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We present a Fourier space density functional approach for hard particles with attractive interactions, which is based on a previously developed two-dimensional approach [S. Hlushak, W. Rżysko, and S. Sokołowski, J. Chem. Phys. 131, 094904 (2009)] for hard-sphere chains. The interactions are incorporated by means of a three-dimensional Fourier image of the direct correlation function that is obtained from the first-order mean-spherical approximation. In order to improve the computational efficiency, we make extensive use of fast Fourier transforms for calculating density convolution integrals. A two-dimensional implementation of the new density functional approach, based on the expansion of the functional around the bulk fluid density, is used to study structure and adsorption of two model fluids in narrow cylindrical pores. We also investigate two methods that improve the accuracy of the theory as compared to the conventional DFT approach, which expands the free energy functional around the bulk fluid density: One a variant of the reference fluid density functional theory used by Gillespie et al. [Phys. Rev. E 68, 031503 (2003)], and the second a weighted density approach with energy route thermodynamics. Results from these two methods are compared to the conventional approach and also to the results of Monte Carlo simulations. We find that the method of Gillespie et al. and the weighted density approach with energy route thermodynamics yield significant improvement over the conventional approach. [ABSTRACT FROM AUTHOR]

Nonequilibrium molecular dynamics (NEMD) simulations were performed and the transient time correlation function (TTCF) method applied to calculate the shear viscosity of n-decane. Using the TTCF method we were able to calculate the viscosity at shear rate orders of magnitude lower than is possible by direct NEMD simulation alone. For the first time for a molecular fluid, we were able to simulate shear rates accessible by experimental measurements, which are typically performed at shear rates well below those accessible by NEMD simulation. The TTCF method allows us to close the gap between the lowest shear rates accessible by MD simulation and the highest shear rates possible in experimental studies. Additionally a multiple time step method for Gaussian thermostatted SLLOD equations of motion was developed following earlier work [G. A. Pan et al., J. Chem. Phys. 122, 4114 (2005)] for atomic fluids. [ABSTRACT FROM AUTHOR]

A statistical associating fluid theory for potentials of variable range to model dipolar fluids is presented. The new theory, termed the SAFT-VR+D equation (the statistical associating fluid theory for potentials of variable range plus dipole), explicitly accounts for dipolar interactions and their effect on the structure of the fluid. This is achieved through the use of the generalized mean spherical approximation (GMSA) to describe a reference fluid of dipolar square-well segments. Isothermal-isobaric and Gibbs ensemble Monte Carlo simulations have been performed in order to test the new theoretical approach. Predictions for the thermodynamic properties and phase behavior of dipolar square-well monomer and chain fluids, in which one or more segments are dipolar, are considered and compared with new computer simulation data. The results show that the equation of state in general provides a good description of the phase behavior of dipolar monomer and chain fluids. Some deviations are seen between the simulation data and theoretical predictions for monomer fluids with large dipole moments and for molecules composed of segments with dipoles in different orientations. This is addressed through the replacement of the GMSA by the linearized exponential approximation. [ABSTRACT FROM AUTHOR]

We report molecular dynamics simulations for telechelic molecules composed of two polyhedral oligomeric silsesquioxane (POSS) cages connected by one hydrocarbon backbone dissolved in liquid normal hexane. Silsesquioxanes are novel hybrid organic-inorganic molecules that are useful as building blocks for the synthesis of nanostructured materials. By including POSS molecules within a polymeric material it is possible to modify mechanical properties such as resistance to heat and glass transition temperatures. Unfortunately, the molecular mechanisms responsible for these enhancements are at present not completely understood. In an effort to elucidate the molecular phenomena responsible for these effects, we have studied the conformation of telechelic POSS molecules in solution, as well as their self-diffusion coefficients, as a function of the length of the hydrocarbon backbone. We focus on molecules in which the radius of gyration of the alkane backbone is comparable to the size of the silsesquioxane cages. Our results indicate that the backbone has a significant influence on both the equilibrium and the transport properties of dissolved telechelic hybrid molecules. These observations are useful for developing strategies to direct the self-assembly of nanostructured materials. [ABSTRACT FROM AUTHOR]

The accuracy of several theories for the thermodynamic properties of the Yukawa hard-sphere chain fluid are studied. In particular, we consider the polymer mean spherical approximation (PMSA), the dimer version of thermodynamic perturbation theory (TPTD), and the statistical associating fluid theory for potentials of variable attractive range (SAFT-VR). Since the original version of SAFT-VR for Yukawa fluids is restricted to the case of one-Yukawa tail, we have extended SAFT-VR to treat chain fluids with two-Yukawa tails. The predictions of these theories are compared with Monte Carlo (MC) simulation data for the pressure and phase behavior of the chain fluid of different length with one- and two-Yukawa tails. We find that overall the PMSA and TPTD give more accurate predictions than SAFT-VR, and that the PMSA is slightly more accurate than TPTD. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The prediction of viscosity by molecular simulation has been a goal of molecular modeling essentially since its inception. With today's computing power, the Newtonian or zero shear viscosity of a low molecular weight fluid can easily be determined using equilibrium and nonequilibrium molecular dynamics simulation methods. However, both methods are constrained to systems with relatively short relaxation times that are accessible on the timescale of a molecular dynamics simulation. Here we demonstrate that using a simple scaling relation enables us to predict the Newtonian viscosity of a molecule at any state point for a small fraction of the time that it takes to obtain the same result through nonequilibrium or equilibrium molecular dynamics simulation. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems involving large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger time steps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regard to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. How the models are parameterised, which typically depends on their application, is also discussed. [ABSTRACT FROM AUTHOR]

Abstract: In recent work [Peng et al. Fluid Phase Equilibr. 227(2) (2009), 131] a molecular-based group contribution SAFT-VR equation of state (GC-SAFT-VR) was proposed as a predictive tool for the study of fluid phase behavior. In the GC-SAFT-VR approach a fluid is modeled by a chain of tangentially bonded segments that each represent the different functional groups in the molecule, such as CH3, CH2 and OH, and so represents a more physically realistic model than that used in other SAFT-based approaches in which the segments of the model chain are identical i.e., have the same model parameters. The molecular parameters of the functional groups are determined by fitting to experimental vapor pressure and saturated liquid density data for selected members of different chemical families in a successive fashion, i.e., alkanes for CH3 and CH2 groups and subsequently alcohols for the OH group. The transferability of the molecular parameters can then be tested by comparing the theoretical predictions with experimental data for the phase behavior of pure fluids not included in the fitting process as well as binary mixtures of both simple fluids and polymer systems. Here, we continue the development of the GC-SAFT-VR approach, and for the first time, test its ability to predict the phase behavior of ternary mixtures. In particular, we consider binary and ternary mixtures of 1-pentanol, dibutyl ether and n-nonane. We find that the GC-SAFT-VR approach provides a good description of the phase equilibria of these binary and ternary systems without the need to fit cross interaction parameters to experimental mixture data. [Copyright &y& Elsevier]

Developing accurate models of water for use in computer simulations is important for the study of many chemical and biological systems, including lipid bilayer self-assembly. The large temporal and spatial scales needed to study such self-assembly have led to the development and application of coarse-grained models for the lipid−lipid, lipid−solvent, and solvent−solvent interactions. Unfortunately, popular center-of-mass-based coarse-graining techniques are limited to modeling water with one water per be ad. In this work, we have utilized the K-means algorithm to determine the optimal clustering of waters to allow the mapping of multiple waters to single coarse-grained beads. Through the study of a simple mixture between water and an amphiphilic solute (1-pentanol), we find a four-water bead model has the optimal balance between computational efficiency and accurate solvation and structural properties when compared to water models ranging from one to nine waters per bead. The four-water model was subsequently utilized in studies of the solvation of hexadecanoic acid and the structure, as measured via radial distribution functions, for the hydrophobic tails and the bulk water phase were found to agree well with experimental data and their atomistic target. [ABSTRACT FROM AUTHOR]

Abstract: The high-pressure phase diagram and other thermodynamic properties of the binary systems of water+hydrogen sulphide have been examined using the SAFT-VR+D equation of state [Zhao and McCabe, J. Chem. Phys. 125 (2006) 104504]. The SAFT-VR+D approach is based on a version of the statistical associating fluid theory that was developed to model dipolar fluids by explicitly accounting for dipolar interactions and their effect on the thermodynamics and structure of a fluid. In the SAFT-VR+D equation this is achieved through the use of the generalized mean spherical approximation (GSMA) to describe a monomer fluid of dipolar square-well segments. In the present work, we further develop the SAFT-VR+D equation to study mixtures of dipolar associating fluids of arbitrary size using the analytical solution of the Ornstein–Zernike equation due to Cummings and Blum [J. Chem. Phys. 84, 1833 (1986)]. The high-pressure phase diagram and other thermodynamic properties of the water+hydrogen sulphide binary mixture are then examined. Both components, hydrogen sulphide and water, are naturally modeled as associating spherical molecules with four off-centre sites to mimic hydrogen bonding and an embedded dipole moment (μ) to describe their polarity. Using simple Lorentz–Berthelot combining rules, the theory is able to predict the phase behavior of the H2O+H2S system from pure component parameters. Specifically, type III phase behavior according to the classification of Scott and van Konynenburg is observed, with a three-phase line at low temperatures that terminates at an upper critical end point and two separate critical lines, one at high temperatures that runs continuously from a gas–liquid critical line to a liquid–liquid critical line at high pressures and a second gas–liquid critical line located at low temperatures. The phase behavior predicted by the SAFT-VR+D approach is in excellent agreement with the experimental data, without requiring any fitted binary interaction parameters. In addition, the theory is also able to describe the excess molar enthalpies and the most important features of the Henry''s constants as a function of temperature. [Copyright &y& Elsevier]

Polyhedral oligomeric silsesquioxane (POSS) molecules when functionalized appropriately and dispersed in polymers show promise as monodisperse organic−inorganic hybrid nanocomposite materials characterized by superior mechanical properties. We report here molecular-simulation results for POSS−POSS radial distribution functions, potentials of mean force, and self-diffusion coefficients for POSS monomers dissolved in poly(dimethylsiloxane) in the temperature range of 300−1000 K. Our results demonstrate that it is possible to modulate the effective POSS−POSS interaction by increasing the temperature or by substituting the hydrogen atoms in the POSS monomer with methyl groups. In addition, our results indicate that the motion of POSS monomers dissolved in poly(dimethylsiloxane) follows a hopping mechanism. [ABSTRACT FROM AUTHOR]

The phase and volumetric behaviour of binary mixtures of n-alkanes and n-perfluoroalkanes at subcritical conditions have been studied using the SAFT–VR equation of state. In previous work [C. McCabe, A. Galindo, A. Gil-Villegas, G. Jackson, Predicting the high-pressure phase equilibria of binary mixtures of perfluoro-n-alkanes plus n-alkanes using the SAFT–VR approach, J. Phys. Chem. B 102 (1998) 8060–8069] the SAFT–VR equation was successfully used to predict the phase behaviour of binary mixtures of low molecular weight n-perfluoroalkanes + n-alkanes. A transferable binary interaction parameter was proposed which enabled the accurate prediction of the critical lines for all the systems studied. In this work we focus on the low pressure liquid–liquid immiscibility displayed by binary mixtures of longer chains (C5ㅡC8). New transferable binary interaction parameters for these mixtures are proposed, based on the reproduction of the UCST and excess volumes for the n-hexane + n-perfluorohexane system. With these parameters, predictions are then made for the vapour–liquid equilibria (VLE), liquid–liquid equilibria (LLE) and excess volumes of other binary mixtures without any additional fitting to experimental data. The resulting predictions from the SAFT–VR equation are in good agreement with the available experimental data. [Copyright &y& Elsevier]

The mechanical properties of sliding carbon nanotubes have been investigated by classical molecular dynamics simulations in the canonical ensemble. In particular we have studied damped oscillations in the separation between the centres of mass of the inner and outer tubes of double-walled carbon nanotubes (DWCN). Incommensurate DWCNs forming (7, 0)@(9, 9) structures were simulated for systems at 298.15 K with axial lengths from 12.21 to 98.24 nm. The oscillations exhibited frequencies in the range of gigahertz with the frequency decreasing as the length of the system increases. The time until oscillations become negligible exhibited a nearly linear dependence on the length of the system. Two macroscopic models were developed in order to understand the forces involved in terms of macroscopic properties like friction and shear. The first model considered constant restoring forces during the whole event, while in the second the value of these constant restoring forces depended on the initial conditions of each oscillation. Both models reproduced the oscillations quite well, while the second model allows us to predict the dynamic shear strength in terms of the axial length of the system for tubes with the same diameters. The calculated dynamic shear strength exhibited monotonic behaviour with an inverse dependence on the length of the system. For systems with unequal axial lengths, the restoring force, which drives the oscillation, is reduced compared to the system with equal lengths, regardless of whether the outer nanotube is longer or shorter. [ABSTRACT FROM AUTHOR]

Shear localization has been observed in liquid lubricants flowing at high pressure. Two kinds have been identified: for stress-controlled plane Couette shear at high values of Nahme No., thermal runaway can result in the appearance of a band at mid-plane where the temperature and shear rate become localized. Alternatively, at high pressure and high shear stress, intermittent slip can be visualized along inclined bands for both planar Couette shear and squeeze film flows. These mechanical shear bands are responsible for the rate independent behavior that characterizes the traction transferred across the lubricant film in concentrated contact. We consider three models for shear band formation: Mohr–Coulomb slip, loss of ellipticity of Navier–Stokes equations, and non-monotonic stress–strain rate response. The observations that slip occurs for a ratio of shear to normal stress of about 0.1 and that bands form in two characteristic directions support both the Mohr–Coulomb failure criterion description and a change of character of the governing differential equations. Some evidence of constitutive instability is also presented; however, band orientation does not support this model. [Copyright &y& Elsevier]

A semi-empirical equation of state was developed for square-well chain fluids on the basis of Monte Carlo (MC) simulation data. The equation was formed by combining terms describing non-bonded square-well segments, hard-sphere chain formation, and a perturbation term describing the square-well contribution to chain formation. The functional dependence on the chain length is the same as that derived in the statistical associating fluid theory (SAFT). Extensive isobaric–isothermal MC simulations were performed for the dimer, 4-mer, 8-mer, and 16-mer square-well fluids at temperatures below or near the critical point. The new equation satisfactorily represents the volumetric properties of square-well chain fluids, up to and including the 100-mer, which was the longest chain length studied. Additionally, the new model accurately reproduces the phase envelopes of the dimer and 4-mer fluids, however, it underestimates the vapor pressures for 8-mer’s and above. [Copyright &y& Elsevier]

SAFT is perhaps the most versatile, fundamentally, based engineering equation of state in use today. However, in common with all analytic equations of state, SAFT exhibits classical behavior in the critical region rather than the non-analytical, singular behavior seen in real fluids. Recently, so-called crossover equations of state have been developed which solve this shortcoming by incorporating the scaling laws valid asymptotically close to the critical point while reducing to the original classical equation of state far from the critical point. We have combined the SAFT-VR equation of state with an analytical crossover technique to obtain the SAFT-VRX equation of state. The SAFT-VRX approach combines the accurate low temperature behavior of SAFT-VR with a precise representation of the critical region. Preliminary results are presented for hydrocarbon systems which illustrate the accuracy of the SAFT-VRX approach over the entire fluid phase region. [Copyright &y& Elsevier]

The product-reactant Ornstein-Zernike approach, represented by the polymer mean-spherical approximation (PMSA), is utilized to describe the structure and thermodynamic properties of the fluid of Yukawa hard sphere chain molecules. An analytical solution of the PMSA for the most general case of the multicomponent freely jointed hard sphere multi-Yukawa chain fluid is presented. As in the case of the regular MSA for the hard sphere Yukawa fluid, the problem is reduced to the solution of a set of nonlinear algebraic equations in the general case, and to a single equation in the case of the factorizable Yukawa potential coefficients. Closed form analytical expressions are presented for the contact values of the monomer-monomer radial distribution function, structure factors, internal energy, Helmholtz free energy, chemical potentials and pressure in terms of the quantities, which follows directly from the PMSA solution. By way of illustration, several different versions of the hard sphere Yukawa chain model are considered, represented by one-Yukawa chains of length m, where m = 2,4,8,16. To validate the accuracy of the present theory, Monte Carlo simulations were carried out and the results are compared systematically with the theoretical results for the structure and thermodynamic properties of the system at hand. In general it is found that the theory performs very well, thus providing an analytical route to the equilibrium properties of a well defined model for chain fluids. [ABSTRACT FROM AUTHOR]

The hard-sphere Yukawa chain (HSYC) fluid is a simple model for chain fluids and polymers in which each molecule is composed of freely-jointed tangent spheres. The spheres each have a hard core and an attractive interaction, written as a single Yukawa potential or as a sum of Yukawa potentials. We have calculated the phase equilibria and PVT behaviour of the HSYC fluid both theoretically and by Monte Carlo simulation. The theoretical approach is based on the analytic solution of the polymer mean spherical approximation for the HSYC fluid. By comparing the theory and simulation we are able to evaluate the accuracy of the theory. We find that in general the theory performs very well, thus, it provides an analytic route to an equation of state for a well-defined model of chain fluids. [ABSTRACT FROM AUTHOR]

We broaden the scope of the statistical associating fluid theory for potentials of variable attractive range (SAFT-VR) to treat heteronuclear chain molecules formed from bonded square-well (BSW) segments. The ideas of the bonded hard sphere (BHS) treatment for distributed-site models composed of hard-sphere segments are applied to square-well sites with the SAFT-VR approach. The results of isothermal-isobaric Monte Carlo simulations are reported for heteronuclear square-well diatomics with different sets of energy and range parameters. The SAFT-VR approach provides an excellent description of the equation of state of the diatomic systems for a wide range of densities. The goal of the work is to provide a rigorous treatment of distributed-site models of fluids, and to establish a framework for a group contribution approach with SAFT-VR. [ABSTRACT FROM AUTHOR]

The properties of alkanes in the C[sub 20]-C[sub 40] mass range are of fundamental importance in industrial applications as they are important constituents of synthetic lubricant base stocks. In an extension to earlier work on alkanes in the C[sub 20]-C[sub 40] carbon number range we present the results of molecular simulations for 9-octylheptadecane, a starlike isomer of C[sub 25]. Both equilibrium (EMD) and nonequilibrium molecular dynamics (NEMD) simulations have been performed under ambient state conditions and to pressures in the gigapascal range. The EMD simulations focus on calculations of the rotational relaxation times, while the NEMD simulations reveal the dependence of the viscosity on strain rate. Additionally, we calculate the viscosity number and pressure-viscosity coefficient for 9-octylheptadecane and compare the results with those obtained experimentally. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems. [ABSTRACT FROM AUTHOR]

Monolayers presenting methyl-terminated (hydrophobic) and hydroxyl-terminated (hydrophilic) surfaces on silica have been studied by molecular dynamics simulation and the effects of hydrogen bonding, chain length, and chain mixing on the frictional properties determined. The hydroxyl-terminated monolayers were found to show large adhesion zones as a result of strong interfacial interlayer hydrogen bonds; the interfacial sliding forces observed in the hydroxyl-terminated monolayers being one order of magnitude higher than the interfacial forces for the hydrophobic surfaces at the characteristic point of zero-load. Mixed hydroxyl- and methyl-terminated monolayers of equal length were found to exhibit intermediate shear stress values between those observed for pure monolayers, with the magnitude of the shear stress depending on the surface content of the hydroxyl-terminated chains. For mixed monolayers of unequal chain lengths, at high loads a maximum in the magnitude of the shear stress as a function of the length of the methyl-terminated chain was observed due to the creation of a buffer zone between the hydroxyl-terminated chains that produces strong hydrogen-bonding interactions. The effect of a constant normal load or constant separation simulation ensemble on the results has also been studied and in general found to have minimal influence on the observed behavior, although some differences are observed for the shear stress at intermediate normal loads due to the formation of stronger hydrogen bond networks at constant load compared to constant separation. [ABSTRACT FROM AUTHOR]

A coarse-grained model has been developed for simulating the self-assembly of nonyl-tethered polyhedral oligomeric silsesquioxane (POSS) nanoparticles in solution. A mapping scheme for groups of atoms in the atomistic molecule onto beads in the coarse-grained model was established. The coarse-grained force field consists of solvent-mediated effective interaction potentials that were derived via a structural-based coarse-graining numerical iteration scheme. The force field was obtained from initial guesses that were refined through two different iteration algorithms. The coarse-graining scheme was validated by comparing the aggregation of POSS molecules observed in simulations of the coarse-grained model to that observed in all-atom simulations containing explicit solvent. At 300 K the effective coarse-grained potentials obtained from different initial guesses are comparable to each other. At 400 K the differences between the force fields obtained from different initial guesses, although small, are noticeable. The use of a different iteration algorithm employing identical initial guesses resulted in the same overall effective potentials for bare cube corner bead sites. In both the coarse-grained and all-atom simulations, small aggregates of POSS molecules were observed with similar local packings of the silsesquioxane cages and tether conformations. The coarse-grained model afforded a savings in computing time of roughly two orders of magnitude. Further comparisons were made between the coarse-grained monotethered POSS model developed here and a minimal model developed in earlier work. The results suggest that the interactions between POSS cages are long ranged and are captured by the coarse-grained model developed here. The minimal model is suitable for capturing the local intermolecular packing of POSS cubes at short separation distances. [ABSTRACT FROM AUTHOR]

The statistical associating fluid theory for potentials of variable range plus dipole (SAFT-VR+D) is extended to study associating dipolar fluids. In the SAFT-VR+D approach dipolar interactions are taken into account through the use of the generalized mean spherical approximation to describe a reference fluid of dipolar square-well segments. This enables the effect of the dipolar interactions on the thermodynamics and structure of fluids to be explicitly described. Predictions for the thermodynamic properties and phase behavior of dipolar associating square-well monomers with one, two, and four association sites are considered and compared with new isothermal-isobaric and Gibbs ensemble Monte Carlo simulation data. The results show that the SAFT-VR+D equation provides a good description of the phase behavior of dipolar associating fluids. Additionally we have applied the new theoretical approach to study the vapor pressure and saturated liquid density of water. [ABSTRACT FROM AUTHOR]

A statistical associating fluid theory to model electrolyte fluids that explicitly accounts for solvent molecules by modeling water as a dipolar square-well associating fluid is presented. Specifically the statistical associating fluid theory for potentials of variable range (SAFT-VR) is combined with integral equation theory and the generalized mean spherical approximation using the nonprimitive model to describe the long-range ion-ion, ion-dipole, and dipole-dipole interactions. Isothermal-isobaric ensemble Monte Carlo simulations have been performed in order to test the new theoretical approach. In particular, simulations are performed for different ion concentrations and different ratios of the cation, anion, and solvent segment diameters. Predictions for the thermodynamic properties from the new equation of state are compared with the computer simulation data. Additionally, results from a combination of the SAFT-VR approach with Debye-Hückel theory and the primitive model are also presented and compared to those obtained with the nonprimitive model to illustrate the advantages of the new statistical associating fluid theory for potentials of variable range plus dipole and electrolytes (SAFT-VR+DE) approach. The results show that the proposed equation of state provides a good description of the PVT properties of electrolyte fluids with different sizes of ions and solvent. [ABSTRACT FROM AUTHOR]

A molecular thermodynamics approach is developed in order to describe the adsorption of fluids on solid surfaces. The new theory is based on the statistical associating fluid theory for potentials of variable range [A. Gil-Villegas et al., J. Chem. Phys. 106, 4168 (1997)] and uses a quasi-two-dimensional approximation to describe the properties of adsorbed fluids. The theory is tested against Gibbs ensemble Monte Carlo simulations and excellent agreement with the theoretical predictions is achieved. Additionally the authors use the new approach to describe the adsorption isotherms for nitrogen and methane on dry activated carbon. [ABSTRACT FROM AUTHOR]

We apply an operator splitting method to develop a simulation algorithm that has complete analytical solutions for the Gaussian thermostated SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] for a system under shear. This leads to a homogeneous algorithm for performing both equilibrium and nonequilibrium isokinetic molecular dynamics simulation. The resulting algorithm is computationally efficient. In particular, larger integration time steps can be used compared to simulations with regular Gaussian thermostated SLLOD equations of motion. The utility and accuracy of the algorithm are demonstrated through application to the Weeks–Chandler–Anderson fluid. Although strict conservation of the kinetic energy suppresses thermal fluctuations in the system, this algorithm does not allow simulations at lower shear rates than those normally afforded by older nonequilibrium molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

In this work, molecular dynamics simulations are used to examine the self-assembly of anisotropically coated "patchy" nanoparticles. Specifically, we use a coarse-grained model to examine silica nanoparticles coated with alkane chains, where the poles of the grafted nanoparticle are bare, resulting in strongly attractive patches. Through a systematic screening process, the patchy nanoparticles are found to form dispersed, string-like, and aggregated phases, dependent on the combination of alkane chain length, coating chain density, and the fractional coated surface area. Correlation analysis is used to identify the ability of various particle descriptors to predict bulk phase behavior from more computationally efficient single grafted nanoparticle simulations and demonstrates that the solvent-accessible surface area of the nanoparticle core is a key predictor of bulk phase behavior. The results of this work enhance our knowledge of the phase space of patchy nanoparticles and provide a powerful approach for future screening of these materials. [ABSTRACT FROM AUTHOR]

A foreword to "Molecular Simulation" is presented.

Investigates coexistence densities of methane and propane by canonical molecular dynamics and Gibbs ensemble Monte Carlo simulations. Computational advantages and drawbacks of both simulations; Description of n-alkanes through the TraPPE-UA force field.

The vapor pressure of four liquidperfluoroalkylalkanes(CF3(CF2)n(CH2)mCH3; n= 3, m= 4,5,7; n= 5, m= 5) was measured as a function of temperature between278 and 328 K. Molar enthalpies of vaporization were calculated fromthe experimental data, and the results were compared with data fromthe literature for the corresponding alkanes and perfluoroalkanes.The heterosegmented statistical associating fluid theory was usedto interpret the results at the molecular level both with and withoutthe explicit inclusion of the dipolar nature of the molecules. Additionally,ab initio calculations were performed for all perfluoroalkylalkanesstudied to determine the dipole moment to be used in the theoreticalcalculations. We demonstrate that the inclusion of a dipolar termis essential for describing the vapor–liquid equilibria ofperfluoroalkylalkanes. It is also shown that vapor–liquidequilibria in these compounds result from a subtle balance betweendipolar interactions, which decrease the vapor pressure, and the relativelyweak dispersive interactions between the hydrogenated and fluorinatedsegments. [ABSTRACT FROM AUTHOR]

Carbohydrate-binding modules (CBMs) are ubiquitous components of glycoside hydrolases, which degrade polysaccharides in nature. CBMs target specific polysaccharides, and CBM binding affinity to cellulose is known to be proportional to cellulase activity, such that increasing binding affinity is an important component of performance improvement. To ascertain the impact of protein and glycan engineering on CBM binding, we use molecular simulation to quantify cellulose binding of a natively glycosylated Family 1 CBM. To validate our approach, we first examine aromatic-carbohydrate interactions on binding, and our predictions are consistent with previous experiments, showing that a tyrosine to tryptophan mutation yields a 2-fold improvement in binding affinity. We then demonstrate that enhanced binding of 3-6-fold over a nonglycosylated CBM is achieved by the addition of a single, native mannose or a mannose dimer, respectively, which has not been considered previously. Furthermore, we show that the addition of a single, artificial glycan on the anterior of the CBM, with the native, posterior glycans also present, can have a dramatic impact on binding affinity in our model, increasing it up to 140-fold relative to the nonglycosylated CBM. These results suggest new directions in protein engineering, in that modifying glycosylation patterns via heterologous expression, manipulation of culture conditions, or introduction of artificial glycosylation sites, can alter CBM binding affinity to carbohydrates and may thus be a general strategy to enhance cellulase performance. Our results also suggest that CBM binding studies should consider the effects of glycosylation on binding and function. [ABSTRACT FROM AUTHOR]

Abstract: We present a fundamental study of the frictional performance of silica microspheres, either 4, 2, or 0.5μm in diameter, on a silicon substrate. The tribological properties of these rolling systems were measured with a ball-on-flat tribometer at various loads. The frictional performance of the rolling systems is found to be highly dependent on load and sphere diameter. Rolling motion was confirmed by imaging the surface of microsphere systems that have been coated with a thin layer of gold. In addition, the surface energy of the lubrication scheme was altered using coatings containing octadecyltrichlorosilane or (tridecafluoro-1,1,2,2-tetrahydrooctyl)-1-trichlorosilane precursors. [ABSTRACT FROM AUTHOR]

The solubility of xenon in liquid n-pentane and n-hexane has been studied experimentally, theoretically, and by computer simulation. Measurements of the solubility are reported for xenon + n-pentane as a function of temperature from 254 to 305 K. The uncertainty in the experimental data is less than 0.15%. The thermodynamic functions of solvation such as the standard Gibbs energy, enthalpy, and entropy of solvation have been calculated from Henry's law coefficients for xenon + n-pentane solutions and also for xenon + n-hexane, which were reported in previous work. The results provide a further example of the similarity between the xenon + n-alkane interaction and the n-alkane + n-alkane interactions. Using the SAFT-VR approach we were able to quantitatively predict the experimental solubility for xenon in n-pentane and semiquantitatively that of xenon in n-hexane using simple Lorentz−Berthelot combining rules to describe the unlikely interaction. Henry's constants at infinite dilution for xenon + n-pentane and xenon + n-hexane were also calculated by Monte Carlo simulation using a united atom force field to describe the n-alkane and the Widom test particle insertion method. [ABSTRACT FROM AUTHOR]

Shear viscosity of n-decane was computed using the molecular stress transient time correlation function (TTCF) formalism for the wide range of shear rates from 1.7 × 1010 s-1 to 2.13 × 104 s-1. In earlier work calculations were presented for the shear viscosity of n-decane using the atomic stress formalism of the TTCF method (G. Pan and C. McCabe, J. Chem. Phys. 125(19), 4527 (2006)) in which we were able to close the gap between the lowest shear rates accessible by direct nonequilibrium molecular dynamics (NEMD) simulations and the highest shear rates possible in experimental studies. Here it is shown that the application of the molecular stress approach within the TTCF formalism, as an alternative to the atomic stress method, significantly reduces the number of NEMD trajectories necessary to obtain the shear viscosity. [ABSTRACT FROM AUTHOR]

Abstract: We present free energy calculations for the Trichoderma reesei Cel7A (cellobiohydrolase I) linker peptide from molecular dynamics simulations directed towards understanding the linker role in cellulose hydrolysis. The calculations predict an energy storage mechanism of the linker under stretching/compression that is consistent with processive depolymerization. The linker exhibits two stable states at lengths of 2.5nm and 5.5nm during extension/compression, with a free energy difference of 10.5kcal/mol between the two states separated by an energy barrier. The switching between stable states supports the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring. [Copyright &y& Elsevier]

The SAFT-VR equation of state is extended to treat heteronuclear chain fluids, focusing, in particular, on symmetric and asymmetric diblock chains. The chain molecules studied are composed of segments of different size and/or energy of interaction. Both symmetric and asymmetric systems are considered. The theoretical predictions are compared with isothermal–isobaric and Gibbs ensemble Monte Carlo simulation data. Excellent agreement is obtained between the hetero-SAFT-VR predictions and the simulation data, validating the use of the SAFT-VR approach for heteronuclear chains in more realistic models of polymers and small molecules composed of different functional groups. [ABSTRACT FROM AUTHOR]

The solubility of xenon in n-hexane and n-perfluorohexane has been studied using both molecular simulation and a version of the SAFT approach (SAFT-VR). The calculations were performed close to the saturation line of each solvent, between 200K and 450K, which exceeds the smaller temperature range where experimental data are available in the literature. Molecular dynamics simulations, associated with Widom's test particle insertion method, were used to calculate the residual chemical potential of xenon in n-hexane and nperfluorohexane and the corresponding Henry's law coefficients. The simulation results overestimate the solubility of xenon in both solvents when simple geometric combining rules are used, but are in good agreement if a binary interaction parameter is included. With the SAFTVR approach we are able to reproduce the experimental solubility for xenon in n-hexane, using simple Lorentz–Berthelot rules to describe the unlike interaction. In the case of nperfluorohexane as a solvent, a binary interaction parameter was introduced, taken from previous work on (Xe + C[sub 2]F[sub 6]) mixtures. Overall, good agreement is obtained between the simulation, theoretical and experimental data. [ABSTRACT FROM AUTHOR]

Grafting polymers to nanoparticles is one approach used to control and enhance the structure and properties of nanomaterials. However, predicting the aggregation behavior of tethered nanoparticles (TNPs) is a somewhat trial and error process as a result of the large number of possible polymer tethers, nanoparticles, and solvent species that can be studied. With the main goal of understanding how to control the dispersion and aggregation of TNP systems, molecular simulations and the hetero-statistical associating fluid theory for potentials of variable range have been used to calculate the fluid phase equilibrium of TNPs in both vacuum and in simple solvents under a wide range of conditions. The role of graft length, graft density, and solvent interactions is examined and trends established. Additionally, the fluid distribution ratio (k value) is used to study the solubility of TNPs in industrially relevant solvents including carbon dioxide, nitrogen, propane, and ethylene. [ABSTRACT FROM AUTHOR]

The fluid-solid phase transition behavior of nano-confined Lennard-Jones fluids as a function of temperature and degree of nanoconfinement has been studied via statistical temperature molecular dynamics (STMD). The STMD method allows the direct calculation of the density of states and thus the heat capacity with high efficiency. The fluids are simulated between parallel solid surfaces with varying pore sizes, wall-fluid interaction energies, and registry of the walls. The fluid-solid phase transition behavior has been characterized through determination of the heat capacity. The results show that for pores of ideal-spacing, the order-disorder transition temperature (TODT) is reduced as the pore size increases until values consistent with that seen in a bulk system. Also, as the interaction between the wall and fluid is reduced, TODT is reduced due to weak constraints from the wall. However, for non-ideal spacing pores, quite different behavior is obtained, e.g., generally TODT are largely reduced, and TODT is decreased as the wall constraint becomes larger. For unaligned walls (i.e., whose lattices are not in registry), the fluid-solid transition is also detected as T is reduced, indicating non-ideality in orientation of the walls does not impact the formation of a solid, but results in a slight change in TODT compared to the perfectly aligned systems. The STMD method is demonstrated to be a robust way for probing the phase transitions of nanoconfined fluids systematically, enabling the future examination of the phase transition behavior of more complex fluids. [ABSTRACT FROM AUTHOR]

Grafting polymers to nanoparticles is one approach used to control and enhance the structure and properties of nanomaterials. However, predicting the aggregation behavior of tethered nanoparticles (TNPs) is a somewhat trial and error process as a result of the large number of possible polymer tethers, nanoparticles, and solvent species that can be studied. With the main goal of understanding how to control the dispersion and aggregation of TNP systems, molecular simulations and the hetero-statistical associating fluid theory for potentials of variable range have been used to calculate the fluid phase equilibrium of TNPs in both vacuum and in simple solvents under a wide range of conditions. The role of graft length, graft density, and solvent interactions is examined and trends established. Additionally, the fluid distribution ratio (k value) is used to study the solubility of TNPs in industrially relevant solvents including carbon dioxide, nitrogen, propane, and ethylene. [ABSTRACT FROM AUTHOR]

The fluid-solid phase transition behavior of nano-confined Lennard-Jones fluids as a function of temperature and degree of nanoconfinement has been studied via statistical temperature molecular dynamics (STMD). The STMD method allows the direct calculation of the density of states and thus the heat capacity with high efficiency. The fluids are simulated between parallel solid surfaces with varying pore sizes, wall-fluid interaction energies, and registry of the walls. The fluid-solid phase transition behavior has been characterized through determination of the heat capacity. The results show that for pores of ideal-spacing, the order-disorder transition temperature (TODT) is reduced as the pore size increases until values consistent with that seen in a bulk system. Also, as the interaction between the wall and fluid is reduced, TODT is reduced due to weak constraints from the wall. However, for non-ideal spacing pores, quite different behavior is obtained, e.g., generally TODT are largely reduced, and TODT is decreased as the wall constraint becomes larger. For unaligned walls (i.e., whose lattices are not in registry), the fluid-solid transition is also detected as T is reduced, indicating non-ideality in orientation of the walls does not impact the formation of a solid, but results in a slight change in TODT compared to the perfectly aligned systems. The STMD method is demonstrated to be a robust way for probing the phase transitions of nanoconfined fluids systematically, enabling the future examination of the phase transition behavior of more complex fluids. [ABSTRACT FROM AUTHOR]

Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (&eh;) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results. [ABSTRACT FROM AUTHOR]

Systems composed of soft matter (e.g. liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a 'bespoke' fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibilitya. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations. [ABSTRACT FROM AUTHOR]

Configurational-bias Monte Carlo has been incorporated into the Wang-Landau method. Although the Wang-Landau algorithm enables the calculation of the complete density of states, its applicability to continuous molecular systems has been limited to simple models. With the inclusion of more advanced sampling techniques, such as configurational-bias, the Wang-Landau method can be used to simulate complex chemical systems. The accuracy and efficiency of the method is assessed using as a test case systems of linear alkanes represented by a united-atom model. With strict convergence criteria, the density of states derived from the Wang-Landau algorithm yields the correct heat capacity when compared to conventional Boltzmann sampling simulations. [ABSTRACT FROM AUTHOR]

The Wang-Landau (WL) Monte Carlo method has been applied to simulate the self-assembly of a lipid bilayer on a 3D lattice. The WL method differs from conventional Monte Carlo methods in that a complete density of states is obtained directly for the system, from which properties, such as the free energy, can be derived. Furthermore, from a single WL simulation, continuous curves of the average energy and heat capacity can be determined, which provide a complete picture of the phase behavior. The lipid model studied consists of 3 or 5 coarse-grained segments on lattices of varying sizes, with the empty lattice sites representing water. A bilayer structure is found to form at low temperatures, with phase transitions to clusters as temperature increases. For 3-segment chains, varying lattice sizes were studied, with the observation that the ratio of chain number to lattice area (i.e., area per lipid) affects the phase transition temperature. At small ratios, only one phase transition occurs between the bilayer and cluster phases, while at high lipid ratios the phase transition occurs in a two-step process with a stable intermediate phase. This second phase transition was not observed in conventional Metropolis Monte Carlo simulations on the same model, demonstrating the advantage of being able to perform a complete scan of the whole temperature range with the WL method. For longer 5-segment chains similar phase transitions are also observed with changes in temperature. In the WL method, due to the extensive nature of the energy, the number of energy bins required to represent the density of states increases as the system size increases and so limits its practical application to larger systems. To improve this, an extension of the WL algorithm, the statistical-temperature Monte Carlo method that allows simulations with larger energy bin sizes, has recently been proposed and is implemented in this work for the 3-segment lattice model. The results obtained are in good agreement with the original WL method and appear to be independent of the energy bin size used. [ABSTRACT FROM AUTHOR]

A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models used to perform a study. Ambiguity in molecular models often stems from inadequate usage documentation of molecular force fields and the fact that force fields are not typically disseminated in a format that is directly usable by software. Specifically, the lack of a generally applicable scheme for the annotation of the rules of a particular force field and a general purpose tool for performing automated parameterization (i.e., atom-typing) based on these rules, may lead to errors in model parameterization that are not easily identified. Here, we present Foyer, an open-source Python tool that enables users to define and apply force field atom-typing rules in a format that is both human- and machine-readable and provides a framework for force field dissemination, thus eliminating ambiguity in atom-typing and improving reproducibility. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type and "overrides" are used to set rule precedence, rather than a rigid hierarchical scheme. Herein we describe the underlying methodology and force field annotation scheme of the Foyer software, demonstrate its application in several use-cases, and discuss specific aspects of the Foyer approach that are designed to improve reproducibility. [ABSTRACT FROM AUTHOR]