Results for “Molecular simulation” — Page 18

NASA NTRS2008

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Yamakov, Vesselin↗

NASA NTRS2008

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Saether, E.↗

NASA NTRS2006

NASA Tech Briefs, April 2006

The topics covered include: 1) Replaceable Sensor System for Bioreactor Monitoring; 2) Unitary Shaft-Angle and Shaft-Speed Sensor Assemblies; 3) Arrays of Nano Tunnel Junctions as Infrared Image Sensors; 4) Catalytic-Metal/PdO(sub x)/SiC Schottky-Diode Gas Sensors; 5) Compact, Precise Inertial Rotation Sensors for Spacecraft; 6) Universal Controller for Spacecraft Mechanisms; 7) The Flostation - an Immersive Cyberspace System; 8) Algorithm for Aligning an Array of Receiving Radio Antennas; 9) Single-Chip T/R Module for 1.2 GHz; 10) Quantum Entanglement Molecular Absorption Spectrum Simulator; 11) FuzzObserver; 12) Internet Distribution of Spacecraft Telemetry Data; 13) Semi-Automated Identification of Rocks in Images; 14) Pattern-Recognition Algorithm for Locking Laser Frequency; 15) Designing Cure Cycles for Matrix/Fiber Composite Parts; 16) Controlling Herds of Cooperative Robots; 17) Modification of a Limbed Robot to Favor Climbing; 18) Vacuum-Assisted, Constant-Force Exercise Device; 19) Production of Tuber-Inducing Factor; 20) Quantum-Dot Laser for Wavelengths of 1.8 to 2.3 micron; 21) Tunable Filter Made From Three Coupled WGM Resonators; and 22) Dynamic Pupil Masking for Phasing Telescope Mirror Segments.

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NASA NTRS2014

Multiscale Analysis of Structurally-Graded Microstructures Using Molecular Dynamics, Discrete Dislocation Dynamics and Continuum Crystal Plasticity

A multiscale modeling methodology is developed for structurally-graded material microstructures. Molecular dynamic (MD) simulations are performed at the nanoscale to determine fundamental failure mechanisms and quantify material constitutive parameters. These parameters are used to calibrate material processes at the mesoscale using discrete dislocation dynamics (DD). Different grain boundary interactions with dislocations are analyzed using DD to predict grain-size dependent stress-strain behavior. These relationships are mapped into crystal plasticity (CP) parameters to develop a computationally efficient finite element-based DD/CP model for continuum-level simulations and complete the multiscale analysis by predicting the behavior of macroscopic physical specimens. The present analysis is focused on simulating the behavior of a graded microstructure in which grain sizes are on the order of nanometers in the exterior region and transition to larger, multi-micron size in the interior domain. This microstructural configuration has been shown to offer improved mechanical properties over homogeneous coarse-grained materials by increasing yield stress while maintaining ductility. Various mesoscopic polycrystal models of structurally-graded microstructures are generated, analyzed and used as a benchmark for comparison between multiscale DD/CP model and DD predictions. A final series of simulations utilize the DD/CP analysis method exclusively to study macroscopic models that cannot be analyzed by MD or DD methods alone due to the model size.

Saether, Erik↗

NASA NTRS2019

Emergence of Simple Ion Channels by Self-Assembly of Short Peptides

As protocells transitioned from structures bound by membranes made of simple amphiphiles, such as fatty acids, to structures containing phospholipid membranes, they became nearly impermeable to charged species. Yet, the ability to transport ions across membranes was vital to regulating cellular volume, pH homeostasis, generating energy and sensing the environment. For this reason, life evolved ion channels, protein structures surrounding water-filled pores in the membrane that facilitated ion transport. In contemporary cells, ion channels are complex protein assemblies. Could the same function be carried out, even if less efficiently and selectively, by much simpler peptides at the origins of life? To answer this question, we turned to trichogen (GAIV), an 11-residue peptide that was found to permeabilize membrane, causing leakage of the vesicle content including ions. Since GAIV is synthesized non-gnomically, it represents as excellent model for the earliest, poorly optimized channels. Understanding the mechanism by which short peptides, such as GAIV, mediate ion transport across membranes provides crucial information on the emergence, structure and the mechanism of action of the earliest ion channels. In this study, we used extensive molecular dynamics (MD) simulations to investigate directly spontaneous assembly of GAIV peptide and its structural dynamics, the formation of an induced water pore across the membrane and consequently ion conduction through the membrane.

Wei, Chenyu↗

NASA NTRSDate not supplied

Interfacial thermodynamics of cryogenic fluids: The effect on non-condensable gas on fluid storage

Propellant tanks that contain cryogenic fluids (CFs) in low gravity conditions are usually pressurized with non-condensable (NC) gases for fast extraction. Unfortunately, the presence of NC gases causes CFs to exhibit higher boil-offs compared to pure CF systems. For optimal utilization of the cryogenic fuels, these higher boil-off rates must be minimized. Our goal is to quantify the effects NC gases have on the evaporation and condensation dynamics of CFs to develop strategies that mitigate the higher boil-offs. The hypothesis is that the NC gas accumulates around the CF’s liquid vapor interface in the Knudsen layer, creating a kinetic barrier for both evaporation and condensation. Testing this hypothesis with experimental methods is difficult due to the transient nature of the Knudsen layer, which is only a few nanometers thick. Furthermore, experimental capabilities are limited in low gravity conditions and extremely expensive. Accordingly, we approach this problem from a theoretical perspective. In this study, we employ molecular dynamics (MD) simulations to probe the interfacial mechanisms that affect CF’s evaporation and condensation at varying concentrations of NC gases. Specifically, we use nitrogen (N2) and oxygen (O2) as our CFs and neon (Ne) as our NC gas. Using MD simulations, we show that Ne accumulates at N2 liquid vapor interface across a wide range of Ne concentrations, thereby impeding mass transport of N2. Our simulations allow for direct computation of the molar flux as well as the mass accommodation coefficient (MAC) which can then be used as input parameters to continuum fluid dynamics (CFD) models for optimal storage tank design.

Michael Robert DeLyser↗

NASA NTRS2022

Resolving the fine structure in the energy landscapes of repeat proteins

Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.

Murilo N. Sanches↗

NASA NTRSDate not supplied

Influence of Microstructural Features on Austenite-Martensite Interfaces in NiTi Shape Memory Alloys

Shape memory alloys (SMAs) exhibit several unique thermomechanical properties due to a reversible martensitic phase transformation. A key aspect of this transformation is the austenite-martensite interface. Here we present a molecular dynamics (MD) simulation methodology to study the atomic-scale features of austenite-martensite interface migration under near-equilibrium conditions. In single crystals, the interfaces migrate rapidly with only a small thermodynamic driving force. In polycrystals, however, interface migration is significantly impeded due to the change in orientation relationship at grain boundaries and the stored elastic energy resulting from microstructural constraints. This behavior can be linked to several mechanisms associated with transformation width and hysteresis in SMAs, properties of great importance for applications involving actuation. Additionally, we will present preliminary MD simulation results on the influence of precipitates on the formation and migration of austenite-martensite interfaces.

Gabriel Plummer↗

NASA NTRSDate not supplied

Profiling of Mars Atmospheric Carbon Dioxide Isotopologues Using 2-Micron Orbiting Lidar

Mars atmospheric characterization is important for investigating the planet climate history and planning future missions. A feasibility study for implementing the 2-um lidar technology for measuring Martian atmospheric carbon dioxide isotopologues is presented in this paper. Instrument reconfigurations include transmitted wavelengths and detection for differential absorption lidar application using an orbiter platform. Spectral analysis focused on the major four carbon dioxide isotopologues using the 2035 nm wavelength range, which results in minimal interference from other molecular species. Lidar simulation indicated the capability of detecting 12C16O2, 13C16O2, and 18O12C16O near surface vertical profiles up to 20 km altitude. Sensing of 17O12C16O isotopologue is challenging due to lower abundance and Martian atmospheric dust. This orbiting lidar provides a valuable tool for future Mars missions.

Tamer F. Refaat↗

NASA NTRSDate not supplied

Influence of Microstructural Features on Austenite-Martensite Interfaces in NiTi Shape Memory Alloys

Shape memory alloys (SMAs) exhibit several unique thermomechanical properties due to a reversible martensitic phase transformation. A key aspect of this transformation is the austenite-martensite interface. Here we present a molecular dynamics (MD) simulation methodology to study the atomic-scale features of austenite-martensite interface migration under near-equilibrium conditions. In single crystals, the interfaces migrate rapidly with only a small thermodynamic driving force. In polycrystals, however, interface migration is significantly impeded due to the change in orientation relationship at grain boundaries and the stored elastic energy resulting from microstructural constraints. This behavior can be linked to several mechanisms associated with transformation width and hysteresis in SMAs, properties of great importance for applications involving actuation. Additionally, we will present preliminary MD simulation results on the influence of precipitates on the formation and migration of austenite-martensite interfaces.

Gabriel Plummer↗

NASA NTRSDate not supplied

Profiling of Mars Atmospheric Carbon Dioxide Isotopologues Using 2-Micron Orbiting Lidar

Mars atmospheric characterization is important for investigating the planet climate history and planning future missions. A feasibility study for implementing the 2-um lidar technology for measuring Martian atmospheric carbon dioxide isotopologues is presented in this paper. Instrument reconfigurations include transmitted wavelengths and detection for differential absorption lidar application using an orbiter platform. Spectral analysis focused on the major four carbon dioxide isotopologues using the 2035 nm wavelength range, which results in minimal interference from other molecular species. Lidar simulation indicated the capability of detecting 12C16O2, 13C16O2, and 18O12C16O near surface vertical profiles up to 20 km altitude. Sensing of 17O12C16O isotopologue is challenging due to lower abundance and Martian atmospheric dust. This orbiting lidar provides a valuable tool for future Mars missions.

Tamer F. Refaat↗

NASA NTRS2024

Molecules in Cool Stars: The A 2 Π − X 2 Σ + and the B 2 Σ + − X 2 Σ + Band Systems of CaCl

Cool red giant stars exhibit absorption bands of calcium monochloride (CaCl) in the optical region. In this work, the bands of CaCl corresponding to the A 2 Π − X 2 Σ + transition with v' ≤ 4 and v'' ≤ 4, and B 2 Σ + − X 2 Σ + transition with v' ≤ 2 and v'' ≤ 2 are rotationally analyzed with PGOPHER, a multipurpose program for simulating and fitting molecular spectra. All bands were analyzed using high-resolution absorption spectra collected at the National Solar Observatory in 1985, calibrated with atomic lines from a high-resolution emission spectrum obtained in a separate hollow cathode experiment. The results are compared with previous laser-induced fluorescence measurements. Overall, the accuracy of spectroscopic constants for the A2Π and B2Σ+ states is improved. Scaled transition dipole moment calculations were used to obtain line strengths. Line lists are provided with Einstein A coefficients and oscillator strengths, which can be used to determine CaCl stellar abundances. Additionally, isotope splittings allowed us to estimate band origins for the 40 Ca 37 Cl isotopologue based on band-head positions.

Léo Lavy↗

NASA NTRSDate not supplied

First-Principles Investigation of Phase Transitions in RuNb, RuTa, and Ru-Nb-Ta Ultrahigh Temperature Shape Memory Alloys

Ultrahigh temperature shape memory alloys (UHT-SMAs) have transition temperatures above 600 C, and they have found applications for sensing and actuating devices in aerospace industry. Among very few such UHT-SMAs currently known are Ru-based alloys such as RuNb and RuTa, whose martensite structures and phase transitions are totally different from those of NiTi-based SMAs and were poorly understood. In this work, we carried out a systematical study of RuNb using first-principles total energy calculations and molecular dynamics (MD) simulations. The transition paths and mechanisms in cubic → tetragonal →monoclinic transitions are revealed. and the transition sequence and martensitic transition temperatures are determined (MTTs) by evaluating the Gibbs free energies using thermodynamic integration. The calculated MTTs are in very good agreement with the experimental data. We found that the monoclinic phase at the second transition has the 𝑃21/m symmetry instead of experimentally identified 𝑃2/m. Our calculations demonstrate that RuTa has very similar phase transitions to those of RuTa. Furthermore, we studied the Ru0.5Nb0.25Ta0.25 ternary. Our results can explain the measured significant drop of MTT (~ 200 C) in the second transition for Ru0.5Nb0.25Ta0.25 compared with those of RuNb and RuTa, while in the first transition its MTT is between MTTs of RuNb and RuTa. The insights gained by this study and the verified ab initio methods for accurate MTT calculations can be applied to fast screen and quantitatively design novel UHT-SMAs having similar properties with desirable MTTs and much reduced cost.

Zhigang Wu↗

NASA NTRSDate not supplied

Multiscale Modeling of Fracture Strength in Fibrous Thermal Protection System Materials

This work presents a multiscale modeling approach to predict the fracture strength of fibrous Thermal Protection System (TPS) materials. The model assumes that system failure is initiated at the joints between individual fibers. We investigated three distinct TPS compositions: amorphous silica, alumina and aluminosilicate fibers. Molecular dynamics (MD) simulations were employed to determine the fracture strength values of these fiber joints for both material systems. These fracture strength values were then integrated into simulations of 3D randomly populated fiber structures, where tensile load transfer occurs through the fiber joints. These microscale properties are upscaled through a renormalization approach [1] to predict macroscale tensile strength of 3D random fiber networks, accounting for joint-dominated failure and effective load-bearing area. The study concludes by demonstrating the resulting strength variation as a function of material composition, fiber density, and morphology. We also show validation of results by comparing them against explicit fiber finite element (FE) modeling [2] where fiber joint fracture is represented by cohesive elements.

Jaehyun Cho↗

NASA NTRS1989

Perception of numerical methods in rarefied gasdynamics

The relationships between various numerical methods applied to problems in rarefied gasdynamics are discussed, with emphasis on conflicting viewpoints and computational requirements associated with physical simulation versus the numerical solution of the Boltzmann equation. The basic differences between the molecular dynamics and direct simulation methods are shown to affect their applicability to dense and rarefied flows. Methods for the probabilistic selection of representative collision in the direct simulation Monte Carlo method are reviewed. A method combining the most desirable features of the earlier methods is presented.

Bird, G. A.↗

NASA NTRS2020

Detectability of Molecular Signatures on TRAPPIST-1e through Transmission Spectroscopy Simulated for Future Space-based Observatories

Discoveries of terrestrial, Earth-sized exoplanets that lie within the habitable zone(HZ)of their host stars continu eto occur at increasing rates. Transit spectroscopy can potentially enable the detection of molecular signatures fromsuch worlds, providing an indication of the presence of an atmosphere and its chemical composition, includinggases potentially indicative of a biosphere. Such planets around nearby M-dwarf stars—such as TRAPPIST-1—provide a relatively good signal, high signal-to-noise ratio, and frequent transits for follow-up spectroscopy.However, even with these advantages, transit spectroscopy of terrestrial planets in the HZ of nearby M-stars willstill be a challenge. Herein, we examine the potential for future space observatories to conduct such observations,using a global climate model, a photochemical model, and a radiative transfer suite to simulate modern-Earth-likeatmospheric boundary conditions on TRAPPIST-1e. The detectability of biosignatures on such an atmosphere viatransmission spectroscopy is modeled for various instruments of the James Webb Space Telescope, Large UV/Optical/Infrared Surveyor, Habitable Exoplanet Observatory, and Origins. We show that only CO2at 4.3μm would be detectable at the>5σlevel in transmission spectroscopy, when clouds are included in our simulations.This is because the impact of clouds on scale height strongly limits the detectability of molecules in the atmosphere. Synergies between space- and ground-based spectroscopy may be essential in order to overcome these difficulties.

Daria Pidhorodetska↗

NASA NTRS2003

Numerical Studies of Properties of Confined Helium

We carry out state of the art simulations of properties of confined liquid helium near the superfluid transition to a degree of accuracy which allows to make predictions for the outcome of fundamental physics experiments in microgravity. First we report our results for the finite-size scaling behavior of heat capacity of superfluids for cubic and parallel-plate geometry. This allows us to study the crossover from zero and two dimensions to three dimensions. Our calculated scaling functions are in good agreement with recently measured specific heat scaling functions for the above mentioned geometries. We also present our results of a quantum simulation of submonolayer of molecular hydrogen deposited on an ideal graphite substrate using path-integral quantum Monte Carlo simulation. We find that the monolayer phase diagram is rich and very similar to that of helium monolayer. We are able to uncover the main features of the complex monolayer phase diagram, such as the commensurate solid phases and the commensurate to incommensurate transition, in agreement with the experiments and to find some features which are missing from the experimental analysis.

Manousakis, Efstratios↗

NASA NTRS1991

A simulation of the collapse and fragmentation of cooling molecular clouds

The application of the Smoothed Particle Hydrodynamics method to the fragmentation of rotating cloud and disk systems is described, allowing for molecular cooling due to H2 and CO. A novel approach to solving Poisson's equation for disklike structures which exploits the multigrid algorithm is also described. Numerical studies are presented which investigate the evolution of both rotating clouds and Maclaurin disks, in each case with both an isothermal equation of state and with molecular cooling. The results establish the influence of molecular cooling on the fragmentation of molecular clouds. The isothermal sequences, if they fragment at all, do so into far fewer lumps than the cooling sequences. This is not due to a cooling instability as such, but rather to the reduced thermal support. One of the sequences shows a remarkable similarity to the W49A star-forming region.

Monaghan, Joe J.↗