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At least 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. In this work, we present a computational tool, Glycan Modeler for in silico N–/O –glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader , a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-μs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler . Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Development of an Advanced Simulator to Model Mobility Control and Geomechanics during CO 2 Floods

The simulator is an isothermal, three-dimensional, four-phase, compositional, equation-of–state (EOS) simulator. We have named the simulator UTDOE-CO2 capable of simulating various recovery processes (i.e., primary, secondary waterflooding, and miscible and immiscible gas flooding). We include both the Peng-Robinson EOS and the Redlich-Kwong EOS models. A Gibbs stability test is also included in the model to perform a phase identification test to consistently label each phase for subsequent property calculations such as relative permeability, viscosity, density, interfacial tension, and capillary pressure. Our time step strategy is based on an IMPEC-type method (implicit pressure and explicit concentration). The gridblock pressure is solved first using the explicit dating of saturation-dependent terms. Subsequently, the material balance equations are solved explicitly for the total concentration of each component. The physical dispersion term is also included in the governing equations. The simulator includes (1) several foam model(s) for gas mobility control, (2) compositional relative permeability models with the hysteresis option, (3) corner point grid and several efficient solvers, (4) geomechanics module to compute stress field as the result of CO 2 injection/production, (5) the format of commercial visualization software, S3graf from Science-soft Ltd., was implemented for user friendly visualization of the simulation results. All tasks are completed and the simulator was fully tested and delivered to the DOE office including a user’s guide and several input files and the executable for Windows Pcs. We have published several SPE papers, presented several posters, and one MS thesis is completed (V. Pudugramam, 2013) resulting from this DOE funded project.

02 PETROLEUM↗
DOE OSTI2015

Prototyping and validating requirements of radiation and nuclear emergency plan simulator

Organizational incapability in developing unrealistic, impractical, inadequate and ambiguous mechanisms of radiological and nuclear emergency preparedness and response plan (EPR) causing emergency plan disorder and severe disasters. These situations resulting from 65.6% of poor definition and unidentified roles and duties of the disaster coordinator. Those unexpected conditions brought huge aftermath to the first responders, operators, workers, patients and community at large. Hence, in this report, we discuss prototyping and validating of Malaysia radiation and nuclear emergency preparedness and response plan simulation model (EPRM). A prototyping technique was required to formalize the simulation model requirements. Prototyping as systems requirements validation was carried on to endorse the correctness of the model itself against the stakeholder’s intensions in resolving those organizational incapability. We have made assumptions for the proposed emergency preparedness and response model (EPRM) through the simulation software. Those assumptions provided a twofold of expected mechanisms, planning and handling of the respective emergency plan as well as in bringing off the hazard involved. This model called RANEPF (Radiation and Nuclear Emergency Planning Framework) simulator demonstrated the training emergency response perquisites rather than the intervention principles alone. The demonstrations involved the determination of the casualties’ absorbed dose range screening and the coordination of the capacity planning of the expected trauma triage. Through user-centred design and sociotechnical approach, RANEPF simulator was strategized and simplified, though certainly it is equally complex.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Transfer Learning of High-Fidelity Opacity Spectra in Autoencoders and Surrogate Models

Simulations of high energy density physics are expensive, largely in part for the need to produce nonlocal thermodynamic equilibrium opacities. High-fidelity spectra may reveal new physics in the simulations not seen with low-fidelity spectra, but the cost of these simulations also scales with the level of fidelity of the opacities being used. Neural networks are capable of reproducing these spectra, but neural networks need data to train them, which limits the level of fidelity of the training data. Here this article demonstrates that it is possible to reproduce high-fidelity spectra with median errors in the realm of 3%–4% using as few as 50 samples of high-fidelity Krypton data by performing transfer learning on a neural network trained on many times more low-fidelity data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1994

A mathematical model for simulating noise suppression of lined ejectors

A mathematical model containing the essential features embodied in the noise suppression of lined ejectors is presented. Although some simplification of the physics is necessary to render the model mathematically tractable, the current model is the most versatile and technologically advanced at the current time. A system of linearized equations and the boundary conditions governing the sound field are derived starting from the equations of fluid dynamics. A nonreflecting boundary condition is developed. In view of the complex nature of the equations, a parametric study requires the use of numerical techniques and modern computers. A finite element algorithm that solves the differential equations coupled with the boundary condition is then introduced. The numerical method results in a matrix equation with several hundred thousand degrees of freedom that is solved efficiently on a supercomputer. The model is validated by comparing results either with exact solutions or with approximate solutions from other works. In each case, excellent correlations are obtained. The usefulness of the model as an optimization tool and the importance of variable impedance liners as a mechanism for achieving broadband suppression within a lined ejector are demonstrated.

Watson, Willie R.↗
NASA NTRS1996

Simulation and Modeling of the Elliptic Streamline Flow

Direct numerical simulation (DNS) was used to study homogeneous turbulence with a mean flow having elliptic streamlines. This flow combines the effects of rotation and strain on the turbulence. There are many important reasons for studying the elliptic streamline flow. This flow contains the effects of both rotation and strain and is therefore similar to the mean flow in a vortex strained in the plane perpendicular to its axis. Such flows provide insight into the fundamental vortical interactions within turbulence. A strained vortex also occurs in airplane wakes, in which each wingtip vortex induces a strain field on the other. The strain field can affect the stability of these vortices and thereby their turbulent structure downstream. The ability to understand and predict the turbulent structure of the vortices is important to the wake hazard problem which is of major concern for the safety of commercial aircraft.

Blaisdell, Gregory A.↗
NASA NTRS2000

Theory and Design Tools For Studies of Reactions to Abrupt Changes in Noise Exposure

Study plans, a pre-tested questionnaire, a sample design evaluation tool, a community publicity monitoring plan, and a theoretical framework have been developed to support combined social/acoustical surveys of residents' reactions to an abrupt change in environmental noise, Secondary analyses of more than 20 previous surveys provide estimates of three parameters of a study simulation model; within individual variability, between study wave variability, and between neighborhood variability in response to community noise. The simulation model predicts the precision of the results from social surveys of reactions to noise, including changes in noise. When the study simulation model analyzed the population distribution, noise exposure environments and feasible noise measurement program at a proposed noise change survey site, it was concluded that the site could not yield sufficient precise estimates of human reaction model to justify conducting a survey. Additional secondary analyses determined that noise reactions are affected by the season of the social survey.

Fields, James M.↗
DOE OSTI2013

Application of MMC model on simulation of shearing process of thick hot-rolled high strength steel plate

Shear operation is widely used as the first step in sheet metal forming to cut the sheet or plate into the required size. The shear of thick hot-rolled High Strength Steel (HSS) requires large shearing force and the sheared edge quality is relatively poor because of the large thickness and high strength compared with the traditional low carbon steel. Bad sheared edge quality will easily lead to edge cracking during the post-forming process. This study investigates the shearing process of thick hot-rolled HSS plate metal, which is generally exploited as the beam of heavy trucks. The Modified Mohr-Coulomb fracture criterion (MMC) is employed in numerical simulation to calculate the initiation and propagation of cracks during the process evolution. Tensile specimens are designed to obtain various stress states in tension. Equivalent fracture strains are measured with Digital Image Correlation (DIC) equipment to constitute the fracture locus. Simulation of the tension test is carried out to check the fracture model. Then the MMC model is applied to the simulation of the shearing process, and the simulation results show that the MMC model predicts the ductile fracture successfully.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Terry Turbopump Expanded Operating Band Modeling and Simulation Efforts in Fiscal Year 2021 Extended Period of Performance (Final Report)

This report documents the progress made under the Terry Turbine Expanded Operating Band (TTEXOB) program's modeling and simulation (MODSIM) initiative at Sandia National Laboratories (SNL ). It describes the US Federal Fiscal Year 2021 (FY21) extended period-of-performance MODSIM work completed since the closure of FY20 with due reference to the Texas A&M University (TAMU) hybrid milestone 5/6 experimental program. This work, which falls under Milestone 7 of the program, provides a counterpart to the various experiments. The overall TTEXOB program and its milestone-based approach are described in the program's Summary Plan. Details of the individual milestone test plans can be found in the corresponding detailed test plan, e.g. the Milestone 3 and 4 Detailed Test Plan. SNL MODISM is conducted alongside experiments performed at TAMU, and SNL technical staff regularly consults with TAMU on the experimental program. In FY21, MELCOR code models and capabilities were exercised in two different contexts: experimental comparisons to the TAMU ZS-1 and GS-2, and stand-alone analyses of a station black-out (SBO) scenario in a generic boiling water reactor (BWR). Code to experiment comparisons met with fair success when turbine losses were well characterized as for the ZS-1 turbine. Both deterministic and Bayesian calibration processes were used to find a recommended turbine torque multiplier for ZS-1 type turbines. This process could be repeated for GS-2 type turbines if GS-2 losses were better understood. Stand-alone generic BWR SBO calculations revealed that three different modes of self-regulating turbopump behavior may be observed depending on certain modeling parameters and choices having to do with turbine nozzles. Aspects of this predicted behavior may have been observed in TAMU GS-2 experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Accelerating nuclear fuel development and qualification: Modeling and simulation integrated with separate-effects testing

In this work, an approach to transform and accelerate nuclear fuel development and qualification is outlined. The approach exploits advanced modeling and simulation at the outset to inform constituent and system selection and to enable integral fuel performance analyses. Analyses using these tools identify and prioritize the most important fuel performance parameters and phenomena for subsequent targeted characterization with separate-effects tests. Separate-effects testing spans out-of-pile and in-pile tests and is meant to iterate with and inform engineering-scale integral fuel performance analyses throughout the development process. Exercising this cycle in an agile fashion will increase confidence in the integral fuel performance predictions while reducing uncertainties. This process sets the stage for executing a much more limited set of well-defined integral irradiation tests designed to validate engineering-scale fuel performance codes and to confirm the performance and safety of the fuel system under prototypic conditions. This approach will reduce the time for development and qualification of a new fuel system, and it will also reduce associated costs.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS1976

An application of the Multi-Purpose System Simulation /MPSS/ model to the Monitor and Control Display System /MACDS/ at the National Aeronautics and Space Administration /NASA/ Goddard Space Flight Center /GSFC/

The Multi-Purpose System Simulator (MPSS) model was used to investigate the current and projected performance of the Monitor and Control Display System (MACDS) at the Goddard Space Flight Center in processing and displaying launch data adequately. MACDS consists of two interconnected mini-computers with associated terminal input and display output equipment and a disk-stored data base. Three configurations of MACDS were evaluated via MPSS and their performances ascertained. First, the current version of MACDS was found inadequate to handle projected launch data loads because of unacceptable data backlogging. Second, the current MACDS hardware with enhanced software was capable of handling two times the anticipated data loads. Third, an up-graded hardware ensemble combined with the enhanced software was capable of handling four times the anticipated data loads.

Mill, F. W.↗
NASA NTRS2011

US Clean Energy Sector and the Opportunity for Modeling and Simulation

The following paper sets forth the current understanding of the US clean energy demand and opportunity. As clean energy systems come online and technology is developed, modeling and simulation of these complex energy programs provides an untapped business opportunity. The US Department of Defense provides a great venue for developing new technology in the energy sector because it is demanding lower fuel costs, more energy efficiencies in its buildings and bases, and overall improvements in its carbon footprint. These issues coupled with the security issues faced by foreign dependence on oil will soon bring more clean energy innovations to the forefront (lighter batteries for soldiers, alternative fuel for jets, energy storage systems for ships, etc).

Inge, Carole Cameron↗
DOE OSTI2023

Modeling and Simulation of Advanced Manufacturing Techniques using MOOSE and MALAMUTE

Advanced manufacturing techniques offer increased geometry complexity, energy and material usage efficiency improvements, and an expanded palette of materials as compared to conventional manufacturing approaches. Advanced-manufacturing-produced parts can experience wide variations in the final microstructure, and these microstructure variations significantly impact the parts’ performance. In this chapter, we present recent code developments within Multiphysics Object-Oriented Simulation Environment (MOOSE) and in the MOOSE Application Library for Advanced Manufacturing UTilitiEs (MALAMUTE). Here we demonstrate applying these modeling and simulation codes to two advanced manufacturing process types: advanced sintering techniques and laser-based additive manufacturing techniques. The multiphysics and multiscale capabilities of these codes enable prediction of the microstructure evolution resulting from variations in the Advanced manufacturing process parameters.

36 MATERIALS SCIENCE↗
NASA NTRS1989

The transient performance of a two-phase fluid reservoir

Thermal control of future large, high power spacecraft will require a two-phase fluid central bus. The two-phase fluid reservoir is a critical component in the two-phase fluid bus. It both controls the saturation temperature and provides a space for volumetric changes. A dynamic reservoir simulation model does not currently exist, but it is needed to expedite efforts and reduce risk. During 1989 an effort was made to develop a simulation model of the transient performance of a two-phase fluid reservoir. As a beginning, a preliminary model was developed. It is based upon component mathematical models in lumped parametric form and build upon five component mathematical models for calculating dynamic responses of two-phase fluid reservoirs, primary feedback elements, controller commands, heater actuators, and reservoir heaters. As much as possible, the model took advantage of the available SINDA'85/FLUINT thermal/fluid integrator. Additional calculation logic and computer subroutines were developed to complete implementation of the model. The model is capable of simulating dynamic response of an equilibrium two-phase fluid reservoir. Modification of the model to include the liquid/vapor nonequilibrium is required for applications of the model to simulate performance of reservoir in which the liquid and vapor phases of the reservoir fluid are not in equilibrium. In addition, the model in its present form, needs to be refined in several respects. More empirical data are needed to guide the model development. The model may then be used to conduct a full parametric study of two-phase fluid reservoirs. More complexities in two-phaes flow regions in laboratory and flight conditions may have to be considered eventually if empirical data cannot be simulated satisfactorily. System with other components arrangement also need to be simulated if optimization is ever to be attained. The present model does, however, preliminarily demonstrates that such analyses are quite possible and offers a far less expensive method to understand the transient of a two-phase fluid reservoir system than a totally headware approach.

Chi, Joseph↗
NASA NTRS2002

Airspace Systems Program: Virtual Airspace Modeling and Simulation Project

The Airspace Systems Program (ASP) has identified a set of goals based on projections of annual passenger demands. The topics of discussion include: 1) Virtual Airspace Modeling and Simulation Project (VAMS) Project Description; 2) VAMS Project Management; 3) VAMS Project Schedule; and 4) Technical Interchange Meeting (TIM). This paper is in viewgraph form.

Jacobsen, Robert↗
DOE OSTI2022

Cloud Radiative Effects on MJO Development in DYNAMO

Observed Madden-Julian Oscillation (MJO) events are examined with the aid of regional model simulations to understand the role of cloud radiative effects in the MJO development. The importance of this role is demonstrated by the absence of MJO in the model simulations that contain no cloud radiative effects. Comparisons of model simulations with and without the cloud radiative effects and observation help identify the major processes arising from those effects. Those processes develop essentially from heating in the upper-troposphere due to shortwave absorption within anvil clouds in the upper troposphere and the convergence of longwave radiation in the middle-upper troposphere, with a peak at 300-hPa, during deep convection. First, that heating adds extra buoyancy and accelerates the rising motion in the upper troposphere in deep convection. The vertical acceleration in the upper troposphere creates a vacuum effect and demands for more deep convection to develop. Second, in response to that demand and required by mass balance arises the large-scale horizontal and vertical mass, moisture, and energy convergence. It strengthens deep convection and, with the feedback from continuing cloud radiative effect, creates conditions that can perpetuate deep convection and MJO development. That perpetuation does not occur however because those processes arising from the cloud radiative heating in the upper troposphere stabilize the troposphere till it supports no further deep convection. Weakening deep convection reduces cloud radiative effects. The subsequent reduction of the vacuum effect in the upper troposphere diminishes deep convection completing an MJO cycle. These results advance our understanding of the development of the MJO in the radiative-convective system over warm waters in the tropics. They show that while the embryo of intraseasonal oscillation may exist in the system its growth/development is largely dependent on cloud radiative effects and feedbacks.

54 ENVIRONMENTAL SCIENCES↗