Integral equation theory of Lennard-Jones fluids: A modified Verlet bridge function approach

EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules

Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL.

Determination of thermodynamic state variables of liquids from their microscopic structures using an artificial neural network

In this work we implement a machine learning method to predict the thermodynamic state of a liquid using only its microscopic structure provided by the radial distribution function (RDF). The main goal is to determine the equation of state of the system. The goal is achieved by predicting the density, temperature or both at the same time using only the RDF. We implement and train a machine learning feed forward artificial neural network (ANN) to address the different cases of interest where single or simultaneous predictions are done. Due to its versatility, in this study the Lennard-Jones (LJ) fluid is used as the reference system. The ANN is trained in a wide range of densities and temperatures, covering the liquid-vapour coexistence, liquid phase and supercritical states. We show that the overall percentage relative error of most of the predictions in different cases of study is around 3%. As a practical case of study we use the ANN predictions to determine the pressure equation of state for different isotherms and we found a very good agreement with respect to the exact results. Our ANN implementation is a versatile and useful tool to predict thermodynamic state variables when some information is unknown and, consequently, to enhance the thermodynamic description of liquids.

Closure for the Ornstein-Zernike equation with pressure and free energy consistency

The Ornstein-Zernike (OZ) integral equation theory is a powerful approach to simple liquids due to its low computational cost and the fact that, when combined with an appropriate closure equation, the theory is thermodynamically complete. However, approximate closures proposed to date exhibit pressure or free energy inconsistencies that produce inaccurate or ambiguous results, limiting the usefulness of the Ornstein-Zernike approach. To address this problem, we combine methods to enforce both pressure and free energy consistency to create a new closure approximation and test it for a single-component Lennard-Jones fluid. The closure is a simple power series in the direct and total correlation functions for which we have derived analytical formulas for the excess Helmholtz free energy and chemical potential. These expressions contain a partial molar volumelike term, similar to excess chemical potential correction terms recently developed. Using our bridge approximation, we have calculated the pressure, Helmholtz free energy, and chemical potential for the Lennard-Jones fluid using the Kirkwood charging, thermodynamic integration techniques, and analytic expressions. These results are compared with those from the hypernetted chain equation and the Verlet-modified closure against Monte Carlo and equations-of-state data for reduced densities of ρ^{*}<1 and temperatures of T^{*}=1.5, 2.74, and 5. Our closure shows consistency among all thermodynamic paths, except for one expression of the Gibbs-Duhem relation, whereas the hypernetted chain equation and the Verlet-modified closure exhibit consistency between only a few relations. Accuracy of the closure is comparable to the Verlet-modified closure and a significant improvement to results obtained from the hypernetted chain equation.

Number Density Distribution of Small Particles around a Large Particle: Structural Analysis of a Colloidal Suspension

Some colloidal suspensions contain two types of particles-small and large particles-to improve the lubricating ability, light absorptivity, and so forth. Structural and chemical analyses of such colloidal suspensions are often performed to understand their properties. In a structural analysis study, the observation of the number density distribution of small particles around a large particle (g_LS) is difficult because these particles are randomly moving within the colloidal suspension by Brownian motion. We obtain g_LS using the data from a line optical tweezer (LOT) that can measure the potential of mean force between two large colloidal particles (Φ_LL). We propose a theory that transforms Φ_LL into g_LS. The transform theory is explained in detail and tested. We demonstrate for the first time that LOT can be used for the structural analysis of a colloidal suspension. LOT combined with the transform theory will facilitate structural analyses of the colloidal suspensions, which is important for both understanding colloidal properties and developing colloidal products.

Number density distribution of solvent molecules on a substrate: a transform theory for atomic force microscopy

Atomic force microscopy (AFM) in liquids can measure a force curve between a probe and a buried substrate. The shape of the measured force curve is related to hydration structure on the substrate. However, until now, there has been no practical theory that can transform the force curve into the hydration structure, because treatment of the liquid confined between the probe and the substrate is a difficult problem. Here, we propose a robust and practical transform theory, which can generate the number density distribution of solvent molecules on a substrate from the force curve. As an example, we analyzed a force curve measured by using our high-resolution AFM with a newly fabricated ultrashort cantilever. It is demonstrated that the hydration structure on muscovite mica (001) surface can be reproduced from the force curve by using the transform theory. The transform theory will enhance AFM's ability and support structural analyses of solid/liquid interfaces. By using the transform theory, the effective diameter of a real probe apex is also obtained. This result will be important for designing a model probe of molecular scale simulations.

Computation of virial coefficients from integral equations

A polynomial-time method of computing the virial coefficients from an integral equation framework is presented. The method computes the truncated density expansions of the correlation functions by series transformations, and then extracts the virial coefficients from the density components. As an application, the method was used in a hybrid-closure integral equation with a set of self-consistent conditions, which produced reasonably accurate virial coefficients for the hard-sphere fluid and Gaussian model in high dimensions.

Model-potential-free analysis of small angle scattering of proteins in solution: insights into solvent effects on protein–protein interaction

The model-potential-free method advances the analysis of small-angle scattering for protein solutions and provides new insights into protein–protein interactions.

Liquid-vapor interfaces in XY -spin fluids: an inhomogeneous anisotropic integral-equation approach

An integral-equation approach is developed to study interfacial properties of anisotropic fluids with planar spins in the presence of an external magnetic field. The approach is based on the coupled set of the Lovett-Mou-Buff-Wertheim integro-differential equation for the inhomogeneous anisotropic one-particle density and the Ornstein-Zernike equation for the orientationally dependent two-particle correlation functions. Using the proposed inhomogeneous angle-harmonics expansion formalism we show that these integral equations can be reduced to a much simpler form similar to that inherent for a system of isotropic fluids. The interfacial orientationally dependent direct correlation function can be consistently constructed by means of a nonlinear interpolation via its values obtained in the coexisting anisotropic bulk phases. A soft mean spherical approximation is employed for the closure relation. This has allowed us to solve the complicated integral equations in the situation when both spatial inhomogeneity and orientational anisotropy are present simultaneously. The approach introduced is applied to an XY fluid model with ferromagnetic spin interactions. As a result, the density-orientation and magnetization profiles at the liquid-vapor interfaces are calculated in a wide range of temperatures up to subcritical regions. The influence of the external field on the microscopic structure of the interfaces and the surface tension is also analyzed in detail.

Optimized theory for simple and molecular fluids

An optimized closure approximation for both simple and molecular fluids is presented. A smooth interpolation between Perkus-Yevick and hypernetted chain closures is optimized by minimizing the free energy self-consistently with respect to the interpolation parameter(s). The molecular version is derived from a refinement of the method for simple fluids. In doing so, a method is proposed which appropriately couples an optimized closure with the variant of the diagrammatically proper integral equation recently introduced by this laboratory [K. M. Dyer et al., J. Chem. Phys. 123, 204512 (2005)]. The simplicity of the expressions involved in this proposed theory has allowed the authors to obtain an analytic expression for the approximate excess chemical potential. This is shown to be an efficient tool to estimate, from first principles, the numerical value of the interpolation parameters defining the aforementioned closure. As a preliminary test, representative models for simple fluids and homonuclear diatomic Lennard-Jones fluids were analyzed, obtaining site-site correlation functions in excellent agreement with simulation data.

Approximative "one particle" bridge function B(1)(r) for the theory of simple fluids

New properties for the one particle bridge function B(1)(r), which are necessary to the calculation of the excess chemical potential betamue), are derived for the hard sphere fluid. The method, which only requires the knowledge of the bridge function B(2)(r), is based on an investigation of the correlation function dependence on the Kirkwood charging parameter. In this framework, the unavoidable question of topological homotopy is addressed. As far as B(2)(r) is considered as exact, this work provides useful information on B(1)(r) in the well identified dynamical regimes of the hard sphere fluid. Signatures of the transitions between these regimes are identified on the trends of B(1)(r). This approach provides self-consistent results for betamue) that agree very well with simulation data.

Liquid-vapor and liquid-liquid interfaces in Ising fluids: An integral equation approach

The microscopic structure and thermodynamic properties of liquid-vapor and liquid-liquid interfaces in Ising fluids are studied using an integral equation approach. The calculations are performed in the absence and presence of an external magnetic field by solving the corresponding set of Lovett-Mou-Buff-Wertheim integrodifferential equations for the one-particle density distribution functions. The two-particle inhomogeneous direct correlation functions are consistently constructed by nonlinear interpolation between the bulk ones. The bulk correlation functions of the coexisting phases are obtained from the Ornstein-Zernike equations with a modified soft mean spherical approximation for the closure relation. As a result, the density and magnetization profiles at liquid-vapor and liquid-liquid interfaces as well as the surface tension and adsorption coefficients are evaluated in a wide temperature range including subcritical regions. The influence of an external magnetic field on the liquid-vapor interfaces is also considered.

How to extend hard sphere density functional approximation to nonuniform nonhard sphere fluids: Applicable to both subcritical and supercritical temperature regions

A methodology for the formulation of density functional approximation (DFA) for nonuniform nonhard sphere fluids is proposed by following the spirit of a partitioned density functional approximation [Zhou, Phys. Rev. E 68, 061201 (2003)] and mapping the hard core part onto an effective hard sphere whose high order part of the functional perturbation expansion is treated by existing hard sphere DFAs. The resultant density functional theory (DFT) formalism only needs a second order direct correlation function and pressure of the corresponding coexistence bulk fluid as inputs and therefore can be applicable to both supercritical and subcritical temperature cases. As an example, an adjustable parameter-free version of a recently proposed Lagrangian theorem-based DFA is imported into the present methodology; the resultant DFA is applied to Lennard-Jones fluid under the influence of external fields due to a single hard wall, two hard walls separated by a small distance, a large hard sphere, and a spherical cavity with a hard wall. By comparing theoretical predictions with previous simulation data and those recently supplied for coexistence bulk fluid situated at "dangerous" regions, it was found that the present DFA can predict subtle structure change of the density profile and therefore is the most accurate among all existing DFT approaches. A detailed discussion is given as to why so excellent DFA for nonhard sphere fluids can be drawn forth from the present methodology and how the present methodology differs from previous ones. The methodology can be universal, i.e., it can be combined with any other hard sphere DFAs to construct DFA for other nonhard sphere fluids with a repulsive core.

Structure of inhomogeneous Lennard-Jones fluid near the critical region and close to the vapor-liquid coexistence curve: Monte Carlo and density-functional theory studies

Results for the density profiles of the Lennard-Jones (LJ) fluid subjected to diverse external fields are presented for the Monte Carlo simulations within the grand canonical ensemble and for the third order and second order perturbation density-functional approximation (DFA). In all cases, the bulk LJ fluid in the particle reservoir to which the nonuniform fluid under consideration is connected, is at the conditions situated at "dangerous" regions of the phase diagram, i.e., near the critical temperature or close to the gas-liquid coexistence curve. It is found that the previously investigated third order and second order perturbation DFA for hard core attractive Yukawa fluid [J. Chem. Phys. 122, 064503 (2005)] can perform successfully also for the nonuniform LJ fluid only on the condition of high accuracy of the required bulk second order direct correlation function. The present report further indicates that the proposed third order and second order perturbation DFA is efficient and suitable for both supercritical and subcritical temperatures.

Phase diagram of complex fluids using an efficient integral equation method

We present an adaptive technique for the determination of the phase diagram of fluids within the integral equation theory. It enables an efficient and accurate systematic mapping of the thermodynamic space in order to construct the binodal and spinodal lines. Results are obtained with the thermodynamically consistent integral equation proposed by Sarkisov [J. Chem. Phys. 114, 9496 (2001)] within the tangent linear technique that yields an exact differentiation of correlation functions. The generality of the numerical approach is assessed by determining both the liquid-vapor coexistence and the critical parameters of the generalized Lennard-Jones (n,6) potentials with varying repulsive part, including the hard-sphere limit.

Molecular dynamics study of the density and temperature dependence of bridge functions in normal and supercritical Lennard-Jones fluids

A systematic study of the density and temperature dependence of bridge functions has been carried out using molecular dynamics simulation studies in one-component Lennard-Jones fluids. In deriving the liquid structure, approximate closures are generally used in integral equation theories of liquids to obtain static density correlations. In the present work, we have directly compared the simulated bridge function to two such commonly used closures, viz., hybrid mean spherical approximation (HMSA) [J. Chem. Phys. 84, 2336 (1986)] and Duh-Henderson [J. Chem. Phys. 104, 6742 (1996)] closures with thermodynamic parameters varying from the normal liquid to the supercritical fluid phase far from and near the critical point. In the normal liquid region, both closures show a qualitative agreement with the simulated bridge function, although the extent of correlation at distances sigma < r < or = 2.5sigma is generally underestimated. A similar behavior is obtained in supercritical fluids far from the critical point where critical fluctuations are no longer important. In contrast, significant deviations are observed in the bridge functions in supercritical fluids near the critical point even at densities as small as 25% or 50% of the critical density. Such behavior appears to have resulted from competing contributions to the bridge function from decreasing indirect correlations and small yet significant cavity correlations persistent even at very low densities.

XY-spin fluids in an external magnetic field: an integral equation approach

We develop an integral equation approach to study anisotropic fluids with planar spins in the presence of an external field. As a result, the integral equation calculations for these systems appear to be no more difficult than those for ordinary isotropic liquids. The method presented is applied to the investigation of phase coexistence properties of ferromagnetic XY-spin fluids in a magnetic field. The soft mean spherical approximation is used for the closure relation connecting the orientationally dependent two-particle direct and total correlation functions. The Lovett-Mou-Buff-Wertheim and Born-Green-Yvon equations are employed to describe the one-particle orientational distribution. The phase diagrams are obtained in the whole range of varying the external field for a wide class of XY-spin fluid models with various ratios of the strengths of magnetic to nonmagnetic Yukawa-like interactions. The influence of changing the screening radii of the interaction potentials is also considered. Different types of the phase diagram topology are identified. They are characterized by the existence of critical, tricritical, critical end, and triple points related to transitions between gas, liquid, and para- and ferromagnetic states, accompanied by different external field dependencies of critical temperatures and densities corresponding to the gas-liquid and liquid-liquid transitions. As is demonstrated, the integral equation approach leads to accurate predictions of the complicated phase diagram behavior which coincide well with those evaluated by the cumbersome Gibbs ensemble simulation and multiple-histogram reweighting techniques.

Chemical potentials and phase equilibria of Lennard-Jones mixtures: a self-consistent integral equation approach

We explore the vapor-liquid phase behavior of binary mixtures of Lennard-Jones-type molecules where one component is supercritical, given the system temperature. We apply the self-consistency approach to the Ornstein-Zernike integral equations to obtain the correlation functions. The consistency checks include not only thermodynamic consistencies (pressure consistency and Gibbs-Duhem consistency), but also pointwise consistencies, such as the zero-separation theorems on the cavity functions. The consistencies are enforced via the bridge functions in the closure which contain adjustable parameters. The full solution requires the values of not only the monomer chemical potentials, but also the dimer chemical potentials present in the zero-separation theorems. These are evaluated by the direct chemical-potential formula [L. L. Lee, J. Chem. Phys. 97, 8606 (1992)] that does not require temperature nor density integration. In order to assess the integral equation accuracy, molecular-dynamics simulations are carried out alongside the states studied. The integral equation results compare well with simulation data. In phase calculations, it is important to have pressure consistency and valid chemical potentials, since the matching of phase boundaries requires the equality of the pressures and chemical potentials of both the liquid and vapor phases. The mixtures studied are methane-type and pentane-type molecules, both characterized by effective Lennard-Jones potentials. Calculations on one isotherm show that the integral equation approach yields valid answers as compared with the experimental data of Sage and Lacey. To study vapor-liquid phase behavior, it is necessary to use consistent theories; any inconsistencies, especially in pressure, will vitiate the phase boundary calculations.

XY spin fluid in an external magnetic field

A method of integral equations is developed to study anisotropic fluids with planar spins in an external field. As a result, the calculations for these systems appear to be no more difficult than those for ordinary homogeneous liquids. The approach proposed is applied to the ferromagnetic XY spin fluid in a magnetic field using a soft mean spherical closure and the Born-Green-Yvon equation. This provides an accurate reproduction of the complicated phase diagram behavior obtained by cumbersome Gibbs ensemble simulation and multiple histogram reweighting techniques.

Criticality of a liquid–vapor interface from an inhomogeneous integral equation theory

A microscopic theory is developed to study the liquid-vapor interfacial properties of simple fluids with ab initio treatment of the inhomogeneous two-body correlation functions, without any interpolation. It consists of the inhomogeneous Ornstein-Zernike equation coupled with the Duh-Henderson-Verlet closure and the Lovett-Mou-Buff-Wertheim equation. For the liquid-vapor interface of the Lennard-Jones fluid, we obtained the density profile and the surface tension, as well as their critical behaviour. In particular, we identified non-classical critical exponents. The theory accurately predicts the phase diagram and the interfacial properties in a very good agreement with simulations. We also showed that the method leads to true capillary-wave asymptotics in the macroscopic limit.

Ising fluids in an external magnetic field: an integral equation approach

The phase behavior of Ising spin fluids is studied in the presence of an external magnetic field with the integral equation method. The calculations are performed on the basis of a soft mean spherical approximation using an efficient algorithm for solving the coupled set of the Ornstein-Zernike equations, the closure relations, and the external field constraint. The phase diagrams are obtained in the whole thermodynamic space including the magnetic field H for a wide class of Ising fluid models with various ratios R of the strengths of magnetic to nonmagnetic Yukawa-like interactions. The influence of varying the inverse screening lengths z(1) and z(2), corresponding to the magnetic and nonmagnetic Yukawa parts of the potential, is investigated too. It is shown that changes in R as well as in z(1) and z(2) can lead to different topologies of the phase diagrams. In particular, depending on the value of R, the critical temperature of the liquid-gas transition either decreases monotonically, behaves nonmonotonically, or increases monotonically with increasing H. The para-ferro magnetic transition is also affected by changes in R and the screening lengths. At H=0, the Ising fluid maps onto a simple model of a symmetric nonmagnetic binary mixture. For H--> infinity, it reduces to a pure nonmagnetic fluid. The results are compared with available simulations and the predictions of other theoretical methods. It is demonstrated that the mean spherical approximation appears to be more accurate compared with mean field theory, especially for systems with short ranged attraction potentials (when z(1) and z(2) are large). In the Kac limit z(1), z(2) -->+0, both approaches tend to nearly the same results.

Partitioned density functional approach for a Lennard-Jones fluid

The existing classical density functional approach for nonuniform Lennard-Jones fluid, which is based on dividing the Lennard-Jones interaction potential into a short-range, repulsive part, and a smoothly varying, long-range, attractive tail, was improved by dividing the bulk second-order direct correlation function into strongly density-depending short-range part and weakly density-depending long-range part. The latter is treated by functional perturbation expansion truncated at the lowest order whose accuracy depends on how weakly the long-range part depends on the bulk density. The former is treated by the truncated functional perturbation expansion which is rewritten in the form of the simple weighted density approximation and incorporates the omitted higher-order terms by applying Lagrangian theorem of differential calculus to the reformulated form. The two approximations are put into the density profile equation of the density functional theory formalism to predict the density distribution for Lennard-Jones fluid in contact with a hard wall or between two hard walls within the whole density range for reduced temperature T(*)=1.35 and a density point for reduced temperature T(*)=1. The present partitioned density functional theory performs much better than several previous density functional perturbation theory approaches and a recently proposed bridge density functional approximation.

Free energies from integral equation theories: enforcing path independence

A variational formalism is constructed for deriving the chemical potential and the Helmholtz free energy in various statistical-mechanical integral equation theories of fluids. Nonzero bridge functions extending the scope of the theories beyond the hypernetted chain approximation can be classified as to whether or not they imply path dependence of the free energy. Classes of bridge functions free of the path dependence problem are derived, based on which a route is devised toward direct computation of free energies from the simulation of a single state.

Bridge function and other structural properties of core-softened model fluids from molecular dynamics simulations

Molecular dynamics (MD) simulations in three dimensions have been performed for a fluid with particles interacting with a continuous version of the Stell-Hemmer core-softened potential that in two dimensions has been known to reproduce most of the static and dynamic anomalies of liquid water. The pair distribution function obtained from the MD simulation is extrapolated with the help of integral equation theory with a suitable closure relation and the bridge function is extracted. A strong dependence of the bridge function on the system size, i.e., the total number of particles (N) used in the simulation box is observed, which leads to spurious values of the structure factor at long wavelengths. A simple self-consistent correction scheme for the finite size effect has been adopted to correct the bridge function and this scheme produces the correct bridge function even for a small system size. The effects of temperature, number density, and potential parameters on the pair distribution functions and extracted bridge functions are extensively studied.