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. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties.

Green-Kubo expressions for transport coefficients from dissipative particle dynamics simulations revisited

This article addresses the debate about the correct application of Green-Kubo expressions for transport coefficients from dissipative particle dynamics simulations. We demonstrate that the Green-Kubo expressions are valid provided that (i) the dynamic model conserves the physical property, whose transport is studied, and (ii) the fluctuations satisfy detailed balance. As a result, the traditional expressions used in molecular dynamics can also be applied to dissipative particle dynamics simulations. However, taking the calculation of the shear viscosity as a paradigmatic example, a random contribution, whose strength scales as 1/δt1/2, with δt the time-step, can cause difficulties if the stress tensor is not separated into the different contributions. We compare our expression to that of Ernst and Brito (M. H. Ernst and R. Brito, Europhys. Lett., 2006, 73, 183-189), which arises from a diametrically different perspective. We demonstrate that the two expressions are completely equivalent and find exactly the same result both analytically and numerically. We show that the differences are not due to the lack of time-reversibility but instead from a pre-averaging of the random contributions. Despite the overall validity of Green-Kubo expressions, we find that the Einstein-Helfand relations (D. C. Malaspina et al. Phys. Chem. Chem. Phys., 2023, 25, 12025-12040) do not suffer from the need to decompose the stress tensor and can readily be used with a high degree of accuracy. Consequently, Einstein-Helfand relations should be seen as the preferred method to calculate transport coefficients from dissipative particle dynamics simulations.

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. It accurately captures the response of RDX under a range of thermal loading conditions compared to atomistic simulations. In addition, the Hugoniot response of the CG model in the overdriven regime reasonably matches atomistic simulations and experiments. Exploiting the model's high computational efficiency, we investigate mesoscale systems involving millions of molecules and characterize size-dependent criticality of hotspots in RDX. The combination of accuracy and computational efficiency of our reactive model provides a tool for investigation of mesoscale phenomena, such as the role of microstructures and defects in the shock-to-deflagration transition, through particle-based simulation.

Transport coefficients from Einstein-Helfand relations using standard and energy-conserving dissipative particle dynamics methods

In this article we demonstrate that contrary to general belief, the standard Einstein-Helfand (EH) formulas are valid for the evaluation of transport coefficients of systems containing dissipative and random forces...

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 property carriers, 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. The mass exchange between mesoparticles is such that the mass of the mesoparticle remains unchanged after the transfer process and requires additional considerations regarding the coupling with other system properties such as the particle internal energy. The proof-of-concept work presented in this article is the first part of a two-part article series. In Part 1, the development of the GenDPDE-M theoretical framework and the derivation of the algorithm are presented in detail. Part 2 of this article series is targeted for practitioners, where applications, demonstrations, and practical considerations for implementing the GenDPDE-M method are presented and discussed.

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. In part 2 of this series, further verification and demonstrations of the GenDPDE-M method are presented for mesoparticles with embedded binary mixtures using the ideal gas (IG) and van der Waals (vdW) equation-of-state (EoS). The targeted readership of part 2 is toward practitioners, where applications and practical considerations for implementing the GenDPDE-M method are presented and discussed, including a numerical discretisztion algorithm for the equations-of-motion. The GenDPDE-M method is verified by reproducing the particle distributions predicted by Monte Carlo simulations for the IG and vdW fluids, along with several demonstrations under both equilibrium and non-equilibrium conditions. GenDPDE-M can be generally applied to multi-component mixtures and to other fundamental EoS, such as the Lennard-Jones or Exponential-6 models, as well as to more advanced EoS models such as Statistical Associating Fluid Theory.

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., Phys Chem Chem Phys, 2019, 21, 24891-24911) to include chemical reactivity, denoted GenDPDE-RX. GenDPDE-RX provides a means of simulating chemical reactivity at the micro- and mesoscales, while exploiting the attributes of density- and temperature-dependent many-body force fields, which include improved transferability and scalability compared to two-body pairwise models. The GenDPDE-RX formulation considers intra-particle reactivity via a coarse-grain reactor construct. Extent-of-reaction variables assigned to each coarse-grain particle monitor the temporal evolution of the prescribed reaction mechanisms and kinetics assumed to occur within the particle. Descriptions of the algorithm, equations of motion, and numerical discretization are presented, followed by verification of the GenDPDE-RX method through comparison with reaction kinetics theoretical model predictions. Demonstrations of the GenDPDE-RX method are performed using constant-volume adiabatic heating simulations of three different reaction models, including both reversible and irreversible reactions, as well as multistep reaction mechanisms. The selection of the demonstrations is intended to illustrate the flexibility and generality of the method but is inspired by real material systems that span from fluids to solids. Many-body force fields using analytical forms of the ideal gas, Lennard-Jones, and exponential-6 equations of state are used for demonstration, although application to other forms of equation of states is possible. Finally, the flexibility of the GenDPDE-RX framework is addressed with a brief discussion of other possible adaptations and extensions of the method.

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. P. Larentzos, A. D. Mackie, and J. K. Brennan, Phys. Chem. Chem. Phys. 21, 24891 (2019)]PPCPFQ1463-907610.1039/C9CP04404C, which has been formulated for an emerging class of density- and temperature-dependent coarse-grain models. In the original work, GenDPDE was formulated to ensure a fundamental link is maintained with the underlying physical system at the higher resolution scale. In this paper, we revisit the formulation of the GenDPDE method, and rederive the particle thermodynamics to ensure consistency at the opposing scale extreme, i.e., between the local thermodynamics in the mesoscopic systems and the corresponding macroscopic properties. We demonstrate this consistency by introducing unambiguous, physically meaningful definitions of the heat and work, which lead to the formulation of an alternative heat flow model that is analogous to Fourier's law of heat conduction. We present further analysis of the internal, unresolved degrees-of-freedom of the mesoparticles by considering the thermodynamics of an individual mesoparticle within the GenDPDE framework. Several key outcomes of the analysis include: (i) demonstration that the choice of the independent variables alters the particle thermodynamic description; (ii) demonstration that the mesoscopic thermodynamic transformations introduce additional terms of the order of the size of the local fluctuations, which prevent an unambiguous definition of both the heat and work; (iii) an emphasis on the importance of the choice of the proper estimators of the thermodynamic properties that are embedded in the chosen thermodynamic description; and (iv) a clearly defined path for determining any thermodynamic quantity dressed by the fluctuations. The further insight provided by this deeper analysis is useful for both readers interested in the GenDPDE theoretical framework, as well as readers interested in the practical ramifications of the analysis, namely, the alternative heat flow model.

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. Compared to the original DPDE method, the formulation of the generalised DPDE method requires a change in the independent variable from the particle internal energy to the particle entropy. As part of the re-formulation, the terms dressed particle entropy and the corresponding dressed particle temperature are introduced, which depict the many-body contributions in the local volume. The generalised DPDE method has similarities to the energy form of the smoothed dissipative particle dynamics method, yet fundamental differences exist, which are described in the manuscript. The basic dynamic equations are presented along with practical considerations for implementing the generalised DPDE method, including a numerical integration scheme based on the Shardlow-like splitting algorithm. Demonstrations and validation tests are performed using analytical equation-of-states for the van der Waals and Lennard-Jones fluids. Particle probability distributions are analysed, where excellent agreement with theoretical estimates is demonstrated. As further validation of the generalised DPDE method, both equilibrium and non-equilibrium simulation scenarios are considered, including adiabatic flash heating response and vapour-liquid phase separation.

Adsorption and Diffusion of C1 to C4 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 C₁ to C₄ 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. We use the TraPPE and Vujić-Lyubartsev force fields along with the Lorentz-Berthelot combining rules to describe adsorbate-adsorbate and adsorbate-adsorbent interactions. The performance of the force fields is assessed by comparing against experimental single-component adsorption isotherms of methane and ethane in microporous ZSM-5/35, which we measured as part of this work. We compare the adsorption isotherms and diffusivities of the adsorbed alkanes in the dual-porosity zeolite with those in microporous ZSM-5/35 and discern the specific behavior at each porosity scale on the overall adsorption, self-diffusion, and transport behavior in zeolites with dual micro/mesoporosities.

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 0.1, 0.3, and 0.6. The relative pressure (P/P_o) 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 (Panne and Thünemann 2010). 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-109. 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 to a benchmark set of experimentally determined values. Overall good agreement and consistency were found between the predictions of most entrants.

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

Several methods are used in sequence to determine the chemical potential of atomistic RDX in the solid and liquid phases, and its corresponding melting point. Results yield the thermodynamic melting point of 488.75 K at 1.0 atm.

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.

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. Chem. Phys. 120, 10896 (2004)] is applied to a polymer system to calculate nonbonded interactions. The inverse Boltzmann inversion method was used to parametrize the bonded and bond-angle bending interactions. Molecular dynamics simulations were performed, and the CG model exhibited a significantly lower modulus compared to the atomistic model at low temperature and high strain rate. In an attempt to improve the CG model performance, several other parametrization schemes were used to build other models from this base model. The first of these models included standard frictional forces through use of the constant-temperature dissipative particle dynamics method that improved the modulus, yet was not transferrable to higher temperatures and lower strain rates. Other models were built by increasing the attraction between CG beads through direct manipulation of the nonbonded potential, where an improvement of the stress response was found. For these models, two parametrization protocols that shifted the force to more attractive values were explored. The first protocol involved a uniform shift, while the other protocol shifted the force in a more localized region. The uniformly shifted potential greatly affected the structure of the equilibrium model as compared to the locally shifted potential, yet was more transferrable to different temperatures and strain rates. Further improvements in the coarse-graining protocol to generate models that more satisfactorily capture mechanical properties are suggested.

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. Parameters for the mSRP are determined from topological, structural, and thermodynamic considerations. The effectiveness of the mSRP in capturing entanglements is demonstrated by calculating the diffusion and mechanical properties of an entangled polymer melt.

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. Both the slit width and the surface interaction strongly influence the phase diagram, especially for the asymmetric systems. For the symmetric and slightly asymmetric diblock copolymer systems, the confinement primarily affects the orientation of the lamellar domains and only marginally influences the domain morphologies. These systems form parallel lamellar phases with different number of lamellae, and perpendicular and mixed lamellar phases. In a narrow portion of the phase diagram, these systems exhibit a parallel perforated lamellar phase, where further insight into the appearance of this phase is provided through free-energy calculations. The confined highly asymmetric diblock copolymer system shows, in addition to nanostructures with parallel and perpendicular cylinders, noncylindrical structures such as parallel lamellae and parallel perforated lamellae. The formation of the various confined nanostructures is further analyzed by calculating structural characteristics such as the mean square end-to-end distance of the diblock copolymers and the nematic order parameter.

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. For surfaces with nanopatterns, we also vary both the mutual area and location of the nanopatterns, where we consider nanopatterns on the opposing surfaces that are vertically (a) aligned, (b) staggered, and (c) partially staggered. In the case of planar slits without nanopatterns, we observe the formation of perpendicular and parallel lamellar phases with different numbers of lamellae. In addition, the symmetric diblock copolymers self-assemble into adsorbed layer and adsorbed layer-parallel lamellar phases and a mixed lamellar phase when the opposing surfaces of the planar slits are modeled by different types of wall beads. In the case of nanopatterned planar slits, we observe novel nanostructures and attempt to rationalize the diblock copolymer self-assembly on the basis of the behavior that we observed in the planar slits without nanopatterns. In particular, we investigate the applicability of predicting the structures formed in the nanopatterned slits by a superposition of the observed structures in slits without nanopatterns.

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. We first consider the relative stability of the parallel and perpendicular phases by applying shear to lamellar structures initially aligned parallel and perpendicular to the shear direction, respectively. The perpendicular lamellar phase persists for all shear rates investigated, whereas the parallel lamellar phase is only stable at low shear rates, and it becomes unstable at high shear rates. At the high shear rates, the parallel lamellar phase first transforms into an unstable diagonal lamellar phase; and upon further increase of the shear rate, the parallel lamellar phase reorients into a perpendicular alignment. We further determine the preferential alignment of the lamellar phases at low shear rate by performing the simulations starting from either the initial transverse lamellar structure or the disordered melt. Since the low shear-rate simulations are plagued by the unstable diagonal lamellar phases, we vary the system size to achieve the natural spacing of the lamellae in the simulation box. In such cases, the unstable diagonal lamellar phases disappear and lamellar phases adopt the preferential alignment, either parallel or perpendicular. In agreement with the experimental observations, the simulations show that the lamellar phase preferentially adopts the parallel orientation at low shear rates and the perpendicular orientation at high shear rates. The simulations further reveal that the perpendicular lamellar phase has lower internal energy than the parallel lamellar phase, whereas the entropy production of the perpendicular lamellar phase is higher with respect to the parallel lamellar phase. Values of the internal energy and entropy production for the unstable diagonal lamellar phases lie between the corresponding values for the parallel and perpendicular lamellar phases. These simulation results suggest that the relative stability of the parallel and perpendicular lamellar phases at low shear rates is a result of the interplay between competing driving forces in the system: (a) the system's drive to adopt a structure with the lowest internal energy and (b) the system's drive to stay in a stationary nonequilibrium state with the lowest entropy production.

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. RxDPD can be used to predict the polydispersity due to various effects, including solvents, additives, temperature, pressure, shear, and confinement. Extensions of the method to other polymer systems are straightforward, including grafted, cross-linked polymers, and block copolymers. To simulate polydispersity, the system contains full polymer chains and a single fractional polymer chain, i.e., a polymer chain with a single fractional DPD particle. The fractional particle is coupled to the system via a coupling parameter that varies between zero (no interaction between the fractional particle and the other particles in the system) and one (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the DPD equations of motion, accompanied by changes in the coupling parameter. The coupling-parameter changes are either accepted with a probability derived from the grand canonical partition function or governed by an equation of motion derived from the extended Lagrangian. The coupling-parameter changes mimic forward and reverse reaction steps, as in RxMC simulations.

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. We analyze the effects of the temperature, nanopore width, bulk pressure, and capillary condensation on the reaction equilibrium with respect to the reaction conversion, fluid structure, and self-diffusion coefficients. We show that the influence of the temperature, nanopore size, and capillary condensation on the confined reaction equilibrium is quite dramatic while the effect of the bulk pressure on the reaction equilibrium in the carbon slit nanopore is only moderate. This work is an extension of previous work by Turner et al. [J. Chem. Phys. 114, 1851 (2001)] on the confined reactive nitric oxide system.

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. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2 +3 H2 <-->2N H3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.

Dual control cell reaction ensemble molecular dynamics: A method for simulations of reactions and adsorption in porous materials

We present a simulation tool to study fluid mixtures that are simultaneously chemically reacting and adsorbing in a porous material. The method is a combination of the reaction ensemble Monte Carlo method and the dual control volume grand canonical molecular dynamics technique. The method, termed the dual control cell reaction ensemble molecular dynamics method, allows for the calculation of both equilibrium and nonequilibrium transport properties in porous materials such as diffusion coefficients, permeability, and mass flux. Control cells, which are in direct physical contact with the porous solid, are used to maintain the desired reaction and flow conditions for the system. The simulation setup closely mimics an actual experimental system in which the thermodynamic and flow parameters are precisely controlled. We present an application of the method to the dry reforming of methane reaction within a nanoscale reactor model in the presence of a semipermeable membrane that was modeled as a porous material similar to silicalite. We studied the effects of the membrane structure and porosity on the reaction species permeability by considering three different membrane models. We also studied the effects of an imposed pressure gradient across the membrane on the mass flux of the reaction species. Conversion of syngas (H2/CO) increased significantly in all the nanoscale membrane reactor models considered. A brief discussion of further potential applications is also presented.

Molecular simulation of the vapor-liquid phase behavior of Lennard-Jones mixtures in porous solids

We present vapor-liquid phase coexistence curves for binary fluid mixtures in a disordered porous solid. The porous material is modeled as a collection of randomly dispersed hard spheres. A variant of the Monte Carlo Gibbs ensemble method [J. K. Brennan and W. Dong, J. Chem. Phys. 116, 8948 (2002)] is used to simulate Lennard-Jones fluid mixtures at several porosities: 0.9, 0.95, and 0.975. Effects based on the size and the energetics of the mixture components are studied. Pressure-composition and pressure-density phase diagrams at reduced temperatures of 0.75 and 1.0 are reported. Compared to the bulk fluid behavior, dramatic shifts in the phase envelope were found for even highly porous structures. Both the Lennard-Jones size and energy mixture parameters were found to strongly influence the resulting shape of the phase envelope.

Molecular simulation of shocked materials using the reactive Monte Carlo method

We demonstrate the applicability of the reactive Monte Carlo (RxMC) simulation method [J. K. Johnson, A. Z. Panagiotopoulos, and K. E. Gubbins, Mol. Phys. 81, 717 (1994); W. R. Smith and B. Tríska, J. Chem. Phys. 100, 3019 (1994)] for calculating the shock Hugoniot properties of a material. The method does not require interaction potentials that simulate bond breaking or bond formation; it requires only the intermolecular potentials and the ideal-gas partition functions for the reactive species that are present. By performing Monte Carlo sampling of forward and reverse reaction steps, the RxMC method provides information on the chemical equilibria states of the shocked material, including the density of the reactive mixture and the mole fractions of the reactive species. We illustrate the methodology for two simple systems (shocked liquid NO and shocked liquid N2), where we find excellent agreement with experimental measurements. The results show that the RxMC methodology provides an important simulation tool capable of testing models used in current detonation theory predictions. Further applications and extensions of the reactive Monte Carlo method are discussed.

Impact of mobilized blood progenitor cell quality determined by the CFU-GM/CD34+ ratio on rapid engraftment after blood stem cell transplantation

To find a parameter to predict the quality of collected mobilized CD34+ blood as hemopoietic reconstituting cells, the ratio of CFU-GM to CD34+ cells was examined. One hundred six consecutive patients who underwent blood stem cell transplantation at the University of Rochester from 01/01/99 to 12/31/99 were examined retrospectively for the number of days to reach an absolute neutrophil count of 500 or 1000 cells/microl and an absolute platelet count of 20,000 or 50,000 cells/microl without transfusion support as measures of engraftment. Linear regression analyses were conducted to determine factors influencing engraftment. The number of CD34+ cells/kg and CFU-GM/kg correlated highly with the number of nucleated blood cells/kg. In this population, in which 90% of patients received >2 x 10(6) CD34+ cells/kg, neither the number of CD34+ cells/kg nor the number of CFU-GM/kg correlated with the time to engraftment as judged by neutrophil or platelet levels. In contrast, the lower the ratio of CFU-GM to CD34+ cells, the more rapid the reconstitution of platelets to 20,000/microl (P = 0.03) and 50,000/microl (P = 0.02). Thus, a lower ratio of the CFU-GM/CD34+ appended to reflect a greater number of hematopoietic reconstituting cells in the blood cell collection. The CFU-GM/CD34+ ratio is an apparent predictor of earlier platelet engraftment, suggesting that the ratio reflects the engraftment potential of mobilized donor progenitor cells.

Thrombotic thrombocytopenic purpura in pulmonary-renal syndromes

Thrombotic thrombocytopenic purpura pathologically consists of a thrombotic microangiopathy that classically spares lung tissues. We describe a case of TTP that presented as a pulmonary-renal syndrome. In reviewing the international literature, pulmonary involvement is not as rare as once was thought, and the diagnosis of TTP should be considered in the differential diagnosis of pulmonary-renal syndromes.