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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.

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]

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]

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]

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]

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]

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]

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]

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.