Effects of molecular siting and adsorbent heterogeneity on the ideality of adsorption equilibria

The ideal adsorbed solution (IAS) theory is the benchmark for the prediction of mixed-gas adsorption equilibria from pure-component isotherms. In this work, we use atomistic grand canonical Monte Carlo simulations to test the effects of molecular siting and adsorbent energetic heterogeneity on the applicability of the IAS theory. Pure-component isotherms generated by atomistic simulation are used to predict binary isobaric isotherms using the IAS theory. These predicted isotherms are compared with those obtained by a full atomistic simulation of the binary mixture. Binary mixtures of argon, methane, and CF4 in silicalite are found to obey IAS theory, while benzene/methane and cyclohexane/methane in silicalite are nonideal. The mixture of argon and CF4 is ideal despite the large difference in the sizes of the two species. This contradicts previous hypotheses in the literature, which state that mixtures of species of unequal size do not adsorb ideally. The nonideal behavior of the benzene/methane and cyclohexane/methane systems occurs because of adsorbent heterogeneity in these systems, which depends on both sorbent and sorbate. In addition, we use a lattice gas model with parameters derived from atomistic simulation to demonstrate analytically that a sufficiently energetically heterogeneous adsorbent will result in the breakdown of IAS theory even in the absence of interactions between sorbates.     

Multiscale coarse-graining of monosaccharides

A systematic multiscale coarse-graining (MS-CG) algorithm is applied to build coarse-grained models for monosaccharides in aqueous solution. The methodology is demonstrated for the example of alpha-D-glucopyranose. The nonbonded interactions are directly derived from the force-matching approach, whereas the bonded interactions are obtained through Boltzmann statistical analyses of the underlying atomistic trajectory. The MS-CG model is shown to reproduce many structural and thermodynamic properties in the constant NPT ensemble. Although the model is derived at a single temperature, pressure, and concentration, it is shown to be reasonably transferable to other thermodynamic states. In this model, long-range interactions are effectively mapped into short-range forces with a moderate cutoff and are evaluated by table look-up. As a result, molecular dynamics employing the MS-CG model is approximately 3 orders of magnitude more efficient than its atomistic counterpart. Consequently, the model is particularly suitable for simulating carbohydrate systems at large length and long time scales. Results for an alpha-(1-->4)-d-glucan with 14 glucose units are also presented, demonstrating that the MS-CG algorithm is also applicable to the coarse-graining of other saccharide systems.     

Fluctuating hydrodynamics for multiscale simulation of inhomogeneous fluids: mapping all-atom molecular dynamics to capillary waves

We introduce a multiscale framework to simulate inhomogeneous fluids by coarse-graining an all-atom molecular dynamics (MD) trajectory onto sequential snapshots of hydrodynamic fields. We show that the field representation of an atomistic trajectory is quantitatively described by a dynamic field-theoretic model that couples hydrodynamic fluctuations with a Ginzburg-Landau free energy. For liquid-vapor interfaces of argon and water, the parameters of the field model can be adjusted to reproduce the bulk compressibility and surface tension calculated from the positions and forces of atoms in an MD simulation. These optimized parameters also enable the field model to reproduce the static and dynamic capillary wave spectra calculated from atomistic coordinates at the liquid-vapor interface. In addition, we show that a density-dependent gradient coefficient in the Ginzburg-Landau free energy enables bulk and interfacial fluctuations to be controlled separately. For water, this additional degree of freedom is necessary to capture both the bulk compressibility and surface tension emergent from the atomistic trajectory. The proposed multiscale framework illustrates that bottom-up coarse-graining and top-down phenomenology can be integrated with quantitative consistency to simulate the interfacial fluctuations in nanoscale transport processes.     

Molecular latent space simulators

Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales. Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing configurational or dynamical coarse-graining of the state space. The learned kinetic models enable the efficient generation of dynamical trajectories over vastly longer time scales than are accessible by MD, but the discretization of configurational space and/or absence of a means to reconstruct molecular configurations precludes the generation of continuous atomistic molecular trajectories. We propose latent space simulators (LSS) to learn kinetic models for continuous atomistic simulation trajectories by training three deep learning networks to (i) learn the slow collective variables of the molecular system, (ii) propagate the system dynamics within this slow latent space, and (iii) generatively reconstruct molecular configurations. We demonstrate the approach in an application to Trp-cage miniprotein to produce novel ultra-long synthetic folding trajectories that accurately reproduce atomistic molecular structure, thermodynamics, and kinetics at six orders of magnitude lower cost than MD. The dramatically lower cost of trajectory generation enables greatly improved sampling and greatly reduced statistical uncertainties in estimated thermodynamic averages and kinetic rates.

Latent space simulators learn kinetic models for atomistic simulations and generate novel trajectories at six orders of magnitude lower cost.     

Multiscale coarse-graining of ionic liquids

A recently developed multiscale coarse-graining (MS-CG) approach for obtaining coarse-grained force fields from fully atomistic molecular dynamics simulation is applied to the challenging case of the EMIM+NO3- ionic liquid. The force-matching in the MS-CG methodology is accomplished with an explicit separation of bonded and nonbonded forces. While the nonbonded forces are adopted from this force-matching approach, the bonded forces are obtained from fitting the statistical configurational data from the atomistic simulations. The many-body electronic polarizability is also successfully broken into effective pair interactions. With a virial constraint fixing the system pressure, the MS-CG models rebuild satisfactory structural and thermodynamic properties for different temperatures. The MS-CG model developed from a modest atomistic simulation is therefore suitable for simulating much larger systems, because the coarse-grained models show significant time integration efficiency. This approach is expected to be general for coarse-graining other ionic liquids, as well as many other liquid-state systems. The limitations of the present coarse-graining procedure are also discussed.     

A multiscale coarse-graining method for biomolecular systems

A new approach is presented for obtaining coarse-grained (CG) force fields from fully atomistic molecular dynamics (MD) trajectories. The method is demonstrated by applying it to derive a CG model for the dimyristoylphosphatidylcholine (DMPC) lipid bilayer. The coarse-graining of the interparticle force field is accomplished by an application of a force-matching procedure to the force data obtained from an explicit atomistic MD simulation of the biomolecular system of interest. Hence, the method is termed a "multiscale" CG (MS-CG) approach in which explicit atomistic-level forces are propagated upward in scale to the coarse-grained level. The CG sites in the lipid bilayer application were associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic data. The resulting CG lipid bilayer model is shown to accurately reproduce the structural properties of the phospholipid bilayer.     

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials

The potential of mean force (PMF) with respect to coarse-grained (CG) coordinates is often calculated in order to study the molecular interactions in atomistic molecular dynamics (MD) simulations. The multiscale coarse-graining (MS-CG) approach enables the computation of the many-body PMF of an atomistic system in terms of the CG coordinates, which can be used to parameterize CG models based on all-atom configurations. We demonstrate here that the MS-CG method can also be used to analyze the CG interactions from atomistic MD trajectories via PMF calculations. In addition, MS-CG calculations at different temperatures are performed to decompose the PMF values into energetic and entropic contributions as a function of the CG coordinates, which provides more thermodynamic information regarding the atomistic system. Two numerical examples, liquid methanol and a dimyristoylphosphatidylcholine lipid bilayer, are presented. The results show that MS-CG can be used as an analysis tool, comparable to various free energy computation methods. The differences between the MS-CG approach and other PMF calculation methods, as well as the characteristics and advantages of MS-CG, are also discussed.     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.     

Co-primary thermolysis molecular modeling simulation of lignin and subbituminous coal via a reactive coarse-grained simplification

Co-pyrolysis of coal and biomass is one immediate approach to reduce net carbon dioxide emissions from heat and power generation. Interestingly there is often co-pyrolysis synergy, commonly enhancing tar and gas yields. To explore the synergy mechanisms requires the ability to predict yields and explore thermolysis of coal and biomass chemistry. The current state-of-knowledge allows individual yield predictions through mathematical modeling, and creation of large-scale molecular representations of lignin (as a biomass simplification) and coal. Yet there is no means of coupling these molecular representations and predicted yields. Here a reactive coarse-grained simulation is used to generate 2D lattice representations from complex large-scale subbituminous coal and generic hardwood lignin structural representations. The chemical percolation devolatilization (CPD) model was used to predict yields of chars and tars/gases during pyrolysis. Scripting within a molecular modeling environment generates the reactive 2D lattice in molecular modeling space and also simulates the primary thermolysis within the lattice to achieve the desired yields through a breaking of labile cross-links between “un-reactive” structural nodes. The approach is used to visualize the dynamic yield differentials between lignin and a subbituminous coal and to generate radical fragments that can be used to explore synergistic interactions. In this paper the coarse-graining and thermolysis processes are described.     

Coarse-graining: a procedure to generate equilibrated and relaxed models of amorphous polymers

We present a coarse-graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation-relaxation strategy previously developed to provide independent atomistic microstructures. The coarse-graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent groups of atoms, through distance, angle and dihedral distribution functions. The interaction energy between pairs of blobs was evaluated through a soft potential, whose parameters were derived from atomistic models. Three levels of coarse-graining that differ in the number of atoms included in the blob have been considered. The structural and energy-related properties calculated using the coarse-grained models developed in this study are in good agreement with those obtained using atomistic simulations.     

Development of a coarse-grained model for simulations of tridecanoin liquid-solid phase transitions

Novel coarse-grained models for molecular dynamics of tridecanoin melts are here proposed as results of a coarse-graining step procedure. The procedure is implemented to develop three coarse-grained models of increasing number of particle types from two to four. Force fields are computed by minimization of the deviations of appropriate distribution functions of the coarse-grained models from those of a reference atomistic one. Density, diffusivity and shear viscosity are computed by numerical simulation and compared with experimental values. The ability of each model to describe liquid-solid transitions is also analyzed. In particular, the model with four types of coarse-grained beads shows a transition from a liquid to a crystal phase.     

A continuum, O(N) Monte Carlo algorithm for charged particles

We introduce a Monte Carlo algorithm for the simulation of charged particles moving in the continuum. Electrostatic interactions are not instantaneous as in conventional approaches, but are mediated by a constrained, diffusing electric field on an interpolating lattice. We discuss the theoretical justifications of the algorithm and show that it efficiently equilibrates model electrolytes and polar fluids. In order to reduce lattice artifacts that arise from the interpolation of charges to the grid we implement a local, dynamic subtraction algorithm. This dynamic scheme is completely general and can also be used with other Coulomb codes, such as multigrid based methods.     

Modeling molecular transport in slit pores

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1-1 nm(-3). Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid-fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation.     

Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics

We present a new coarse-grained (CG) model of cholesterol (CHOL) for the electrostatic-based ELBA force field. A distinguishing feature of our CHOL model is that the electrostatics is modeled by an explicit point dipole which interacts through an ideal vacuum permittivity. The CHOL model parameters were optimized in a systematic fashion, reproducing the electrostatic and nonpolar partitioning free energies of CHOL in lipid/water mixtures predicted by full-detailed atomistic molecular dynamics simulations. The CHOL model has been validated by comparison to structural, dynamic and thermodynamic properties with experimental and atomistic simulation reference data. The simulation of binary DPPC/cholesterol mixtures covering the relevant biological content of CHOL in mammalian membranes is shown to correctly predict the main lipid behavior as observed experimentally.     

Particle-based multiscale coarse graining with density-dependent potentials: application to molecular crystals (hexahydro-1,3,5-trinitro-s-triazine)

We describe the development of isotropic particle-based coarse-grain models for crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX). The coarse graining employs the recently proposed multiscale coarse-graining (MS-CG) method, which is a particle-based force-matching approach for deriving free-energy effective interaction potentials. Though one-site and four-site coarse-grain (CG) models were parameterized from atomistic simulations of non-ordered (molten and ambient temperature amorphous) systems, the focus of the paper is a detailed study of the one-site model with a brief recourse to the four-site model. To improve the ability of the one-site model to be applied to crystalline phases at various pressures, it was found necessary to include explicit dependence on a particle density, and a new theory of local density-dependent MS-CG potentials is subsequently presented. The density-dependency is implemented through interpolation of MS-CG force fields derived at a preselected set of reference densities. The computationally economical procedure for obtaining the reference force fields starting from the interaction at ambient density is also described. The one-site MS-CG model adequately describes the atomistic lattice structure of α-RDX at ambient and high pressures, elastic and vibrational properties, pressure-volume curve up to P = 10 GPa, and the melting temperature. In the molten state, the model reproduces the correct pair structure at different pressures as well as higher order correlations. The potential of the MS-CG model is further evaluated in simulations of shocked crystalline RDX.