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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2017

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗
NASA NTRS2002

Computational Nanomechanics of Carbon Nanotubes and Composites

Nanomechanics of individual carbon and boron-nitride nanotubes and their application as reinforcing fibers in polymer composites has been reviewed with interplay of theoretical modeling, computer simulations and experimental observations. The emphasis in this work is on elucidating the multi-length scales of the problems involved, and of different simulation techniques that are needed to address specific characteristics of individual nanotubes and nanotube polymer-matrix interfaces. Classical molecular dynamics simulations are shown to be sufficient to describe the generic behavior such as strength and stiffness modulus but are inadequate to describe elastic limit and nature of plastic buckling at large strength. Quantum molecular dynamics simulations are shown to bring out explicit atomic nature dependent behavior of these nanoscale materials objects that are not accessible either via continuum mechanics based descriptions or through classical molecular dynamics based simulations. As examples, we discus local plastic collapse of carbon nanotubes under axial compression and anisotropic plastic buckling of boron-nitride nanotubes. Dependence of the yield strain on the strain rate is addressed through temperature dependent simulations, a transition-state-theory based model of the strain as a function of strain rate and simulation temperature is presented, and in all cases extensive comparisons are made with experimental observations. Mechanical properties of nanotube-polymer composite materials are simulated with diverse nanotube-polymer interface structures (with van der Waals interaction). The atomistic mechanisms of the interface toughening for optimal load transfer through recycling, high-thermal expansion and diffusion coefficient composite formation above glass transition temperature, and enhancement of Young's modulus on addition of nanotubes to polymer are discussed and compared with experimental observations.

Srivastava, Deepak↗
NASA NTRSDate not supplied

Semi-Empirical Interatomic Potential for Large-Scale Molecular Dynamics Simulation of Metal-Oxide Systems

Classical molecular dynamics (MD) simulation can be applied to systems containing billions of atoms during times up to microseconds. However, utilization of a large-scale MD simulation requires reliable but computationally cheap interatomic potentials. In the case of metallic systems, embedded atom method (EAM) and Finnis-Sinclair (FS) potentials are the reasonable choices, but their development for multicomponent alloys is a challenge. Addition of oxygen atoms makes the problem of developing semi-empirical potentials even more difficult because the long-range Coulomb interaction cannot be neglected, and different atoms have different charges which vary during MD relaxation such that a charge equilibration procedure should be applied every MD step. As results researchers tend to avoid simulating metal-oxide systems. In this talk, a new Finnis-Sinclair (FS) Ni-Co-Cr potential will be presented. Special attention will be paid to reproducing of the element melting temperatures and clustering. Next, a charge transfer ionic potential (CTIP) developed to simulate the NiO properties will be presented. This potential utilizes the Ni FS potential and accounts for the Coulomb interaction in the vicinity of oxygen atoms. Fitting of the CTIP parameters and FS potential functions describing the interaction with oxygen atoms to the available experimental and ab initio data will be discussed. Results of MD simulation of interaction of NiO particles with dislocations in Ni will be shown.

molecular dynamics simulation↗
NASA NTRS2020

Ultrafast Melting at Metal-Semiconductor Interfaces: A Molecular Dynamics Study

Quantifying the thermodynamics of interfacial melting is important for several applications such as laser machining and designing radiation hardened electronic devices. Due to the short time and length scales that are involved in the process, molecular simulations provide an ideal path for understating the interfacial melting phenomena. In this work we investigate tungsten (W) – silicon carbide (SiC) interfaces which are relevant in modern high-power electronic devices. Classical molecular dynamics simulations along with the two-temperature model (TTM) were used to study the radiation induced melting of the interface while a neural network-based machine learning framework was used to track the transient re-crystallization process. The damage endured by the semiconductor at the interface following the radiation event is discussed in detail while the re-crystallization of the metal is described in terms of the classical nucleation theory.

Ashwin Ravichandran↗
NASA NTRS1998

Nanoscale Etching and Indentation of Silicon(001) Surface with Carbon Nanotube Tips

The possibility of nanoscale etching and indentation of Si(001)(2x1) surface by (8,0) and (10,10) carbon nanotube tips is demonstrated, for the first time, by classical molecular dynamics simulations employing Tersoff's many-body potential for a mixed C/Si/Ge system. In the nanotube tip barely touching the surface scenario atomistic etching is observed, where as in the nanoindentation scenario nanotube tip penetrates the surface without much hindrance. The results are explained in terms of the relative strength of C-C, C-Si, and Si-Si bonds.

Dzegilenko, Fendor N.↗
NASA NTRSDate not supplied

REACTER 2.0: Quantum-Informed Reaction Constraints and Automated Interaction Typing

REACTER is a heuristic method for modeling chemical reactions in classical molecular dynamics simulations, implemented in LAMMPS as fix bond/react. The authors recently extended LAMMPS to support alphanumeric labels for atom types, bond types etc., which enables the pre- and post-reaction templates required by the REACTER protocol to be portable between different simulations and greatly simplifies the task of creating simulation-ready reaction templates. To further increase the generality of reaction templates, support for wildcard characters within atom types has been added, along with the automatic assignment of interaction types for new bonds, angles, etc. based on the involved atom types. In some cases, this feature can express a class of reactions with one pair of reaction templates, where previously dozens may have been required. 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, as well as a custom constraint that leverages LAMMPS’ powerful built-in variable framework. Other new features include variable support for various inputs (e.g., to allow reaction rates or cutoffs to be dependent on overall conversion), on-the-fly update of molecule IDs, and the ability to create new atoms positioned with respect to the reaction site. The new features are applied to modeling polymeric, thermosetting and composite materials, and advanced applications of the new reaction constraints are demonstrated. For example, REACTER is shown to accurately reproduce mechanically-induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a constraint on the total potential energy of the involved atoms.

polymer simulations↗
NASA NTRS1998

Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.

Srivastava, Deepak↗
NASA NTRS2001

Thermodynamic Behavior of Nano-sized Gold Clusters on the (001) Surface

We have studied thermal expansion of the surface layers of the hexagonally reconstructed Au (001) surface using a classical Molecular Dynamics (MD) simulation technique with an Embedded Atomic Method (EAM) type many-body potential. We find that the top-most hexagonal layer contracts as temperature increases, whereas the second layer expands or contracts depending on the system size. The magnitude of expansion coefficient of the top layer is much larger than that of the other layers. The calculated thermal expansion coefficients of the top-most layer are about -4.93 x 10(exp -5)Angstroms/Kelvin for the (262 x 227)Angstrom cluster and -3.05 x 10(exp -5)Angstroms/Kelvin for (101 x 87)Angstrom cluster. The Fast Fourier Transform (FFT) image of the atomic density shows that there exists a rotated domain of the top-most hexagonal cluster with rotation angle close to 1 degree at temperature T less than 1000Kelvin. As the temperature increases this domain undergoes a surface orientational phase transition. These predictions are in good agreement with previous phenomenological theories and experimental studies.

Paik, Sun M.↗
NASA NTRS2001

Thermal Expansion and Diffusion Coefficients of Carbon Nanotube-Polymer Composites

Classical molecular dynamics (MD) simulations employing Brenner potential for intra-nanotube interactions and van der Waals forces for polymer-nanotube interface have been used to investigate thermal expansion and diffusion characteristics of carbon nanotube-polyethylene composites. Addition of carbon nanotubes to polymer matrix is found to significantly increase the glass transition temperature Tg, and thermal expansion and diffusion coefficients in the composite above Tg. The increase has been attributed to the temperature dependent increase of the excluded volume for the polymer chains, and the findings could have implications in the composite processing, coating and painting applications.

Wei, Chengyu↗
NASA NTRS1998

Nanoscale Etching and Indentation of Silicon Surfaces with Carbon Nanotubes

The possibility of nanolithography of silicon and germanium surfaces with bare carbon nanotube tips of scanning probe microscopy devices is considered with large scale classical molecular dynamics (MD) simulations employing Tersoff's reactive many-body potential for heteroatomic C/Si/Ge system. Lithography plays a key role in semiconductor manufacturing, and it is expected that future molecular and quantum electronic devices will be fabricated with nanolithographic and nanodeposition techniques. Carbon nanotubes, rolled up sheets of graphene made of carbon, are excellent candidates for use in nanolithography because they are extremely strong along axial direction and yet extremely elastic along radial direction. In the simulations, the interaction of a carbon nanotube tip with silicon surfaces is explored in two regimes. In the first scenario, the nanotubes barely touch the surface, while in the second they are pushed into the surface to make "nano holes". The first - gentle scenario mimics the nanotube-surface chemical reaction induced by the vertical mechanical manipulation of the nanotube. The second -digging - scenario intends to study the indentation profiles. The following results are reported in the two cases. In the first regime, depending on the surface impact site, two major outcomes outcomes are the selective removal of either a single surface atom or a surface dimer off the silicon surface. In the second regime, the indentation of a silicon substrate by the nanotube is observed. Upon the nanotube withdrawal, several surface silicon atoms are adsorbed at the tip of the nanotube causing significant rearrangements of atoms comprising the surface layer of the silicon substrate. The results are explained in terms of relative strength of C-C, C-Si, and Si-Si bonds. The proposed method is very robust and does not require applied voltage between the nanotube tips and the surface. The implications of the reported controllable etching and hole-creating for nanolithography on silicon are discussed in detail.

Dzegilenko, Fedor N.↗
NASA NTRS1999

Nanomechanics of Carbon and CxByNz Nanotubes: Via a Quantum Molecular Dynamics Method

Nanomechanics of single-wall C, BN and BC$_3$ and B doped C nanotubes under axial compression and tension are investigated through a generalized tight-binding molecular dynamics (GTBMD) and {\it ab-initio} electronic structure methods. The dynamic strength of BN, BC$_3$ and B doped C nanotubes for small axial strain are comparable to each other. The main difference is in the critical strain at which structural collapse occurs. For example, even a shallow doping with B lowers the value of critical strain for C nanotubes. The critical strain for BN nanotube is found to be more than that for the similar C nanotube. Once the structural collapse starts to occur we find that carbon nanotubes irreversibly go into plastic deformation regime via the formation of tetrahedral (four-fold coordinated) bonds at the location of sharp pinches or kinks. This finding is considerably different from the classical MD (molecular dynamics) simulation results known so far. The energetics and electronic densities of states of the collapsed structures, investigated with {\it ab-initio) methods, will also be discussed.

Srivastava, Deepak↗
NASA NTRS2020

Molecular Simulations of Ultrafast Radiation Induced Melting at Metal-Semiconductor Interfaces

Understanding radiation induced ultrafast melting at material interfaces is essential in designing robust electronic devices for aviation/space applications and in laser machining. While it is difficult to achieve the spatial and temporal resolution required to quantify the phenomenon experimentally, simulations can provide the detailed mechanisms of the structural changes that happen during phase transition. In this work, we use molecular simulations to study the effect of radiation damage on silicon carbide (SiC) - tungsten (W) interfaces which is of interest in high power electronics. A multi-scale approach is involved wherein the reactions at the interfaces are quantified using ab-initio molecular dynamics (MD) simulations and classical MD simulations are employed to understand the structural and diffusional changes across the material interface. Finally, coarse-grained Lennard-Jones type models are used to study the larger scale mechanisms and structures obtained due to the induced damages. We show that the response of the material to radiation damage depends on factors such as energy of the incident radiation, thermal properties, and molecular structure of the material.

Ravichandran, Ashwin↗
NASA NTRS2008

State of the Art Assessment of Simulation in Advanced Materials Development

Advances in both the underlying theory and in the practical implementation of molecular modeling techniques have increased their value in the advanced materials development process. The objective is to accelerate the maturation of emerging materials by tightly integrating modeling with the other critical processes: synthesis, processing, and characterization. The aims of this report are to summarize the state of the art of existing modeling tools and to highlight a number of areas in which additional development is required. In an effort to maintain focus and limit length, this survey is restricted to classical simulation techniques including molecular dynamics and Monte Carlo simulations.

Wise, Kristopher E.↗
NASA NTRS2003

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗
NASA NTRS1973

Equilibrium properties of a one-dimensional kinetic system.

One-dimensional systems of N = 500 and 250 particles in equilibrium are numerically simulated utilizing the method of molecular dynamics. Periodic boundary conditions are imposed. The classical two-body interaction potential is short range, repulsive and has a corresponding finite force. The equations of state are determined for densities both less and greater than one. Corresponding theoretical isochores are determined from models based on nearest-neighbor interactions and on a truncated virial expansion, and a comparison is made with the experimental isochores. Time independent radial distributions are constructed numerically and discussed. A change of state from a solidlike state to a fluid-gas state based on the penetrability of the particles is predicted. The transition temperatures are estimated from the radial distribution functions and the nearest-neighbor model. Self-diffusion is observed and the corresponding constants are determined from the velocity autocorrelation functions.

Williams, J. H.↗
NASA NTRS2022

Building and Breaking Carbon Composites with REACTER

Carbon-based composites have become indispensable materials in aerospace and other high-performance applications, yet obtaining a detailed, nanoscale understanding of their morphology and failure mechanisms using only experimental methods remains a difficult challenge. REACTER is a versatile computational modeling tool for atomistic molecular dynamics simulations designed to model chemical reactions at the speed and length scales of classical force fields. In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites: carbon nanotube (CNT) composites and carbon fiber reinforced polymers (CFRP). A network of CNTs was grown dynamically using the new ‘create atoms’ feature of REACTER. The CNT filler was embedded into a polyarylacetylene (PAA) matrix by simulated in situ polymerization to obtain the final composite model. To generate the second class of carbon composite, fully carbonized (graphitic) carbon fiber morphologies were created by the method of Desai et al. [1], but using the advanced reaction constraints framework of REACTER. Two fiber models were created, representing a circular carbon fiber core and a flat surface, and similarly infiltrated with resin to obtain the final CFRP structure. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third order DFT-based tight-binding simulations, via a reaction constraint on the total potential energy of the involved atoms.

Polymer↗
NASA NTRSDate not supplied

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗
NASA NTRS1984

Computer simulation of surface and film processes

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

Tiller, W. A.↗