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Results for “polymer simulations, molecular dynamics”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Jaffe, Richard↗
NASA NTRS2002

The Stress-strain Behavior of Polymer-Nanotube Composites from Molecular Dynamics Simulations

Stress-strain curves of polymer-carbon nanotube composites are derived from molecular dynamics simulations of a single-walled carbon nanotube embedded in polyethylene. A comparison is made between the response to mechanical loading of a composite with a long, continuous nanotube (replicated via periodic boundary conditions) and the response of a composite with a short, discontinuous nanotube. Both composites are mechanically loaded in the direction of and transverse to the NT axis. The long-nanotube composite shows an increase in the stiffness relative to the polymer and behaves anisotropically under the different loading conditions. The short-nanotube composite shows no enhancement relative to the polymer, most probably because of its low aspect ratio. The stress-strain curves are compared with rule-of-mixtures predictions.

Frankland, S. J. V.↗
DOE OSTI2025

The Work of Mechanical Degradation in Elongating Polymer Melts

Molecular dynamics simulations are used to study the mechanical degradation of well-entangled polymer melts during uniaxial extensional flow. Simulations measure the transient rise in extensional stresses and relate them to the molecular alignment and scission of chain backbones. Intermolecular entanglements couple chain scission in space and time, making degradation sensitive to deformation history and strain rate in ways not displayed by dilute polymer solutions. The rate of chain scission is nonmonotonic and peaks at strains corresponding to the maximum extensibility of entanglement segments but prior to the full extension of chain backbones. We measure a specific work per scission event w* and decompose it into separate contributions associated with chain alignment, chemical bond breaking, and scission-induced plasticity. We find chain scission in melts requires activating plastic dissipation that is multiple orders of magnitude larger than the chemical work required to break a covalent backbone bond. Our findings underscore the critical need to consider bulk polymer mechanics and rheology in designing efficient mechanical degradation and mechanochemical processes.

36 MATERIALS SCIENCE↗
NASA NTRS2018

Molecular Dynamics Simulations of Liquid and Polymer Electrolytes for Energy Storage Devices

Advancing beyond current lithium-ion technology is necessary in order to enable energy storage devices for electric airplanes. Electrolyte stability is a key limiting factor, yet the design of improved electrolytes remains a formidable challenge. Molecular dynamics (MD) simulations are a powerful tool for studying electrolytes, since they can be used to evaluate structural, thermodynamic, and transport properties, and can provide molecular-level detail often inaccessible to experimental techniques. Our computational materials groups at the NASA Ames Research Center has developed models and methods to accurately simulate both liquid and polymer electrolytes.We report the results from atomistic MD simulations of several electrolyte materials, with lithium salts dissolved in ionic liquids, dimethoxyethane (DME), and polyethylene oxide (PEO). For improved accuracy, we employ polarizable models, where each atom is given an environment-dependent atomic dipole. The simulations accurately predict bulk transport properties, including viscosity, diffusion, and ionic conductivity, in quantitative agreement with available experimental data. Moreover, the simulations provide important insights into the solvation structure of the lithium ions.We also report the results from coarse-grained MD simulations of polyanion electrolytes. In order to more efficiently capture the longer length- and time-scales of these systems, we employ a generic bead-spring model. These simulations provide important insight into how the polymer chain architecture and ionic interaction strengths affect the ionic aggregation behavior and cation dynamics. Despite the simplicity of the model, the simulations yield qualitative agreement with experimental data for similar systems.

Abbott, Lauren J.↗
NASA NTRSDate not supplied

Building and Breaking Carbon Composites with REACTER

Carbon composites have become indispensable for aerospace and other high-performance applications, and a detailed picture of their morphology and failure mechanisms remains difficult to obtain through experiment. REACTER is a versatile computational modeling tool for atomistic molecular dynamics designed to model chemical reactions at the speed and length scales of classical force fields.1 In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites, carbon-fiber reinforced polymers (CFRP) and carbon nanotube (CNT) composites. Carbon fiber core morphologies were created by the method of Desai et al.,2 but using the advanced reaction constraints framework of REACTER, their proposed multistep procedure was reduced to a single uninterrupted molecular dynamics simulation. The carbon fiber filler was embedded into a polymer matrix by simulated in situ polymerization of several thermosetting resins, including bismaleimide and polyarylacetylene, to obtain the final CFRP model. To generate the second class of carbon composite, CNT networks were grown dynamically using the new ‘create atoms’ feature of REACTER, and similarly infiltrated with resin to obtain CNT composites. The resulting models were compared directly to experiment using simulated high resolution transmission electron microscopy and x-ray diffraction. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a reaction constraint on the total potential energy of the involved atoms.

Molecular Dynamics↗
NASA NTRS2004

[Using Molecular Simulations to Understand Complex Nanoscale Dynamic Phenomena in Polymer Solutions]

The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.

Smith, Grant↗
DOE OSTI2026

Solubilization of PET in binary mixtures of HFIP and DCM

The dissolution of polyethylene terephthalate (PET) is a critical step for a solvent-based process, yet it typically requires highly corrosive or toxic solvents. Here, we investigate the solubilization and conformational behavior of PET in binary mixtures of hexafluoro-2-propanol (HFIP) and dichloromethane (DCM) as a strategy to reduce HFIP usage while maintaining effective dissolution. Small-angle neutron scattering (SANS) measurements reveal that PET remains molecularly dissolved in HFIP/DCM mixtures up to 50 vol% DCM. Analysis of PET chain conformations shows a transition from Gaussian behavior at low HFIP fractions to more swollen chains at intermediate compositions, accompanied by a counter-intuitive minimum in the radius of gyration at 50% HFIP. Complementary SANS measurements of the binary solvents demonstrate that compositional heterogeneity is maximized at this same solvent composition, suggesting a direct coupling between solvent microstructure and polymer dimensions. Molecular dynamics simulations corroborate the experimental findings, revealing solvent domain formation, preferential solvation of PET by HFIP, and a “caging” effect arising from solvent heterogeneity that leads to polymer coil compaction. Together, these results provide molecular-level insight into polymer behavior in mixed solvent systems and establish HFIP/DCM mixtures as a promising, more sustainable solvent platform for the PET post-process.

Arifuzzaman, Arif [ORNL]↗
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 NTRSDate not supplied

Machine-Learned Committor Functions for Reactive Molecular Dynamics

Reactive molecular dynamics (MD) is a powerful tool for atomistic-scale modeling of a diverse range of chemical processes. However, scaling these simulations to large systems and long times scales remains a challenge because of the complexity of the potential energy function required. The authors previously developed a heuristic approach, called REACTER, that incorporates reactivity in MD simulations in a less general but much more computationally efficient manner. REACTER uses standard, fixed valence force fields as the underlying potentialenergy surface for describing all interatomic interactions but adds a procedure for enforcing user-defined reactions that occur when certain geometric constraints on relative atomic positions are satisfied. Further, these bonding changes can be accepted or rejected with a probability related tothe local thermal energy. This work seeks to generalize this approach by replacing the set of user defined geometric constraints and energetic criteria with a committor function that specifies the probability of a reaction occurring on the basis of the local atomic configuration. The committor function is a useful mathematical tool for modeling rare events but, unfortunately, is very difficult to compute for realistic systems in a general way. This work describes a method for approximating the committor function using a machine learning approach, specifically a deep neural network trained with data from reactive MD and DFT-based dynamics simulations. This network is coupled to the existing REACTER protocol, as implemented in the LAMMPS MD package, and used to make on-the-fly predictions of reaction probabilities without the more extensive user input previously required. The new method is demonstrated using the polymerization of polystyrene as a case study. Although very dependent on the quality and quantity of training data, machine-learned committor functions show promise as a method for incorporating reaction probability from higher level calculations into highly scalable MD simulations.

polymer simulations↗
NASA NTRSDate not supplied

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↗
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 NTRSDate not supplied

Predicting Char Yield of High-Temperature Resins

A simulation protocol is developed to predict the char yield of organic resins during high-temperature processing. Such in silico methods can help screen promising new formulations for advanced materials, but previously no chemistry-sensitive technique existed to predict the important experimental value of char yield. The method utilizes a reactive force field (ReaxFF) to model the chemical transformation of precursor monomers into carbonized structures during three processing stages: ramp-up to processing temperatures (~3000 K), pyrolysis, and quenching. Achieving good agreement with experimental char yields requires continuous removal of small byproduct molecules to mimic outgassing, and the application of high pressure to eliminate porosity and encourage graphitization. More than ten different resin chemistries are investigated, including arylacetylenes, cyanate esters, phthalonitriles, and polyimides, representing a diverse group of precursors with respect to initial cyclic content, heteroatoms and reactive groups. The protocol correctly predicts the relative char yield between the investigated chemistries and provides quantitative agreement with experimental values, especially for high char yield resins. The properties of the resins during processing are compared, including outgassing products, morphology of the final chemical configurations, cyclic content and mechanical properties.

polymer simulations, molecular dynamics↗