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At least 1,747 records · Page 97

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, in this work, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

59 BASIC BIOLOGICAL SCIENCES↗

Integrated Computational Materials Engineering Development of Advanced High Strength Steel for Lightweight Vehicles

The goal of the ICME 3GAHSS project was to successfully demonstrate the applicability of Integrated Computational Materials Engineering (ICME) for the development and deployment of third generation advanced high strength steels (3GAHSS) for immediate weight reduction in passenger vehicles. The ICME approach integrated results from well-established computational and experimental methodologies to develop a suite of material constitutive models (deformation and failure), manufacturing process and performance simulation modules, a properties database, as well as the computational environment linking them together for both performance prediction and material optimization. This is the Final Report for the ICME 3GAHSS project, which achieved the fol-lowing objectives: 1) Developed a 3GAHSS ICME model, which includes atomistic, crystal plasticity, state variable and forming models. The 3GAHSS model was implemented in commercially available LS-DYNA and a user guide was developed to facilitate use of the model. 2) Developed and produced two 3GAHSS alloys using two different chemistries and manufacturing processes, for use in calibrating and validating the 3GAHSS ICME Model. 3) Optimized the design of an automotive subassembly by substituting 3GAHSS for AHSS yielding a design that met or exceeded all baseline performance requirements with a 30% mass savings. A technical cost model was also developed to estimate the cost per pound of weight saved when substituting 3GAHSS for AHSS. The project demonstrated the potential for 3GAHSS to achieve up to 30% weight savings in an automotive structure at a cost penalty of up to $0.32 to $1.26 per pound of weight saved. The 3GAHSS ICME Model enables the user to design 3GAHSS to desired mechanical properties in terms of strength and ductility.

36 MATERIALS SCIENCE↗

Effects of boundary hydraulics, dissolved oxygen, and dissolved organic carbon on growth and death dynamics of aerobic microbes in riverbed dune-induced hyporheic zones

Surface and groundwater interact in the hyporheic zone beneath and adjacent to rivers in the presence of a diverse microbial community. Heterotrophic bacteria mediate a range of environmentally important reactions, yet few studies have quantified bacterial growth and death dynamics in the hyporheic zone, and none have systematically analyzed their response to variations in hydraulic or chemical conditions. Here we used MODFLOW and SEAM3D to simulate hydraulics; dissolved oxygen (DO) and dissolved organic carbon (DOC) transport; and aerobic microbial metabolism, growth, and death in hyporheic zones induced by riverbed dunes. We ran simulations both with and without growth/death processes, and varied hydraulic parameters and DO/DOC boundary concentrations. Microbial biomass reached steady state (t = 3 days) in every simulation, at which time there was greater biomass and DOC biodegradation rates in the hyporheic flowcell (300% and 85% higher for the base case, respectively) when accounting for microbial growth dynamics. This occurred as microbial biomass tailored its spatial distribution to the availability of DO and DOC, demonstrating the importance of simulating growth/death processes. Biomass generally increased with hyporheic flow cell area as upwelling groundwater decreased. When varying surface water DO and DOC source concentrations relative to the base case, the greatest effect on biomass occurred when increasing DOC and decreasing DO. We determined minimum DO and DOC steady-state concentrations required for microbial growth, but the minimums were not absolute or related by stoichiometry. Increasing DOC created a smaller area of microbes with higher concentrations relative to the base case. Increasing DO slightly increased the area occupied by microbes while keeping the total biomass nearly constant. Overall, microbial growth and death dynamics depend on DO and DOC availability in the hyporheic zone, which is dependent on DOC/DO boundary concentrations and hyporheic flow paths, and in turn the hydraulic interaction between surface water and groundwater.

54 ENVIRONMENTAL SCIENCES↗

Visualization of Capsule Reentry Vehicle Heat Shield Ablation Using Naphthalene PLIF

The Orion Multi-Purpose Crew Vehicle (MPCV) will use an ablative heat shield and improved understanding of the ablation process would be beneficial for design purposes. Given that ablation is a multi-physics process involving heat and mass transfer, codes aiming to predict heat shield ablation are in need of experimental data pertaining to the turbulent transport of ablation products for validation. At The University of Texas at Austin, a technique is being developed that uses planar laser-induced fluorescence (PLIF) of a low-temperature sublimating ablator (naphthalene) to visualize the transport of ablation products in a supersonic flow. Since ablation at reentry temperatures can be difficult to recreate in a laboratory setting it is desirable to create a limited physics problem and simulate the ablation process at relatively low temperature conditions using naphthalene. A scaled Orion MPCV model with a solid naphthalene heat shield has been tested in a Mach 5 wind tunnel at various angles of attack in the current work. PLIF imaging reveals the distribution of the ablation products as they are transported into the heat-shield boundary layer and over the capsule shoulders into the separated shear layer and backshell recirculation region. Visualizations of the capsule shear layer using both naphthalene PLIF and Schlieren imaging compared favorably. High concentrations of naphthalene in the capsule separated flow region, intermittent turbulent structures on the heat shield surface, and interesting details of the capsule shear layer structure were observed using the naphthalene PLIF technique. The capsule shear layer was also shown to generally appear to be more turbulent at lower angles of attack. Furthermore, the PLIF signal increased steadily over the course of a run indicating that during a wind tunnel run the model heated up and the rate of naphthalene ablation increased. The shear layer showed increasing signs of turbulence over the course of a wind tunnel run as well, likely because of the combination of increased surface roughness and surface blowing rate. PLIF imaging also detected regions with a relatively low concentration of naphthalene in the capsule backshell recirculation region that are most likely the result of cross-flow-induced vortices on the capsule afterbody.

Combs, Christopher S.↗

Celeritas Midterm SciDAC Report

Celeritas is a new Monte Carlo (MC) code that helps satisfy the increasing demand for high energy physics (HEP) detector simulation, using Graphics Processing Unit (GPU) hardware on high performance computing (HPC) systems to model Large Hadron Collider (LHC) experiments and beyond. This report details the project’s progress midway through its SciDAC funding period, highlighting the first complete implementation of standard electromagnetic (EM) physics on GPUs, initial results for performance and scalability on Leadership Computing Facilities (LCFs), and preliminary integration into the CMS and ATLAS experiments. By integrating HEP domain knowledge with expertise in MC transport, Celeritas has catalyzed a shift in the HEP community’s perception of GPU platforms as the future for HPC simulations.

97 MATHEMATICS AND COMPUTING↗

Model-based data center cooling controls comparative co-design

This article presents a comparative simulation-based control logic design process. It uses the Control Description Language (CDL) and the ASHRAE Guideline 36 high-performing building control sequences with the Modelica Buildings Library (MBL) to demonstrate a comparative analysis of two control designs for a data center chilled water plant. Details include a description of the closed-loop plant and control design methodology, including sizing and parameterization, base and alternative (Guideline 36) control logic with software implementation structure, and outline of the simulation experimentation process. The selected control designs are paired with comparable chilled water plant configurations. The models include a chiller, a water-side economizer, and an evaporative cooling tower. The plant provides cooling at 27ºC zone supply air temperature to a data center in Sacramento, CA. The comparative simulation results examined the impacts of a selected control logic detail, and present an example model-based design application. Overall, the simulation results showed a 25% annual and a 18% summer energy use reduction for alternative controls. This shows that simulation-based control logic design performance evaluation can improve energy efficiency and resilience aspects of system controls at large.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Chemical and Radiological Compatibility Testing of 3D Printed Materials

To dramatically increase the adaptability, performance, and safety of processes in support of the Defense Waste Processing Facility (DWPF), Savannah River National Lab (SRNL) plans to perform chemical and radiological compatibility testing on a wide variety of 3D printed materials of interest. The 3D printing process provides numerous strategic operational benefits such as rapid prototyping of complex designs and geometry specific to the needs of the nuclear waste disposition process, as well as on-demand rapid prototyping and iteration with materials that aren’t as accessible through traditional manufacturing methods. Reaction chemistry in simulated waste batches can be matched closely to its radioactive counterpart, but glass reactor vessels have limitations. Vessel geometry can play a big factor in mixing transport limitations, process chemistry, and degradation reaction kinetics. In addition, additive manufacturing allows for much more detailed vessel design than traditional alternatives. Waste processing techniques in DWPF also encounter extreme chemical environments including high pH, strong acids, abrasive slurries, and significant irradiation. To meet these challenges, a matrix of various polymer, ceramic, and metal additive manufacturing materials have been exposed to a suite of chemical environments of interest as well as radioactive dose (such as gamma radiation from 60 Co) to properly test their durability under these conditions. Mass change has been monitored over a period of up to a week in these conditions, as well as added characterization for surface modification through Scanning Electron Microscopy/Electron Dispersive X-ray analysis (SEM/EDX). Further chemical characterization has been monitored through Fourier-Transform InfraRed Spectroscopy (FTIR), with planned investigation via thermal and tensile strength degradation. While the direct product of this research is identification of material(s) that can withstand specific hazardous environments encountered by the mercury water wash tank in DWPF process simulation experiments, the reference base of materials will be used for many other nuclear processes in the pursuit of rapidly developed, cost-efficient, and highly specific devices for environmental remediation and much more.

Wilson, Nathan W. [Savannah River National Laborat↗

Monte Carlo Simulation of Alloy Design Techniques: Fracture and Welding Studied Using the BFS Method for Alloys

Large-scale simulations of dynamic processes at the atomic level have developed into one of the main areas of work in computational materials science. Until recently, severe computational restrictions, as well as the lack of accurate methods for calculating the energetics, resulted in slower growth in the area than that required by current alloy design programs. The Computational Materials Group at the NASA Lewis Research Center is devoted to the development of powerful, accurate, economical tools to aid in alloy design. These include the BFS (Bozzolo, Ferrante, and Smith) method for alloys (ref. 1) and the development of dedicated software for large-scale simulations based on Monte Carlo- Metropolis numerical techniques, as well as state-of-the-art visualization methods. Our previous effort linking theoretical and computational modeling resulted in the successful prediction of the microstructure of a five-element intermetallic alloy, in excellent agreement with experimental results (refs. 2 and 3). This effort also produced a complete description of the role of alloying additions in intermetallic binary, ternary, and higher order alloys (ref. 4).

Bozzolo, Guillermo H.↗

JSPEC: A Program for IBS and Electron Cooling Simulation

Intrabeam scattering is an important collective effect that can deteriorate the properties of a high-intensity beam, and electron cooling is a method to mitigate the IBS effect. JSPEC (JLab Simulation Package for Electron Cooling) is an open-source program developed at Jefferson Lab, which simulates the evolution of the ion beam under the IBS and/or the electron cooling effect. JSPEC has been benchmarked with BETACOOL and experimental data. In this report, we will introduce the features of JSPEC, including the friction force calculation, the IBS expansion rate and electron cooling rate calculation, and the beam-dynamic simulations for the electron cooling process; explain how to set up the simulations in JSPEC; and demonstrate the benchmarking results.

Zhang, He↗

Thin-Entrance Window Process for Soft X-Ray Sensors

New free electron lasers, such as SLAC’s LCLS-II, will provide unique scientific imaging opportunities. In order to fully utilize these facilities, we need to develop detectors with shallow entrance windows that will enable detection of soft x-rays from 250 eV to 1.5 KeV. Achieving adequately shallow entrance windows is challenging because the high temperature anneal needed to activate the dopant also drives the dopant profile deeper, growing the region that is insensitive to soft x-rays. A new microwave annealing technology provides an efficient way to achieve shallow entrance windows in fully depleted high-resistivity silicon sensors. The microwave anneal technique can activate dopants at low substrate temperature, with minimal dopant diffusion, and can be used to fabricate both n-type and p-type entrance windows. SRP and SIMS measurements were used to verify dopant activation with negligible dopant diffusion. We then applied the microwave anneal process to a planar sensor wafer, using the new process to create the backside diode contact. Electrical test of the resulting sensors shows good reverse bias characteristics. The sensors have been bump-bonded to a read-out ASIC and used successfully to measure an Fe-55 x-ray spectrum. Process and device simulations were performed to characterize the quantum efficiency of the entrance window for soft x-rays. This technique is useful for other sensor applications requiring a shallow entrance window, including detectors for UV photons, low energy ions and low energy electrons.

47 OTHER INSTRUMENTATION↗

26th JANNAF Airbreathing Propulsion Subcommittee Meeting

This volume, the first of four volumes, is a collection of 28 unclassified/unlimited-distribution papers which were presented at the Joint Army-Navy-NASA-Air Force (JANNAF) 26th Airbreathing Propulsion Subcommittee (APS) was held jointly with the 38th Combustion Subcommittee (CS), 20th Propulsion Systems Hazards Subcommittee (PSHS), and 2nd Modeling and Simulation Subcommittee. The meeting was held 8-12 April 2002 at the Bayside Inn at The Sandestin Golf & Beach Resort and Eglin Air Force Base, Destin, Florida. Topics covered include: scramjet and ramjet R&D program overviews; tactical propulsion; space access; NASA GTX status; PDE technology; actively cooled engine structures; modeling and simulation of complex hydrocarbon fuels and unsteady processes; and component modeling and simulation.

Fry, Ronald S.↗

Application of Satellite SAR Imagery in Mapping the Active Layer of Arctic Permafrost

The objective of this project is to map the spatial variation of the active layer over the arctic permafrost in terms of two parameters: (i) timing and duration of thaw period and (ii) differential frost heave and thaw settlement of the active layer. To achieve this goal, remote sensing, numerical modeling, and related field measurements are required. Tasks for the University of Colorado team are to: (i) determine the timing of snow disappearance in spring through changes in surface albedo (ii) simulate the freezing and thawing processes of the active layer and (iii) simulate the impact of snow cover on permafrost presence.

Zhang, Ting-Jun↗

Characterization of NUW-LHT-5m, A Lunar Highland Simulant

A new simulant of the lunar highlands regolith, NUW-LHT-5M, was designed by NASA and manufactured by Washington Mills. The simulant was based on Apollo 16 data and is a member of the NU-LHT-series. NASA’s Marshall Space Flight Center and Johnson Space Center have already purchased 3 metric tons of the simulant for advanced engineering work. In support of engineering uses of the simulant, we provided measurements of the simulant including: mineral abundance and composition, liberation, X-ray fluorescence (XRF), ferrous iron, carbon, sulfur, 60 element inductively coupled plasma (ICP), loss on ignition, particle size, both 2D and 3D particle shape, specific surface area, shear, cohesion, internal friction, helium pycnometry, minimum index density, tap density, magnetic susceptibility, cryogenic and high temperature permittivity, visible and near-infrared (VNIR) and middle infra-red spectroscopy (MIR), differential scanning calorimetry (DSC), viscosity, thermal diffusivity, thermal conductivity, thermal gravimetric analysis (TGA), evolved gas analysis (EGA), and spark sintering. For the crystalline components the design of the simulant called for two rocks from the Stillwater Complex, Montana: 17.6 wt% norite, 37.7% anorthosite, and 4.7 wt% olivine from an unspecified commercial source. The other 40% of the simulant was a high calcium (An100), vesicular glass that Washington Mills made specifically for the simulant. Fabrication and quality control processes for both the glass and the simulant are described. Importantly, most of the graphs and tables presented herein provide values for both the new simulant and data for the older NASA mare simulant, JSC-1A. Finally, we discussed the current limitations of NUW-LT-5M and most other lunar regolith simulants to replicate the lunar material.

lunar regolith simulant↗

Low-Frequency Oscillations and Transport Processes Induced by Multiscale Transverse Structures in the Polar Wind Outflow: A Three-Dimensional Simulation

Multiscale transverse structures in the magnetic-field-aligned flows have been frequently observed in the auroral region by FAST and Freja satellites. A number of multiscale processes, such as broadband low-frequency oscillations and various cross-field transport effects are well correlated with these structures. To study these effects, we have used our three-dimensional multifluid model with multiscale transverse inhomogeneities in the initial velocity profile. Self-consistent-frequency mode driven by local transverse gradients in the generation of the low field-aligned ion flow and associated transport processes were simulated. Effects of particle interaction with the self-consistent time-dependent three-dimensional wave potential have been modeled using a distribution of test particles. For typical polar wind conditions it has been found that even large-scale (approximately 50 - 100 km) transverse inhomogeneities in the flow can generate low-frequency oscillations that lead to significant flow modifications, cross-field particle diffusion, and other transport effects. It has also been shown that even small-amplitude (approximately 10 - 20%) short-scale (approximately 10 km) modulations of the original large-scale flow profile significantly increases low-frequency mode generation and associated cross-field transport, not only at the local spatial scales imposed by the modulations but also on global scales. Note that this wave-induced cross-field transport is not included in any of the global numerical models of the ionosphere, ionosphere-thermosphere, or ionosphere-polar wind. The simulation results indicate that the wave-induced cross-field transport not only affects the ion outflow rates but also leads to a significant broadening of particle phase-space distribution and transverse particle diffusion.

Ganguli, Supriya B.↗

A geometrical model for shepherding

Shepherding is the process by which a satellite secularly exchanges angular momentum with a nearby particle or gaseous disk. The sense of the torque is such that the separation between the orbits of the particles and the shepherd increases secularly with time. I devised a new technique to analyze the physical nature of shepherding through study of evolution of the vector eccentricity of the particles. This method appears to analyze the physical nature of shepherding in sparse particle disks. Thus, it may be very useful in calculating the torque on Neptune's rings and on protoplanets in the solar nebula. Moreover, the techniques are useful in estimating how long numerical simulations of resonant processes must be run in order to reach a quasi-steady state.

Lissauer, Jack J.↗

A Multi-scale Modeling System: Developments, Applications and Critical Issues

A multi-scale modeling framework (MMF), which replaces the conventional cloud parameterizations with a cloud-resolving model (CRM) in each grid column of a GCM, constitutes a new and promising approach. The MMF can provide for global coverage and two-way interactions between the CRMs and their parent GCM. The GCM allows global coverage and the CRM allows explicit simulation of cloud processes and their interactions with radiation and surface processes. A new MMF has been developed that is based the Goddard finite volume GCM (fvGCM) and the Goddard Cumulus Ensemble (GCE) model. This Goddard MMF produces many features that are similar to another MMF that was developed at Colorado State University (CSU), such as an improved .surface precipitation pattern, better cloudiness, improved diurnal variability over both oceans and continents, and a stronger, propagating Madden-Julian oscillation (MJO) compared to their parent GCMs using conventional cloud parameterizations. Both MMFs also produce a precipitation bias in the western Pacific during Northern Hemisphere summer. However, there are also notable differences between two MMFs. For example, the CSU MMF simulates less rainfall over land than its parent GCM. This is why the CSU MMF simulated less overall global rainfall than its parent GCM. The Goddard MMF overestimates global rainfall because of its oceanic component. Some critical issues associated with the Goddard MMF are presented in this paper.

Tao, Wei-Kuo↗

Generic Environment for Simulating Launch Operations

GEM-FLO (A Generic Simulation Environment for Modeling Future Launch Operations) is a computer program that facilitates creation of discrete-event simulation models of ground processes in which reusable or expendable launch vehicles (RLVs) are prepared for flight. GEM-FLO includes a component, developed in Visual Basic, that generates a graphical user interface (GUI) and a component, developed in the Arena simulation language, that creates a generic discrete-event simulation model. Through the GUI, GEM-FLO elicits RLV design information from the user. The design information can include information on flight hardware elements, resources, and ground processes. GEM-FLO translates the user s responses into mathematical variables and expressions that populate the generic simulation model. The variables and expressions can represent processing times, resource capacities, status variables, and other process parameters needed to configure a simulation model that reflects the ground processing flow and requirements of a specific RLV. Upon execution of the model, GEMFLO puts out data on many measures of performance, including the flight rate, turnaround time, and utilization of resources. This information can serve as the basis for determining whether design goals can be met, and for comparing characteristics of competing RLV designs

Steele, Martin↗

Aeroacoustic Simulations of the High-Lift Common Research Model and Validation with Experiment

Aerodynamic and acoustic data from unsteady numerical simulations of the High-Lift Common Research Model are compared with experimental measurements from an open-jet wind tunnel test of a 10\-scale model. Time-averaged surface pressure data is in good agreement for all of the configurations evaluated during the test. Unsteady surface pressure spectra from the leading-edge slat and the nose of the main element are presented, demonstrating that the highest levels are associated with the wakes of slat brackets. At these locations the simulations and experiment match reasonably well at low enough frequencies (f < 10 kHz based on the model scale) before excessive numerical dissipation leads to a rapid roll off in the predicted frequency spectra. The agreement is inconsistent at other locations on the slat and main-element surfaces, where the pressure fluctuation levels are lower. Noise predictions using a synthetic microphone array are compared with equivalent experimental results, and the changes in levels predicted between three configurations are similar to those measured. However, some details of the noise predictions are inconsistent with the experiment, and the use of solid- instead of porous-surface data for the acoustic processing of the simulations likely contributes to the discrepancies. All of the simulations were completed before the test, and, despite some shortcomings, they provided valuable insight into the aeroacoustic performance of the model that greatly aided test planning and execution. Hence, the post-test comparisons presented here allow an assessment of the predictive methodology in the context of a realistic high-lift configuration.

High-lift↗