Joshua D. Moore

Coarse-Grain Model Simulations of Nonequilibrium Dynamics in Heterogeneous Materials

A suite of computational tools is described for particle-based mesoscale simulations of the nonequilibrium dynamics of energetic solids, including mechanical deformation, phase transitions, and chemical reactivity triggered by shock or thermal loading. The method builds upon our recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics (DPD) that includes chemical reactions. To describe chemical reactivity, a coarse-grain particle equation-of-state was introduced into the constant-energy DPD variant that rigorously treats complex chemical reactions and the associated chemical energy release. As illustration of these developments, we present simulations of shock compression of an RDX crystal and its thermal decomposition under high temperatures. We also discuss our current efforts toward a highly scalable domain-decomposition implementation that extends applicability to micrometer-size simulations. With appropriate parametrization, the method is applicable to other materials whose dynamic response is driven by microstructural heterogeneities.

Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes

This work focuses on the dynamic properties and energetics of the protein/peptide drug during its transport through carbon nanotubes (CNTs). A systematic study was performed on the interaction between the peptide and the CNTs. In the molecular dynamics (MD) simulations, the protein/peptide molecule Zadaxin is observed to be encapsulated inside the nanotube after its spontaneous insertion and oscillates around the center of the tube, where the van der Waals interaction energy is observed to be a minimum. Furthermore, it is found by performing steered MD simulations that the pulling force applied to the peptide reaches a maximum value, which demonstrates the ability of the CNTs to trap protein/peptide drugs. Such effects, attributed to van der Waals interactions, can be influenced by varying the lengths and diameters of the CNTs. Longer nanotubes provide a broader area to trap the peptide, while smaller nanotubes are able to encapsulate the peptide with a deeper interaction energy well. This investigation provides insights into nanoscale pharmaceutical drug delivery devices.

Transition from single-file to Fickian diffusion for binary mixtures in single-walled carbon nanotubes

The transition from single-file diffusion to Fickian diffusion in narrow cylindrical pores is investigated for systems of rigid single-walled armchair carbon nanotubes, solvated with binary mixtures of Lennard-Jones fluids (Ar/Ne, Ar/Kr, and Ar/Xe). A range of effects is examined including the mixture concentration, the size ratio of the two components, and the nanotube diameter. The transition from single-file to Fickian diffusion in varying carbon nanotube diameters is analyzed in terms of the Fickian self-diffusivity and the single-file mobility of the mixture components. It is found that the single-file to Fickian carbon nanotube transition diameter is a unique property of the individual molecules diameter and remains unchanged regardless of the mixture composition. In applications of binary mixtures, each component may crossover from single-file to Fickian diffusion in a different carbon nanotube diameter, giving rise to bimodal diffusion in some nanotubes. This transition allows for one species to diffuse in single-file while the other diffuses by a Fickian mechanism, yielding orders of magnitude difference between the self-diffusional rates of the two molecules. This phenomenon might be further extended to alter the diffusional motion of molecules in nanoporous materials.

A coarse-grain force field for RDX: Density dependent and energy conserving

We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.

Parallel implementation of isothermal and isoenergetic Dissipative Particle Dynamics using Shardlow-like splitting algorithms

Abstract A parallel implementation of the Shardlow splitting algorithm (SSA) for Dissipative Particle Dynamics (DPD) simulations is presented. The isothermal and isoenergetic SSA implementations are compared to the DPD version of the velocity-Verlet integrator in terms of numerical stability and performance. The integrator stability is assessed by monitoring temperature, pressure and total energy for both the standard and ideal DPD fluid models. The SSA requires special consideration due to its recursive nature resulting in more inter-processor communication as compared to traditional DPD integrators. Nevertheless, this work demonstrates that the SSA exhibits stability over longer time steps that justify its regular use in parallel, multi-core applications. For the computer architecture used in this study, a factor of 10–100 speedup is achieved in the overall time-to-solution for isoenergetic DPD simulations and a 15–34 speedup is achieved for the isothermal DPD simulations.

Particle based multiscale modeling of the dynamic response of RDX

We used multiscale modeling to bridge the atomistic and microscale levels of description by coarse-graining hexahydro-1,3,5-trinitro-s-triazine (RDX) onto a single interaction site through forcematching, resulting in density-dependent potentials which span 0 to 10 GPa in bulk pressure. The resulting model reproduces several atomistic properties but cannot account for accurate energy exchange due to coarse-graining of the intramolecular degrees of freedom. To correct this, we account for momentum and energy transfer in mechanical shock treatments by utilizing constant energy dissipative particle dynamics (DPD-E). We present preliminary results for the parameterization of DPD-E for RDX via bulk simulations and mechanical shock loading, with results assessed by comparison to atomistic simulation.

Adsorption, X-ray Diffraction, Photoelectron, and Atomic Emission Spectroscopy Benchmark Studies for the Eighth Industrial Fluid Properties Simulation Challenge

The primary goal of the eighth industrial fluid properties simulation challenge was to test the ability of molecular simulation methods to predict the adsorption of organic adsorbates in activated carbon materials. The challenge focused on the adsorption of perfluorohexane in the activated carbon standard BAM-P109. Entrants were challenged to predict the adsorption of perfluorohexane in the activated carbon at a temperature of 273 K and at relative pressures of 0.1, 0.3, and 0.6. The relative pressure (P/Po) is defined as that relative to the bulk saturation pressure predicted by the fluid model at a given temperature (273 K in this case). The predictions were judged by comparison to a set of experimentally determined values, which are published here for the first time and were not disclosed to the entrants prior to the challenge. Benchmark experimental studies, described herein, were also carried out and provided to entrants in order to aid in the development of new force fields and simulation methods to be employed in the challenge. These studies included argon, carbon dioxide, and water adsorption in the BAM-P109 activated carbon as well as X-ray diffraction, X-ray microtomography, photoelectron spectroscopy, and atomic emission spectroscopy studies of BAM-P109. Several concurrent studies were carried out for the BAM-P108 activated carbon. These are included in the current manuscript for comparison.

The Eighth Industrial Fluids Properties Simulation Challenge

The goal of the eighth industrial fluid properties simulation challenge was to test the ability of molecular simulation methods to predict the adsorption of organic adsorbates in activated carbon materials. In particular, the eighth challenge focused on the adsorption of perfluorohexane in the activated carbon BAM-P109. Entrants were challenged to predict the adsorption in the carbon at 273 K and relative pressures of 0.1, 0.3, and 0.6. The predictions were judged by comparison with a benchmark set of experimentally determined values. Overall, good agreement and consistency were found between the predictions of most entrants.