Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB).

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. We present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates.

A coarse-grain reactive model of RDX: Molecular resolution at the μm scale.

Predictive models for the thermal, chemical, and mechanical response of high explosives at extreme conditions are important for investigating their performance and safety. We introduce a particle-based, reactive model of 1,3,5-trinitro-1,3,5-triazinane (RDX) with molecular resolution utilizing generalized energy-conserving dissipative particle dynamics with reactions. The model is parameterized with respect to the data from atomistic molecular dynamics simulations as well as from quantum mechanical calculations, thus bridging atomic processes to the mesoscales, including microstructures and defects.

Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 2: Applications and Demonstrations.

We present the second part of a two-part paper series intended to address a gap in computational capability for coarse-grain particle modeling and simulation, namely, the simulation of phenomena in which diffusion via mass transfer is a contributing mechanism. In part 1, we presented a formulation of a dissipative particle dynamics method to simulate interparticle mass transfer, termed generalized energy-conserving dissipative particle dynamics with mass transfer (GenDPDE-M). In the GenDPDE-M method, the mass of each mesoparticle remains constant following the interparticle mass exchange.

Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 1: Theoretical Foundation and Algorithm.

An extension of the generalized energy-conserving dissipative particle dynamics method (GenDPDE) that allows mass transfer between mesoparticles via a diffusion process is presented. By considering the concept of the mesoparticles as , the complexity and flexibility of the GenDPDE framework were enhanced to allow for interparticle mass transfer under isoenergetic conditions, notated here as GenDPDE-M. In the formulation, diffusion is described via the theory of mesoscale irreversible processes based on linear relationships between the fluxes and thermodynamic forces, where their fluctuations are described by Langevin-like equations.

Generalized Energy-Conserving Dissipative Particle Dynamics with Reactions.

We present an extension of the generalized energy-conserving dissipative particle dynamics method (J. Bonet Avalos, et al., , 24891-24911) to include chemical reactivity, denoted GenDPDE-RX.

Generalized energy-conserving dissipative particle dynamics revisited: Insight from the thermodynamics of the mesoparticle leading to an alternative heat flow model.

Recently we introduced the generalized energy-conserving dissipative particle dynamics method (GenDPDE) [J. Bonet Avalos, M. Lísal, J.

Generalised dissipative particle dynamics with energy conservation: density- and temperature-dependent potentials.

We present a generalised, energy-conserving dissipative particle dynamics (DPDE) method appropriate for the non-isothermal simulation of particle interaction force fields that are both density- and temperature-dependent. A detailed derivation is formulated in a bottom-up manner by considering the thermodynamics of small systems with the appropriate consideration of the fluctuations. Connected to the local volume is a local density and corresponding local pressure, which is determined from an equation-of-state based force field that depends also on a particle temperature.

Dissipative particle dynamics with reactions: Application to RDX decomposition.

We present a general, flexible framework for a constant-energy variant of the dissipative particle dynamics method that allows chemical reactions (DPD-RX). In our DPD-RX approach, reaction progress variables are assigned to each particle that monitor the time evolution of an extent-of-reaction associated with the prescribed reaction mechanisms and kinetics assumed to occur within the particle, where chemistry can be modeled using complex or reduced reaction mechanisms. We demonstrate our DPD-RX method by considering thermally initiated unimolecular decomposition of the energetic material, cyclotrimethylene trinitramine (RDX), into a molecular gas mixture.

Adsorption and Diffusion of C to C Alkanes in Dual-Porosity Zeolites by Molecular Simulations.

We employ grand canonical Monte Carlo and molecular dynamics simulations to systematically study the adsorption and diffusion of C to C alkanes in hierarchical ZSM-5 zeolite with micropores (∼1 nm) and mesopores (>2 nm). The zeolite is characterized by a large surface area of active sites on the microporous scale with high permeability and access to the active sites, which arises from the enhanced transport at the mesoporous scale. We model this zeolite as a microporous Na-exchanged alumino-sillicate zeolite ZSM-5/35 (Si/Al = 35) in which cylindrical mesopores with a diameter of 4 nm have been built by deleting atoms accordingly.

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 (Panne and Thünemann 2010). 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.

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-109. Entrants were challenged to predict the adsorption in the carbon at 273 K and relative pressures of 0.

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.

Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model.

We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference.

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.

Exploring the ability of a multiscale coarse-grained potential to describe the stress-strain response of glassy polystyrene.

A new particle-based bottom-up method to develop coarse-grained models of polymers is presented and applied to polystyrene. The multiscale coarse-graining (MS-CG) technique of Izvekov et al. [J.

An enhanced entangled polymer model for dissipative particle dynamics.

We develop an alternative polymer model to capture entanglements within the dissipative particle dynamics (DPD) framework by using simplified bond-bond repulsive interactions to prevent bond crossings. We show that structural and thermodynamic properties can be improved by applying a segmental repulsive potential (SRP) that is a function of the distance between the midpoints of the segments, rather than the minimum distance between segments. The alternative approach, termed the modified segmental repulsive potential (mSRP), is shown to produce chain structures and thermodynamic properties that are similar to the softly repulsive, flexible chains of standard DPD.

Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.

Numerical integration schemes based upon the Shardlow-splitting algorithm (SSA) are presented for dissipative particle dynamics (DPD) approaches at various fixed conditions, including a constant-enthalpy (DPD-H) method that is developed by combining the equations-of-motion for a barostat with the equations-of-motion for the constant-energy (DPD-E) method. The DPD-H variant is developed for both a deterministic (Hoover) and stochastic (Langevin) barostat, where a barostat temperature is defined to satisfy the fluctuation-dissipation theorem for the Langevin barostat. For each variant, the Shardlow-splitting algorithm is formulated for both a velocity-Verlet scheme and an implicit scheme, where the velocity-Verlet scheme consistently performed better.

Adsorptive behavior of CO2, CH4 and their mixtures in carbon nanospace: a molecular simulation study.

Using molecular simulation, four types of nanoporous carbons are examined as adsorbents for the separation of CO(2)/CH(4) mixtures at ambient temperature and pressures up to 10 MPa. First, the adsorption selectivity of CO(2) is investigated in carbon slit pores and single-walled carbon nanotube bundles in order to find the optimal pore dimensions for CO(2) separation. Then, the adsorptive properties of the optimized slit pore and nanotube bundle are compared with two realistic nanoporous carbon models: a carbon replica of zeolite Y and an amorphous carbon.

Self-assembly of lamellar- and cylinder-forming diblock copolymers in planar slits: insight from dissipative particle dynamics simulations.

We present a dissipative particle dynamics simulation study on nanostructure formation of symmetric and asymmetric diblock copolymers confined between planar surfaces. We consider symmetric and slightly asymmetric diblock copolymers that form lamellar nanostructures in the bulk, and highly asymmetric diblock copolymers that form cylindrical nanostructures in the bulk. The formation of the diblock copolymer nanostructures confined between the planar surfaces is investigated and characterized by varying the separation width and the strength of the interaction between the surfaces and the diblock copolymers.

Self-assembly of symmetric diblock copolymers in planar slits with and without nanopatterns: insight from dissipative particle dynamics simulations.

We present a dissipative particle dynamics simulation study on the formation of nanostructures of symmetric diblock copolymers confined between planar surfaces with and without nanopatterns. The nanopatterned surface is mimicked by alternating portions of the surface that interact differently with the diblock copolymers. The formation of the diblock-copolymer nanostructures confined between the planar surfaces is investigated and characterized by varying the separation width and the strength of the interaction between the surfaces and the diblock copolymers.

Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics with reaction ensemble Monte Carlo. II. Supramolecular diblock copolymers.

We present an alternative formulation of the reaction ensemble dissipative particle dynamics (RxDPD) method [M. Lisal, J. K.

Alignment of lamellar diblock copolymer phases under shear: insight from dissipative particle dynamics simulations.

Sheared self-assembled lamellar phases formed by symmetrical diblock copolymers are investigated through dissipative particle dynamics simulations. Our intent is to provide insight into the experimental observations that the lamellar phases adopt parallel alignment at low shear rates and perpendicular alignment at high shear rates and that it is possible to use shear to induce a transition from the parallel to perpendicular alignment. Simulations are initiated either from lamellar structures prepared under zero shear where lamellae are aligned into parallel, perpendicular, or transverse orientations with respect to the shear direction or from a disordered melt obtained by energy minimization of a random structure.

Mesoscale simulation of polymer reaction equilibrium: combining dissipative particle dynamics with reaction ensemble Monte Carlo. I. Polydispersed polymer systems.

We present a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics (RxDPD) method, for studying reaction equilibrium of polymer systems. The RxDPD method combines elements of dissipative particle dynamics (DPD) and reaction ensemble Monte Carlo (RxMC), allowing for the determination of both static and dynamical properties of a polymer system. The RxDPD method is demonstrated by considering several simple polydispersed homopolymer systems.

Chemical reaction equilibrium in nanoporous materials: NO dimerization reaction in carbon slit nanopores.

We present a molecular-level simulation study of the effects of confinement on chemical reaction equilibrium in nanoporous materials. We use the reaction ensemble Monte Carlo (RxMC) method to investigate the effects of temperature, nanopore size, bulk pressure, and capillary condensation on the nitric oxide dimerization reaction in a model carbon slit nanopore in equilibrium with a bulk reservoir. In addition to the RxMC simulations, we also utilize the molecular-dynamics method to determine self-diffusion coefficients for confined nonreactive mixtures of nitric oxide monomers and dimers at compositions obtained from the RxMC simulations.

Reaction ensemble molecular dynamics: direct simulation of the dynamic equilibrium properties of chemically reacting mixtures.

A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics.