be used in studies of material in the warm dense matter (WDM) regime, and ion beam/hydrodynamic coupling experiments relevant to heavy ion based inertial fusion energy. We discuss recent efforts to adapt the 3D ALE-AMR code to model WDM experiments on NDCX II. The code, which combines Arbitrary Lagrangian Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR), has physics models that include ion deposition, radiation hydrodynamics, thermal diffusion, anisotropic material strength with material time history, and advanced models for fragmentation. Experiments at NDCX-II will explore the process of bubble and droplet formation (two-phase expansion) of superheated metal solids using ion beams. Experiments at higher temperatures will explore equation of state and heavy ion fusion beam-to-target energy coupling efficiency. Ion beams allow precise control of local beam energy deposition providing uniform volumetric heating on a timescale shorter than that of hydrodynamic expansion. The ALE-AMR code does not have any export control restrictions and is currently running at the National Energy Research Scientific Computing Center (NERSC) at LBNL and has been shown to scale well to thousands of CPUs. New surface tension models that are being implemented and applied to WDM experiments. Some of the approaches use a diffuse interface surface tension model that is based on the advective Cahn-Hilliard equations, which allows for droplet breakup in divergent velocity fields without the need for imposed perturbations. Other methods require seeding or other methods for droplet breakup. We also briefly discuss the effects of the move to exascale computing and related computational changes on general modeling codes in fusion energy.

42 ENGINEERING↗
DOE OSTI2024

Status of Mercury and Imp: Two Monte Carlo Transport Codes Developed Using Shared Infrastructure at Lawrence Livermore National Laboratory

The Monte Carlo Transport Project at Lawrence Livermore National Laboratory develops two Monte Carlo transport codes used in production by a sizable internal user community. Mercury is a Monte Carlo particle transport code used to model the interaction of neutrons, gammas, and light ions with a material. Imp is an implicit Monte Carlo thermal x-ray photon transport code used to model the interaction of x-ray photons with a material. This paper describes the two codes and highlights recent developments.

Pozulp, Michael↗
DOE OSTI2010

Simulations of one- and two-dimensional complex plasmas using a modular, object-oriented code

In a complex plasma, charged microparticles ('dust') are added to a background of ions, electrons, and neutral particles. This dust fully interacts with the surrounding plasma and self-consistently alters the plasma environment leading to the emergence of new plasma behavior. Numerical tools that complement experimental investigations can provide important insights into the properties of complex plasmas. This paper discusses a newly developed code, named DEMON (dynamic exploration of microparticle clouds optimized numerically), for simulating a complex plasma. The DEMON code models the behavior of the charged particle component of a complex plasma in a uniform plasma background. The key feature of the DEMON code is the use of a modular force model that allows a wide variety of experimental configurations to be studied without varying the core code infrastructure. Examples of the flexibility of this modular approach are presented using examples of one- and two-dimensional complex plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Experimental realization of the analogy of quantum dense coding in classical optics

We report on the experimental realization of the analogy of quantum dense coding in classical optical communication using classical optical correlations. Compared to quantum dense coding that uses pairs of photons entangled in polarization, we find that the proposed design exhibits many advantages. Considering that it is convenient to realize in optical communication, the attainable channel capacity in the experiment for dense coding can reach 2 bits, which is higher than that of the usual quantum coding capacity (1.585 bits). This increased channel capacity has been proven experimentally by transmitting ASCII characters in 12 quaternary digitals instead of the usual 24 bits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Comparison of four large-eddy simulation research codes and effects of model coefficient and inflow turbulence in actuator-line-based wind turbine modeling

Here, large-eddy simulation (LES) of a wind turbine under uniform inflow is performed using an actuator line model (ALM). Predictions from four LES research codes from the wind energy community are compared. The implementation of the ALM in all codes is similar and quantities along the blades are shown to match closely for all codes. The value of the Smagorinsky coefficient in the subgrid-scale turbulence model is shown to have a negligible effect on the time-averaged loads along the blades. Conversely, the breakdown location of the wake is strongly dependent on the Smagorinsky coefficient in uniform laminar inflow. Simulations are also performed using uniform mean velocity inflow with added homogeneous isotropic turbulence from a public database. The time-averaged loads along the blade do not depend on the inflow turbulence. Moreover, and in contrast to the uniform inflow cases, the Smagorinsky coefficient has a negligible effect on the wake profiles. It is concluded that for LES of wind turbines and wind farms using ALM, careful implementation and extensive cross-verification among codes can result in highly reproducible predictions. Moreover, the characteristics of the inflow turbulence appear to be more important than the details of the subgrid-scale modeling employed in the wake, at least for LES of wind energy applications at the resolutions tested in this work.

17 WIND ENERGY↗
DOE OSTI2019

Comparative collisionless alpha particle confinement in stellarator reactors with the XGC gyrokinetic code

Whole volume simulations of stellarators are necessary to address a number of important physics and engineering issues, including turbulent transport prediction and optimising divertor operation. In this work, advances in development of a whole volume stellarator capability for the global gyrokinetic particle-in-cell code XGC are detailed. A 3D interpolation of the equilibrium magnetic eld to the last close flux surface, calculated using the VMEC ideal magnetohydrodynamic equilibrum code, has been implemented. Orbit tracing with the XGC code is verified for the Wendelstein 7-X stellarator by comparison with the BEAMS3D and EUTERPE codes. The XGC stellarator version has then been used to consider collisionless alpha particle con nement in representative quasi-isodynamic and quasi-axisymmetric designs. It has been shown that, at least without further optimisation for energetic particle confinement, the Wendelstein 7-X-like quasi-isodynamic reactor design exhibits better alpha particle confinement.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Verification of the global gyrokinetic stellarator code XGC-S for linear ion temperature gradient driven modes

XGC (X-point Gyrokinetic Code) is a whole-volume, total-f gyrokinetic particle-in-cell code developed for modeling tokamaks. Recently, XGC has been extended to model more general 3D toroidal magnetic configurations, such as stellarators. These improvements have concluded in the XGC-S version. In this paper, XGC-S is benchmarked in the reduced delta-f limit for linear electrostatic ion temperature gradient-driven microinstabilities, which can underlie turbulent transport in stellarators. An initial benchmark of XGC-S in tokamak geometry shows good agreement with the XGC1, ORB5, and global GENE codes. A benchmark between XGC-S and the EUTERPE global gyrokinetic code for stellarators has also been performed, here in the geometry of the optimized stellarator Wendelstein 7-X. Good agreement has been discovered for the mode number spectrum, mode structure, and growth rate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Cross-code comparison of the impact of the fill tube on high yield implosions on the National Ignition Facility

Fill tubes are used to inject deuterium and tritium fuel into inertial confinement fusion capsules fielded on the National Ignition Facility. These fill tubes have been shown to have a detrimental effect on capsule performance, primarily by introducing a low-density pathway into the central fuel region that enables the jetting of ablation material into the hot spot. Due to the complexity of the highly nonlinear flow associated with the fill tube and the challenge of diagnosing the evolution of the fill tube jet late in the implosion experiments, the uncertainty in how this perturbation source evolves is great. In this work, we report on the results of a detailed code comparison performed to understand uncertainties in computational modeling of the impact of fill tubes on implosion performance. The study employed two radiation-hydrodynamics codes, HYDRA and xRAGE, which employ very different meshing strategies and hydrodynamics solvers, as well as two radiation transport methodologies, discrete ordinates and multi-group diffusion. Our results demonstrate generally good agreement between codes through most of the implosion although they indicate sensitivity to opacity averaging methods. Late in the implosion, differences arise in the distribution and amount of contaminant although these differences have a remarkably small impact on the amount of yield reduction due to the fill tube. While these results demonstrate sensitivity in fill tube modeling to algorithmic choices, the observed differences between codes are small relative to known sensitivities due to expected variations in the fill tube geometry. Finally, we have developed a methodology for performing multi-group diffusion simulations that show good agreement with the more accurate discrete ordinates method

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Benchmark between antenna code TOPICA, RAPLICASOL and Petra-M for the ICRH ITER antenna

ITER will be equipped with three plasma heating systems: neutral beam (NB), electron cyclotron (EC), and ion cy-clotron resonance heating (ICRH). The latter consists of two identical ICRH antennas to deliver 20 MW to the plasma (baseline, upgradable to 40 MW). ICRH will play a crucial role in the ignition and sustainment of burning plasmas in ITER. A high fidelity and robust modeling effort to understand the interaction of the IC waves with the scrape-off-layer (SOL) plasma is a very important aspect. Among the main important research topics, we have the assessment of the antenna loading for different plasma scenarios, the role of the lower hybrid resonance in front of the antenna and how to include it in our models, and the RF sheath boundary conditions to evaluate the antenna impurity generation. In this work, we tackle the first of these by reporting on ICRF simulations employing the Petra-M code, which is an electromagnetic simulation tool for modeling RF wave propagation based on MFEM [http://mfem.org] for the ITER ICRH antenna. Moreover, a benchmark between the well tested antenna codes TOPICA, RAPLI-CASOL, which is based on COMSOL [www.comsol.com], and the Petra-M code is also presented. In conclusion, S- and Z-matrices and wave electric field are compared showing an excellent agreement among these codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Simulation of an inductively coupled plasma with a two-dimensional Darwin particle-in-cell code

A two-dimensional particle-in-cell code for the simulation of low-frequency electromagnetic processes in laboratory plasmas has been developed. The code uses the Darwin method omitting the electromagnetic wave propagation. The Darwin method separates the electric field into solenoidal and irrotational parts. The solenoidal electric field is calculated with a new algorithm based on the equation for the electric field vorticity. The system of linear equations in the new algorithm is readily solved using a standard iterative method. The irrotational electric field is the electrostatic field calculated with the direct implicit algorithm. The code is verified by reproducing the two-stream instability, electron electromagnetic waves, and shear Alfvén waves. The code is applied to simulate an inductively coupled plasma with the driving current flowing around the plasma region. In this simulation, a ring of dense plasma forms at the initial stage but then the density becomes maximal in the center and decays monotonically toward the walls. The skin effect is in the transitional mode between local and non-local, and the electron velocity distribution function is non-Maxwellian.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2011

Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Assessment of the Subchannel Code CTF for Single- and Two-Phase Flows

As part of the Consortium for Advanced Simulation of Light Water Reactors, the subchannel code CTF is being used for single-phase and two-phase flow analysis under light water reactor operating conditions. Accurate determination of flow distribution, pressure drop, and void content is crucial for predicting margins to thermal crisis and ensuring more efficient plant performance. In preparation for the intended applications, CTF has been validated against data from experimental facilities comprising the General Electric (GE) 3 × 3 bundle, the boiling water reactor full-size fine-mesh bundle tests (BFBTs), the Risø tube, and the pressurized water reactor subchannel and bundle tests (PSBTs). Meanwhile, the licensed, well-recognized subchannel code VIPRE-01 was used to generate a baseline set of simulations for the targeted tests and solution parameters were compared to the CTF results.The flow split verification problem and single-phase GE 3 × 3 results are essentially in perfect agreement between the two codes. For the two-phase GE 3 × 3 cases, flow and quality discrepancies arise in the annular-mist flow regime, yet significant improvement is observed in CTF when void drift and two-phase turbulent mixing enhancement are considered. The BFBT pressure drop benchmark shows close agreement between predicted and measured results in general, although considerable overprediction by CTF is observed at relatively high void locations of the facility. This overestimation tendency is confirmed by the Risø cases. While overall statistics are satisfactory, both BFBT and PSBT bubbly-to-churn flow void contents are markedly overpredicted by CTF.The issues with two-phase closures such as turbulent mixing, interfacial and wall friction, and subcooled boiling heat transfer need to be addressed. As a result, preliminary sensitivity studies are presented herein, but more advanced models and code stability analysis require further investigation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

Multigroup Cross-Section Generation with the OpenMC Monte Carlo Particle Transport Code

High-fidelity deterministic transport codes require highly accurate multigroup cross sections (MGXS). Monte Carlo is increasingly cited as a reactor-agnostic approach to MGXS generation since it is unconstrained by the engineering-based approximations that limit the applicability of deterministic MGXS generation tools. This paper introduces a new framework that uses the OpenMC Monte Carlo code to generate MGXS for use in multigroup transport codes. The openmc.mgxs module is built atop OpenMC's Python application programming interface to process tally data output by the OpenMC executable. This paper validates the module to generate MGXS that enable the multigroup OpenMOC transport code to compute eigenvalues to within 50 pcm and fission rates to within 1% of reference solutions for two heterogeneous pressurized water reactor benchmarks.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Structural Design and Modeling of MARVEL Primary Coolant System Using the ASME Section III, Division 5, Code

This paper presents the structural design and supporting analysis for the Microreactor Applications Research Validation and Evaluation (MARVEL) primary coolant system (PCS) using the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code Section III, Division 5, rules. MARVEL is a liquid metal–cooled microreactor intended to provide experimental capabilities for the rapid testing and development of microreactor technologies. The PCS utilizes high-temperature sodium-potassium liquid metal as the primary coolant and operates at a design temperature of 570°C, necessitating the consideration of creep-related failure mechanisms. The base metal for the PCS is 316H stainless steel, and the weldments are made with a 16-8-2 filler. The design approach incorporates the current base code rules along with ASME code cases N-924, N-861, and N-862 to address primary load, ratcheting, and creep-fatigue evaluations, respectively. The reactor’s operation involves complex thermal and mechanical interactions due to natural convective flow and differential thermal expansion between components. In conclusion, this paper discusses the structural engineering challenges encountered, such as managing thermal stresses in the distribution plenum and guard vessel, and outlines the strategies implemented to meet the code requirements, including design modifications and operational constraints.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗
DOE OSTI2018

A Test Problem for Codes Solving the Discretized Diffusion Equation in Cartesian Geometry Derived Via Discrete Green’s Functions

We obtain here a solution to a zone-centered discretization of the one dimensional time-dependent diffusion equation with arbitrary initial conditions and source, constant absorption and scattering opacity, and constant zone size and time step. The solution is obtained using the discrete Green’s functions of the discretized equation. The solution of the discretized equation is useful in the testing of computer codes, because the code can be expected to agree with the solution to the discrete equation, to within small errors caused by roundoff. This is in contrast to solutions of the differential equation, with which the code results only approximately agree. Finally, the usefulness of the solution for tests of an inertial confinement fusion code is demonstrated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

THE McGill PLANAR HYDROGEN ATMOSPHERE CODE (McPHAC)

The McGill Planar Hydrogen Atmosphere Code (McPHAC) v1.1 calculates the hydrostatic equilibrium structure and emergent spectrum of an unmagnetized hydrogen atmosphere in the plane-parallel approximation, at surface gravities appropriate for neutron stars. McPHAC incorporates several improvements over previous codes for which tabulated model spectra are available: (1) Thomson scattering is treated anisotropically, which is shown to result in a 0.2%-3% correction in the emergent spectral flux across the 0.1-5 keV passband; (2) the McPHAC source code is made available to the community, allowing it to be scrutinized and modified by other researchers wishing to study or extend its capabilities; and (3) the numerical uncertainty resulting from the discrete and iterative solution is studied as a function of photon energy, indicating that McPHAC is capable of producing spectra with numerical uncertainties <0.01%. The accuracy of the spectra may at present be limited to {approx}1%, but McPHAC enables researchers to study the impact of uncertain inputs and additional physical effects, thereby supporting future efforts to reduce those inaccuracies. Comparison of McPHAC results with spectra from one of the previous model atmosphere codes (NSA) shows agreement to {approx}<1% near the peaks of the emergent spectra. However, in the Wien tail a significant deficit of flux in the spectra of the previous model is revealed, determined to be due to the previous work not considering large enough optical depths at the highest photon frequencies. The deficit is most significant for spectra with T{sub eff} < 10{sup 5.6} K, though even there it may not be of much practical importance for most observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2010

A MULTIDIMENSIONAL RELATIVISTIC HYDRODYNAMIC CODE WITH A GENERAL EQUATION OF STATE

The ideal gas equation of state with a constant adiabatic index, although commonly used in relativistic hydrodynamics, is a poor approximation for most relativistic astrophysical flows. Here we propose a new general equation of state for a multi-component relativistic gas which is consistent with the Synge equation of state for a relativistic perfect gas and is suitable for numerical (special) relativistic hydrodynamics. We also present a multidimensional relativistic hydrodynamic code incorporating the proposed general equation of state, based on the HLL scheme, which does not make use of a full characteristic decomposition of the relativistic hydrodynamic equations. The accuracy and robustness of this code is demonstrated in multidimensional calculations through several highly relativistic test problems taking into account nonvanishing tangential velocities. Results from three-dimensional simulations of relativistic jets show that the morphology and dynamics of the relativistic jets are significantly influenced by the different equation of state and by different compositions of relativistic perfect gases. Our new numerical code, combined with our proposed equation of state, is very efficient and robust, and unlike previous codes, it gives very accurate results for thermodynamic variables in relativistic astrophysical flows.

79 ASTRONOMY AND ASTROPHYSICS↗