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At least 19 records

REACTER: A Versatile Tool for Large-Scale Reactive Molecular Dynamics

Accurately describing reactive events over long length and time scales remains a grand challenge of computational materials science. REACTER is a general protocol for modeling chemical reactions using classical force fields, and is implemented in the popular molecular dynamics software LAMMPS. REACTER has a growing user base and has been used as a model-building tool for a variety of materials, including thermoplastics, thermosets, glassy materials and composites. The method has also been applied to accelerated modeling of reversible chemical reactions, such as the formation of electrochemical components for batteries. Recently, the REACTER protocol has received some major upgrades to enhance its ability to predict when reactions occur and to make it easier to use. Force field parameters can now be automatically assigned to newly created bonds, angles and other interactions. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, and a constraint based on the total potential energy of the atoms involved in a reactive site. This potential energy constraint allows for the accurate reproduction of DFT-based tight-binding (DFTB3) predicted bond dissociation curves for mechanically induced bond breaking.

polymer simulations, molecular dynamics

Antigenic Protein In Microgravity-Grown Human Mixed Mullerian Tumor (LN1) Cells Preserved In RNA Stabilizing Agent

Cells treated with RNAlater(TradeMark) have previously been shown to contain antigenic proteins that can be visualized using Western blot analysis. These proteins seem to be stable for several months when stored in RNA stabilizer at 4 C. Antigenic protein can be recovered from cells that have been processed using an Ambion RNAqueous(Registered TradeMark) kit to remove RNA. In this set of experiments, human mixed Mullerian tumor (LNI) cells grown on the International Space Station during Expedition 3 were examined for antigenic stability after removal of RNA. The cells were stored for three months in RNAlater(TradeMark) and RNA was extracted. The RNA filtrate containing the protein was precipitated, washed, and suspended in buffer containing sodium dodecyl sulfate (SDS). Samples containing equal concentrations of protein were loaded onto SDS-polyacrylamide gels. Proteins were separated by electrophoresis and transferred by Western blot to polyvinylidene fluoride (PVDF) membrane. The Western blots were stained with an enhanced chemiluminescent ECL(Registered Trademark) Plus detection kit (Amersham) and scanned using a Storm 840 gel image analyzer (Amersham, Molecular Dynamics). ImageQuant(Registered TradeMark) software was used to quantify the densities of the protein bands. The ground control and flight LN1 cell samples showed a similar staining pattern over time with antibodies to vimentin, glyceraldehyde-3-phosphate dehydrogenase, and epithelial membrane antigens.

Hammond, Dianne K.

Antigenic Protein In Microgravity-Grown Human Mixed Mullerian Tumor (LN1) Cells Preserved In RNA Stabilizing Agent

Cells treated with RNAlater(TradeMark) have previously been shown to contain antigenic proteins that can be visualized using Western blot analysis. These proteins seem to be stable for several months when stored in RNA stabilizer at 4 C. Antigenic protein can be recovered from cells that have been processed using an Ambion RNAqueous(Registered TradeMark) kit to remove RNA. In this set of experiments, human mixed Mullerian tumor (LN1) cells grown on the International Space Station during Expedition 3 were examined for antigenic stability after removal of RNA. The cells were stored for three months in RNAlater(TradeMark) and RNA was extracted. The RNA filtrate Containing the protein was precipitated, washed, and suspended in buffer containing sodium dodecyl sulfate (SDS). Samples containing equal concentrations of protein were loaded onto SDS-polyacrylamide gels. Proteins were separated by electrophoresis and transferred by Western blot to polyvinylidene fluoride (PVDF) membrane. The Western blots were stained with an enhanced chemiluminescent ECL(Registered TradeMark)Plus detection kit (Amersham) and scanned using a Storm 840 gel image analyzer (Amersham, Molecular Dynamics). ImageQuant(Registered TradeMark)a software was used to quantify the densities of the protein bands. The ground control and flight LN1 cell samples showed a similar staining pattern over time with antibodies to vimentin, glyceraldehyde-3-phosphate dehydrogenase, and epithelial membrane antigens.

Hammond, Dianne K.

Overview of Ablative TPS Modeling at NASA Ames

Over the past decade, NASA has invested in efforts to build predictive thermal protection system (TPS) material models from the micro-scale to the macro-scale. To complement the mission design cycle process and reduce the need for extensive testing, NASA is developing modeling and simulation tools that enable characterizing material properties and response to hot plasma experienced during atmospheric entry. Traditional material response and ablation modeling tools, such as the heritage code FIAT, and its multidimensional siblings, TITAN and 3dFIAT, are being complemented with newly developed software such as Icarus and PATO. Both of these programs are three-dimensional, finite-volume solvers that use unstructured meshes and 21st century programming paradigms to allow for efficient parallel simulations. FIAT and Icarus are also used for TPS sizing purposes. Today, these traditional tools are being supplemented with computational materials models at the atomistic level. The scales of interest range from computational chemistry (Density Functional Theory [DFT]), to atomistic simulations (Molecular Dynamics [MD]), to the microscale with the Porous Microstructure Analysis (PuMA) software that was recently awarded the 2022 NASA Software of the Year award. Finally, thermo-structural modeling is also of interest to the TPS Materials branch and done using commercial tools such as MSC MARC, MENTAT, NASTRAN and PATRAN. The present talk will also link the use of these computational tools to current NASA missions and projects associated with challenging and complex vehicles entries/reentries.

materials modeling

Ndarts

Ndarts software provides algorithms for computing quantities associated with the dynamics of articulated, rigid-link, multibody systems. It is designed as a general-purpose dynamics library that can be used for the modeling of robotic platforms, space vehicles, molecular dynamics, and other such applications. The architecture and algorithms in Ndarts are based on the Spatial Operator Algebra (SOA) theory for computational multibody and robot dynamics developed at JPL. It uses minimal, internal coordinate models. The algorithms are low-order, recursive scatter/ gather algorithms. In comparison with the earlier Darts++ software, this version has a more general and cleaner design needed to support a larger class of computational dynamics needs. It includes a frames infrastructure, allows algorithms to operate on subgraphs of the system, and implements lazy and deferred computation for better efficiency. Dynamics modeling modules such as Ndarts are core building blocks of control and simulation software for space, robotic, mechanism, bio-molecular, and material systems modeling.

Jain, Abhinandan

Photonic Interrogation and Control of Nano Processes

My research activities for the summer of 2003 consisted of two projects: One project was concerned with determining a method for predicting the static and dynamic assembly properties of nano-structures using laser tweezers. The other project was to investigate the generation of Laguerre-Gaussian modes using a spatial light modulator incorporated into an optical tweezers system. Concerning the first project, I initially pursued the approach suggested by my NASA colleague Dr. Art Decker. This approach involved mimicking the model of the structure of atomic nucleus for the assembly of 1 to 100 atoms using allowed quadruple transitions induced by orbital angular momentums of a Laguerre- Gaussian (Doughnut) laser mode. After realizing the inaptness of the nuclear model with the nanostructure model as far as the binding forces and transitions were concerned, I focused on using quantum dot modei. This model was not attuned also for the host lattice influences the electronic structure of the quantum dot. Thus one other option that I decided to pursue was the approach of molecular quantum mechanics. In this approach the nanostructure is treated as a large (10-100 nm) molecule constructed from single element or multi-elements. Subsequent to consultation with Dr. Fred Morales, a chemical engineer at NASA GRC, and Dr. David Ball, a computational chemist at Cleveland State University, I acquired a molecular-quantum computation software, Hyperchem 7.0. This software allows simulation of different molecular structures as far as their static and dynamic behaviors are concerned. The time that I spent on this project was about eight weeks. Once this suitable approach was identified, I realized the need to collaborate with a computational quantum chemist to pursue searching for stable nanostructures in the range of 10-100 nm that we can be assembled using laser tweezers. The second project was about generating laser tweezers that possess orbital angular momentum. As shown, we were able to generate laser tweezers modes of different orbital angular momentum using a spatial light modulator incorporated into a laser tweezers system. The motivation for investigating these types of modes stems from being able to spin particles at high speeds and also to orient two particles in separate traps and then join them together. Also, there has been recent intense interest on fundamental physics research on orbital angular momentum of light. The fact that circularly polarized light may have associated with it angular momentum that relates to the spin of individual photons (spin 0 for the plane polarized light, spin +1 for the right-circularly polarized light and spin -1 for the left-circularly polarized light) was first demonstrated by Beth in 1936. Orbital angular momentum is, however, distinct from spin in that the spin angular momentum of light is intrinsically linked to the behavior of the electric field in the light whereas orbital angular momentum is a consequence of inclined wavefronts. In 1992 L. Allen, et al showed that the Laguerre-Gaussian (LG) modes could possess well-defined orbital angular momentum that can exceed 1 planck's constant, i.e. l plancks constant per photon, where l is the azimuthal index of the mode.

Jassemnejad, Baha

Modeling Molecules

The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

Source record

High-Resolution Spectroscopic Database for the NASA Earth Observing System Program

The purpose of this project is to develop and enhance the HITRAN molecular spectroscopic database and associated software to support the observational programs of the Earth Observing System (EOS). In particular, the focus is on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The data requirements of these programs in terms of spectroscopy are varied, but usually call for additional spectral parameters or improvements to existing molecular bands. In addition, cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use of HITRAN functional to the EOS program.

Rothman, Laurence S.

High Resolution Spectroscopic Database for the NASA Earth Observing System Program

The purpose of this project has been to develop and enhance the HITRAN molecular spectroscopic database and associated software to support the observational programs of the Earth Observing System (EOS). Emphasis has been on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The HITRAN program is also involved in the Ozone Monitoring Experiment (OMI). The data requirements of these programs in terms of spectroscopy are varied with respect to constituents being observed, required remote-sensing parameters, and spectral coverage. A general requisite is for additional spectral parameters and improvements to existing molecular bands sufficient for the simulation of the observations leading to retrieval of the atmospheric state. In addition, cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use of HITRAN functional to the EOS program.

Rothman, Laurence

High-Resolution Spectroscopic Database for the NASA Earth Observing System Program

The purpose of this project is to develop and enhance the HITRAN molecular spectroscopic database and associated software to support the observational programs of the Earth Observing System (EOS). In particular, the focus is on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The HITRAN program is also involved in the Ozone Monitoring Experiment (OMI). The data requirements of these programs in terms of spectroscopy are varied with respect to constituents being observed, required remote-sensing parameters, and spectral coverage. A general requisite is for additional spectral parameters and improvements to existing molecular bands sufficient for the simulation of the observations leading to retrieval of the atmospheric state. In addition, cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use of HITRAN functional to the EOS program.

Rothman, Laurence

High-Resolution Spectroscopic Database for the NASA Earth Observing System Program

The purpose of this project is to develop and enhance the HITRAN molecular spectroscopic database and associated - software to support the observational programs of the Earth observing System (EOS). In particular, the focus is on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The HITRAN program is also involved in the Ozone Monitoring Experiment (OMI). The data requirements of these programs in terms of spectroscopy are varied with respect to constituents being observed, required remote-sensing parameters, and spectral coverage. A general requisite is for additional spectral parameters and improvements to existing molecular bands sufficient for the simulation of the observations leading to retrieval of the atmospheric state. In addition cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use HITRAN functional to the EOS program.

Rothman, Laurence S.

Hierarchical Coupling of Molecular Dynamics and Micromechanics to Predict the Elastic Properties of Three-Phase and Four-Phase Silicon Carbide Composites

The results obtained from previously conducted molecular dynamics analysis of silicon carbide (-SiC (6H, 4H, & 2H-SiC), -SiC (3C SiC)), silicon and boron nitride, were utilized as inputs in the MAC/GMC micromechanics software to model and evaluate the elastic properties of three-phase SiC/BN/SiC and four-phase SiC/BN/Si/SiC composites. This method of analysis eliminates the need for back-calculation of the apparent properties of the base constituents from the measured ceramic matrix composites properties. The multiscale models are validated against the available data in literature.

Aluko, Olanrewaju

Molecular Dynamics Simulations of Silicon Carbide, Boron Nitride and Silicon for Ceramic Matrix Composite Applications

A comprehensive computational molecular dynamics study is presented for crystalline α-SiC (6H, 4H, and 2H SiC), β-SiC (3C SiC), layered boron nitride, amorphous boron nitride and silicon, the constituent materials for high-temperature SiC/SiC compositions. Large-scale Atomic/Molecular Parallel Simulator software package was used. The Tersoff Potential force field was utilized to evaluate their mechanical characteristics of most of the materials, and the Reax force field was used to model silicon when the Tersoff Potential did not provide accurate results. Their mechanical behaviors were evaluated at a strain rate of 10(exp 7)/s and the results agree with the experimental data in the literature. The results are foundational for linking constituent behavior to composite performance, particularly when test data is unavailable or suspect.

Aluko, Olanrewaju

Thermoplastic Matrix Composite Design for Cryotanks Using Multiscale Modeling and Bayesian Optimization

Designing lightweight, robust cryogenic storage tanks is critical for future launch vehicles, in-space propellant storage, and hydrogen powered aircraft. This work presents a multiscale modeling and Bayesian optimization framework for the design of thermoplastic matrix composite cryotanks. Molecular dynamics simulations are first used to determine temperature-dependent constituent properties for candidate thermoplastic matrices, which are homogenized to the lamina scale using NASA’s Multiscale Analysis Tool (NASMAT). These lamina properties, in combination with laminate family generation rules, are evaluated in HyperX structural optimization software to identify stacking sequences that meet all cryogenic load requirements. A Bayesian optimization framework is applied, with HyperX in the loop (via the HyperX API) to efficiently search across material and laminate design variables, yielding an optimized cryotank configuration with significant reductions in design cycle time compared to exhaustive search approaches.

thermoplastics

Large Eddy Simulation (LES) of Particle-Laden Temporal Mixing Layers

High-fidelity models of plume-regolith interaction are difficult to develop because of the widely disparate flow conditions that exist in this process. The gas in the core of a rocket plume can often be modeled as a time-dependent, high-temperature, turbulent, reacting continuum flow. However, due to the vacuum conditions on the lunar surface, the mean molecular path in the outer parts of the plume is too long for the continuum assumption to remain valid. Molecular methods are better suited to model this region of the flow. Finally, granular and multiphase flow models must be employed to describe the dust and debris that are displaced from the surface, as well as how a crater is formed in the regolith. At present, standard commercial CFD (computational fluid dynamics) software is not capable of coupling each of these flow regimes to provide an accurate representation of this flow process, necessitating the development of custom software. This software solves the fluid-flow-governing equations in an Eulerian framework, coupled with the particle transport equations that are solved in a Lagrangian framework. It uses a fourth-order explicit Runge-Kutta scheme for temporal integration, an eighth-order central finite differencing scheme for spatial discretization. The non-linear terms in the governing equations are recast in cubic skew symmetric form to reduce aliasing error. The second derivative viscous terms are computed using eighth-order narrow stencils that provide better diffusion for the highest resolved wave numbers. A fourth-order Lagrange interpolation procedure is used to obtain gas-phase variable values at the particle locations.

Bellan, Josette

Parallel Grand-Canonical Monte Carlo (ParaGrandMC) User’s Manual Version 2.0

This manual describes the commands and command line options for the Parallel Grand Canonical Monte Carlo version 2.0 (ParaGrandMC.2.0) simulation code. This is a highly scalable parallel FORTRAN 2003 code for simulating the thermodynamic evolution of materials at the atomic level, and predicting their thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is specifically designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces. In addition to performing Monte Carlo (MC) simulations, the code can also perform Molecular Dynamics (MD) and Langevin Dynamics (LD) simulations, which can be combined and interchanged with MC for faster and more efficient system evolution. A detailed description of the MC part of the code is provided in the NASA ParaGrandMC report: NASA/CR–2016-219202; http://www.sti.nasa.gov.

High performance computing

26th Space Simulation Conference Proceedings. Environmental Testing: The Path Forward

Topics covered include: A Multifunctional Space Environment Simulation Facility for Accelerated Spacecraft Materials Testing; Exposure of Spacecraft Surface Coatings in a Simulated GEO Radiation Environment; Gravity-Offloading System for Large-Displacement Ground Testing of Spacecraft Mechanisms; Microscopic Shutters Controlled by cRIO in Sounding Rocket; Application of a Physics-Based Stabilization Criterion to Flight System Thermal Testing; Upgrade of a Thermal Vacuum Chamber for 20 Kelvin Operations; A New Approach to Improve the Uniformity of Solar Simulator; A Perfect Space Simulation Storm; A Planetary Environmental Simulator/Test Facility; Collimation Mirror Segment Refurbishment inside ESA s Large Space; Space Simulation of the CBERS 3 and 4 Satellite Thermal Model in the New Brazilian 6x8m Thermal Vacuum Chamber; The Certification of Environmental Chambers for Testing Flight Hardware; Space Systems Environmental Test Facility Database (SSETFD), Website Development Status; Wallops Flight Facility: Current and Future Test Capabilities for Suborbital and Orbital Projects; Force Limited Vibration Testing of JWST NIRSpec Instrument Using Strain Gages; Investigation of Acoustic Field Uniformity in Direct Field Acoustic Testing; Recent Developments in Direct Field Acoustic Testing; Assembly, Integration and Test Centre in Malaysia: Integration between Building Construction Works and Equipment Installation; Complex Ground Support Equipment for Satellite Thermal Vacuum Test; Effect of Charging Electron Exposure on 1064nm Transmission through Bare Sapphire Optics and SiO2 over HfO2 AR-Coated Sapphire Optics; Environmental Testing Activities and Capabilities for Turkish Space Industry; Integrated Circuit Reliability Simulation in Space Environments; Micrometeoroid Impacts and Optical Scatter in Space Environment; Overcoming Unintended Consequences of Ambient Pressure Thermal Cycling Environmental Tests; Performance and Functionality Improvements to Next Generation Thermal Vacuum Control System; Robotic Lunar Lander Development Project: Three-Dimensional Dynamic Stability Testing and Analysis; Thermal Physical Properties of Thermal Coatings for Spacecraft in Wide Range of Environmental Conditions: Experimental and Theoretical Study; Molecular Contamination Generated in Thermal Vacuum Chambers; Preventing Cross Contamination of Hardware in Thermal Vacuum Chambers; Towards Validation of Particulate Transport Code; Updated Trends in Materials' Outgassing Technology; Electrical Power and Data Acquisition Setup for the CBER 3 and 4 Satellite TBT; Method of Obtaining High Resolution Intrinsic Wire Boom Damping Parameters for Multi-Body Dynamics Simulations; and Thermal Vacuum Testing with Scalable Software Developed In-House.

Packard, Edward A.

Rayleigh Scattering Diagnostic for Dynamic Measurement of Velocity Fluctuations in High Speed Jets

A flow diagnostic technique based on the molecular Rayleigh scattering of laser light is used to obtain dynamic density and velocity data in a high speed flow. The technique is based on analyzing the Rayleigh scattered light with a Fabry-Perot interferometer used in the static, imaging mode. An analysis is presented that established a lower bound for measurement uncertainty of about 20 m/sec for individual velocity measurements obtained in a 100 microsecond time interval. Software and hardware interfaces were developed to allow computer control of all aspects of the experiment and data acquisition. The signals from three photomultiplier tubes were simultaneously recorded using photon counting at a 10 kHz sampling rate and 10 second recording periods. Density and velocity data, including distribution functions and power spectra, taken in a Mach 0.8 free jet, are presented.

Seasholtz, Richard G.