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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 1,675 records · Page 93

Cry1A(b)16 toxin from Bacillus thuringiensis : Theoretical refinement of three‐dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms

ABSTRACT Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody–peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248–1257. © 2017 Wiley Periodicals, Inc.

Plácido, Alexandra↗

A method for data handling numerical results in parallel OpenFOAM simulations

Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit{sup ®}[1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms.

42 ENGINEERING↗

A generic multibody simulation

Described is a dynamic simulation package which can be configured for orbital test scenarios involving multiple bodies. The rotational and translational state integration methods are selectable for each individual body and may be changed during a run if necessary. Characteristics of the bodies are determined by assigning components consisting of mass properties, forces, and moments, which are the outputs of user-defined environmental models. Generic model implementation is facilitated by a transformation processor which performs coordinate frame inversions. Transformations are defined in the initialization file as part of the simulation configuration. The simulation package includes an initialization processor, which consists of a command line preprocessor, a general purpose grammar, and a syntax scanner. These permit specifications of the bodies, their interrelationships, and their initial states in a format that is not dependent on a particular test scenario.

Hopping, K. A.↗

A verification library for multibody simulation software

A multibody dynamics verification library, that maintains and manages test and validation data is proposed, based on RRC Robot arm and CASE backhoe validation and a comparitive study of DADS, DISCOS, and CONTOPS that are existing public domain and commercial multibody dynamic simulation programs. Using simple representative problems, simulation results from each program are cross checked, and the validation results are presented. Functionalities of the verification library are defined, in order to automate validation procedure.

Kim, Sung-Soo↗

Constraint methods that accelerate free-energy simulations of biomolecules

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulating the dynamic interaction of a robotic arm and the Space Shuttle remote manipulator system

Industrial robots are usually attached to a rigid base. Placing the robot on a compliant base introduces dynamic coupling between the two systems. The Vehicle Emulation System (VES) is a six DOF platform that is capable of modeling this interaction. The VES employs a force-torque sensor as the interface between robot and base. A computer simulation of the VES is presented. Each of the hardware and software components is described and Simulink is used as the programming environment. The simulation performance is compared with experimental results to validate accuracy. A second simulation which models the dynamic interaction of a robot and a flexible base acts as a comparison to the simulated motion of the VES. Results are presented that compare the simulated VES motion with the motion of the VES hardware using the same admittance model. The two computer simulations are compared to determine how well the VES is expected to emulate the desired motion. Simulation results are given for robots mounted to the end effector of the Space Shuttle Remote Manipulator System (SRMS). It is shown that for fast motions of the two robots studied, the SRMS experiences disturbances on the order of centimeters. Larger disturbances are possible if different manipulators are used.

Garrahan, Steven L.↗

Comparison of human driver dynamics in simulators with complex and simple visual displays and in an automobile on the road

As part of a comprehensive program exploring driver/vehicle system response in lateral steering tasks, driver/vehicle system describing functions and other dynamic data have been gathered in several milieu. These include a simple fixed base simulator with an elementary roadway delineation only display; a fixed base statically operating automobile with a terrain model based, wide angle projection system display; and a full scale moving base automobile operating on the road. Dynamic data with the two fixed base simulators compared favorably, implying that the impoverished visual scene, lack of engine noise, and simplified steering wheel feel characteristics in the simple simulator did not induce significant driver dynamic behavior variations. The fixed base vs. moving base comparisons showed substantially greater crossover frequencies and phase margins on the road course.

Mcruer, D. T.↗

Civil (French/US) certification of the Coast Guard's HH-65A Dauphin

Certification programs with particular emphasis on handling qualities requirements are described. A dynamic simulator was designed and constructed to support and verify the dynamic aspects of the avionics system, particularly the Automatic Flight Control System (AFCS). The role of the Dynamic Simulator is discussed.

Hart, J. C.↗

Adaptive two-regime method: Application to front propagation

The Adaptive Two-Regime Method (ATRM) is developed for hybrid (multiscale) stochastic simulation of reaction-diffusion problems. It efficiently couples detailed Brownian dynamics simulations with coarser lattice-based models. The ATRM is a generalization of the previously developed Two-Regime Method [Flegg et al., J. R. Soc., Interface 9, 859 (2012)] to multiscale problems which require a dynamic selection of regions where detailed Brownian dynamics simulation is used. Typical applications include a front propagation or spatio-temporal oscillations. In this paper, the ATRM is used for an in-depth study of front propagation in a stochastic reaction-diffusion system which has its mean-field model given in terms of the Fisher equation [R. Fisher, Ann. Eugen. 7, 355 (1937)]. It exhibits a travelling reaction front which is sensitive to stochastic fluctuations at the leading edge of the wavefront. Previous studies into stochastic effects on the Fisher wave propagation speed have focused on lattice-based models, but there has been limited progress using off-lattice (Brownian dynamics) models, which suffer due to their high computational cost, particularly at the high molecular numbers that are necessary to approach the Fisher mean-field model. By modelling only the wavefront itself with the off-lattice model, it is shown that the ATRM leads to the same Fisher wave results as purely off-lattice models, but at a fraction of the computational cost. The error analysis of the ATRM is also presented for a morphogen gradient model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular simulation study of dynamical properties of room temperature ionic liquids with carbon pieces

Room temperature ionic liquids (RTILs) with dispersed carbon pieces exhibit distinctive physiochemical properties. In order to explore the molecular mechanism, RTILs/carbon pieces mixture we investigated it by molecular dynamics (MD) simulation in this work. Rigid and flexible carbon pieces in the form of graphene with different thicknesses and carbon nanotubes in different sizes were dispersed in a representative RTIL 1-butyl-3-methyl-imidazolium dicyanamide ([Bmim][DCA]). Our study demonstrated that the diffusion coefficients of RTILs in the presence of flexible carbons are similar to those of bulk RTILs at varying temperatures, which is in contrast to the decreased diffusion of RTILs in the presence of rigid carbons. In addition, interfacial ion number density at rigid carbon surfaces was higher than that at flexible ones, which is correlated with the accessible external surface area of carbon pieces. The life time of cation-anion pair in the presence of carbon pieces also exhibited a dependence on carbon flexibility. RTILs with dispersed rigid carbon pieces showed longer ion pair life time than those with flexible ones, in consistence with the observation in diffusion coefficients. Furthermore, this work highlights the necessity of including the carbon flexibility when performing MD simulation of RTILs in the presence of dispersed carbon pieces in order to obtain the reliable dynamical and interfacial structural properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subdiffusive High-Pressure Hydrogen Gas Dynamics in Elastomers

We report elastomeric rubber materials serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. High-pressure exposure and subsequent rapid decompression often lead to cavitation and stress-induced damage of the elastomer due to localization of the hydrogen gas. Here, we use all-atom classical molecular dynamics simulations to assess the impact of compositional variations on gas diffusion within the commonly used elastomer ethylene–propylene–diene monomer (EPDM). With the aim to build a predictive understanding of precursors to cavitation and to motivate material formulations that are less sensitive to hydrogen-induced failure, we perform systematic simulations of gas dynamics in EPDM as a function of temperature, gas concentration, and cross-link density. Our simulations reveal anomalous, subdiffusive hydrogen motion at pressure and intermediate times. We identify two groups of gas with different mobilities: one group exhibiting high mobility and one group exhibiting low mobility due to their motion being impeded by the polymer. With decreasing temperatures, the low-mobility group shows increased gas localization, the necessary precursor for cavitation damage in these materials. At lower temperatures, increasing cross-link density led to greater hydrogen gas mobility and a lower fraction of caged hydrogen, indicating that increasing cross-link density may reduce precursors to cavitation. Finally, we use a two-state kinetic model to determine the energetics associated with transitions between these two mobility states.

36 MATERIALS SCIENCE↗

NPP Simulators for Coupled Thermal and Electric Power Dispatch

The Light Water Reactor Sustainability (LWRS) program within the United States Department of Energy supports extending the operation of the U.S. commercial nuclear power plant (NPP) fleet. Within the LWRS program, the Flexible Plant Operation and Generation (FPOG) Pathway works to diversify the revenue streams of light water reactors (LWRs) by opening opportunities for the co-generation of non-electric products in addition to supplying electrical power to the grid. Recent events have added greater motivation to these efforts. For example, the recent Inflation Reduction Act (IRA) passed by the U.S. federal government offers substantial tax incentives for producing clean hydrogen, the technology readiness level of dispatchable and high-efficiency hydrogen production has dramatically increased in a short time, and societal response to world climate change is driving a transition away from fossil fuels. Producing hydrogen with maximum efficiency using nuclear power requires dispatching both electrical and thermal power from the nuclear plant to the hydrogen plant, so testing concepts of operations for combined electrical and thermal power dispatch (TPD) from an NNP to a hydrogen plant is of interest. This report documents achievement of the Light Water Reactor Sustainability (LWRS) program milestone “Install and demonstrate a vendor-developed simulator on the Human Systems Simulation Laboratory (HSS) for dispatch of LWR electrical power to a close-coupled electrolysis plant” with a due date of Dec. 22, 2022. Several factors provide motivation for this effort. Coupling the power generation deck of a nuclear power plant to a hydrogen production facility introduces new possibilities for operational transients that must be addressed. In particular, the performance of the integrated system during startup and shutdown of the hydrogen production facility, as well as offnormal conditions, need to be evaluated to ensure there are no adverse effects on the operation of the existing NPP. The concept of operations involving the NPP, the hydrogen plant, and the electric power grid must be tested using NPP simulators and operating procedures that have been modified for TPD operations. These tests must also include dynamic simulations of the coupled tertiary thermal and electric loads as well as coordinated activities with NPP operators, tertiary load operators and grid power coordinators. The report summarizes progress in developing and testing full-scope NPP simulators at the HSSL, including a generic BWR simulator from GSE Systems, Inc. and generic PWR simulator from Westinghouse. In the case of the TPD-GBWR Simulator from GSE Systems, Inc., a BWR is thermally coupled to a high temperature electrolysis (HTE) plant that produces hydrogen and oxygen from de-ionized water. The hydrogen plant is not explicitly simulated but only included as a transient heat sink. A thermal power dispatch (TPD) system transfers heat between the steam systems at the BWR and the hydrogen plant. Operational results from two versions of the modified simulator are presented. The first version uses synthetic oil as a heat transfer fluid in a closed delivery heat loop (DHL) that generates steam at the hydrogen plant. The second version uses steam as the heat transfer fluid in a delivery steam line (DSL) to provide steam to the hydrogen plant. For both versions, the estimated thermal power delivery distance is approximately one kilometer. The amount of thermal power dispatched in the simulators is 15% of the total reactor thermal power such that the simulators provide a tool to study the feasibility of coupling a BWR to industrial processes that benefit from a combination electrical and thermal power dispatch. Ongoing work within a CRADA is also developing a full-scope PWR simulator provided by Westinghouse for both thermal and electric power coupling. This simulator is based on a PWR plant with two three-loop Westinghouse reactors. Westinghouse PWRs are sufficiently similar that a simulator of a three-loop reactor is an appropriate representation for two-loop and four-loop PWR reactors. The three-loop simulator will initially be modified for close-coupling to a 100 MW HTE hydrogen production plant that will require approximately 25 MW of thermal power while operating at its maximum rated capacity. The simulator testing will include full coupling to dynamic simulations of a hydrogen production plant and a representative bulk electric grid. The simulator provided by Westinghouse is similar to the GPWR simulator that INL has already obtained from GSE Systems but has a few important added benefits. First, the Westinghouse simulator is based on digital controls and has additional screens that can be called up to show parameter trends to assist operators in decision-making. The Westinghouse simulator also has upgrades to the controls and hardware representations, such as valve actuators, that make it more realistic and flexible in terms of accurately sim

99 GENERAL AND MISCELLANEOUS↗

Simulating the Effects of Carbon Nanotube Continuity and Interfacial Bonding on Composite Strength and Stiffness

Molecular dynamics simulations of carbon nanotube (CNT) composites, in which the CNTs are continuous across the periodic boundary, overestimate the experimentally measured mechanical properties of CNT composites along the fiber direction. Since the CNTs in these composites are much shorter than the composite dimensions, load must be transferred either directly between CNTs or through the matrix, a mechanism that is absent in simulations of effectively continuous CNTs. In this study, the elastic and fracture properties of high volume fraction discontinuous carbon nanotube/amorphous carbon composite systems were compared to those of otherwise equivalent continuous CNT composites using ReaxFF reactive molecular dynamics simulations. These simulations were used to show how the number of nanotube-matrix interfacial covalent bonds affect composite mechanical properties. Furthermore, the mechanical impact of interfacial bonding was decomposed to reveal its effect on the properties of the CNTs, the interfacial layer of matrix, and the bulk matrix. For the composites with continuous reinforcement, it was found that any degree of interfacial bonding has a negative impact on axial tensile strength and stiffness. This is due to disruption of the structure of the CNTs and interfacial matrix layer by the interfacial bonds. For the discontinuous composites, the modulus was maximized between 4%-7% interfacial bonding and the strength continues to increase up to the highest levels of interfacial bonding studied. Areas of low stress and voids were observed in the simulated discontinuous composites at the ends of the tubes, from which fracture was observed to initiate. Experimental carbon nanotube yarn composites were fabricated and tested. The results were used to illustrate knockdown factors relative to the mechanical performance of the tubes themselves.

Benjamin D Jensen↗

Operator splitting method for simulation of dynamic flows in natural gas pipeline networks

Here, we develop an operator splitting method to simulate flows of isothermal compressible natural gas over transmission pipelines. The method solves a system of nonlinear hyperbolic partial differential equations (PDEs) of hydrodynamic type for mass flow and pressure on a metric graph, where turbulent losses of momentum are modeled by phenomenological Darcy-Weisbach friction. Mass flow balance is maintained through the boundary conditions at the network nodes, where natural gas is injected or withdrawn from the system. Gas flow through the network is controlled by compressors boosting pressure at the inlet of the adjoint pipe. Our operator splitting numerical scheme is unconditionally stable and it is second order accurate in space and time. The scheme is explicit, and it is formulated to work with general networks with loops. We test the scheme over range of regimes and network configurations, also comparing its performance with performance of two other state of the art implicit schemes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Colloidal suspension simulates linear dynamic pressure profile

Missile nose fairings immersed in colloidal suspension prepared with various specific gravities simulate pressure profiles very similar to those encountered during reentry. Stress and deflection conditions similar to those expected during atmospheric reentry are thus attained in the laboratory.

Mc Cann, R. J.↗

Body-centered orthorhombic C 16 : A novel topological node-line semimetal

We identify by ab initio calculations a novel topological semimetal carbon phase in all-sp 2 bonding networks with a 16-atom body-centered orthorhombic unit cell, termed bco-C 16 . Total-energy calculations show that bco-C 16 is comparable to solid fcc-C 60 in energetic stability, and phonon and molecular dynamics simulations confirm its dynamical stability. This all-sp 2 carbon allotrope can be regarded as a three-dimensional modification of graphite, and its simulated x-ray diffraction (XRD) pattern matches well a previously unexplained diffraction peak in measured XRD spectra of detonation and chimney soot, indicating its presence in the specimen. Electronic band structure calculations reveal that bco-C 16 is a topological node-line semimetal with a single nodal ring. Lastly, these findings establish a novel carbon phase with intriguing structural and electronic properties of fundamental significance and practical interest.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Numerical Simulation of Dynamic Stall Using Near-Body Adaptive Mesh Refinement

Time-dependent Reynolds-averaged Navier-Stokes simulations have been carried out for a NACA 0012 airfoil and a flexible UH-60A rotor undergoing dynamic stall. The OVERFLOW computational fluid dynamics (CFD) code is used to explore the use of near-body adaptive mesh refinement (NB-AMR) for the first time on a flexible helicopter rotor in forward flight. Emphasis is placed on understanding the temporal and spatial convergence of the solutions, their numerical efficiency and stability, and establishing a grid-converged solution. Some of the remaining differences between CFD and flight-test measurements are discussed. Time-dependent flow visualization is used to provide an improved understanding of the physical mechanisms involved with two-dimensional and three-dimensional dynamic stall, and the NB-AMR process.

Near-Body↗

Impact of pH on Aqueous-Phase Phenol Hydrogenation Catalyzed by Carbon-Supported Pt and Rh

In aqueous phase, the rates of hydrogenation of aromatic substrates such as phenol on Pt/C and Rh/C are influenced by varying activity of hydronium ions. Decreasing the pH from 8 to 1 increases the rate of hydrogenation of phenol on Pt at 20 bar H 2 and 80 °C by 15-fold. This increase is attributed to weakening of the hydrogen binding energy (HBE) on the metal surface with decreasing pH. A weaker HBE at lower pH is also predicted by ab initio molecular dynamics simulations, providing atomistic insight into the impact of electrolyte ion distribution and interfacial solvent reorganization on HBE. The lower HBE results in a decrease in the activation energy for addition of adsorbed H from the metal to the adsorbed organic (with a Brønsted–Evans–Polanyi slope of ~1). In conclusion, the kinetic model derived accounts also for the lack of pH dependence at low hydrogen coverages (at 1 bar H 2 on Pt or up to 70 bar H 2 on Rh), when the weakening of the HBE decreases the hydrogen coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗