Search

A comprehensive and detailed account is presented for the finite-temperature many-body perturbation theory for electrons that expands in power series all thermodynamic functions on an equal footing. Algebraic recursions in the style of the Rayleigh-Schr\"{o}dinger perturbation theory are derived for the grand potential, chemical potential, internal energy, and entropy in the grand canonical ensemble and for the Helmholtz energy, internal energy, and entropy in the canonical ensemble, leading to their sum-over-states analytical formulas at any arbitrary order. For the grand canonical ensemble, these sum-over-states formulas are systematically transformed to sum-over-orbitals reduced analytical formulas by the quantum-field-theoretical techniques of normal-ordered second quantization and Feynman diagrams extended to finite temperature. It is found that the perturbation corrections to energies entering the recursions have to be treated as a nondiagonal matrix, whose off-diagonal elements are generally nonzero within a subspace spanned by degenerate Slater determinants. They give rise to a unique set of linked diagrams -- renormalization diagrams -- whose resolvent lines are displaced downwards, which are distinct from the well-known anomalous diagrams of which one or more resolvent lines are erased. A linked-diagram theorem is introduced that proves the size-consistency of the finite-temperature many-body perturbation theory at any order. General-order algorithms implementing the recursions establish the convergence of the perturbation series towards the finite-temperature full-configuration-interaction limit unless the series diverges. Normal-ordered Hamiltonian at finite temperature sheds light on the relationship between the finite-temperature Hartree--Fock and first-order many-body perturbation theories., Comment: 29 pages, 21 figures, 8 tables

We present a wave function representation for the canonical ensemble thermal density matrix by projecting the thermofield double state against the desired number of particles. The resulting canonical thermal state obeys an imaginary time-evolution equation. Starting with the mean-field approximation, where the canonical thermal state becomes an antisymmetrized geminal power wave function, we explore two different schemes to add correlation: by number-projecting a correlated grand-canonical thermal state, and by adding correlation to the number-projected mean-field state. As benchmark examples, we use number-projected configuration interaction and an AGP-based perturbation theory to study the Hydrogen molecule in a minimal basis and the six-site Hubbard model., Comment: 8 pages, 3 figures, 1 supplemental information

Polarizable force fields based on classical Drude oscillators offer a practical and computationally efficient avenue to carry out molecular dynamics (MD) simulations of large biomolecular systems. To treat the polarizable electronic degrees of freedom, the Drude model introduces a virtual charged particle that is attached to its parent nucleus via a harmonic spring. Traditionally, the need to relax the electronic degrees of freedom for each fixed set of nuclear coordinates is achieved by performing an iterative self-consistent field (SCF) calculation to satisfy a selected tolerance. This is a computationally demanding procedure that can increase the computational cost of MD simulations by nearly one order of magnitude. To avoid the costly SCF procedure, a small mass is assigned to the Drude particles, which are then propagated as dynamic variables during the simulations via a dual-thermostat extended Lagrangian algorithm. To help clarify the significance of the dual-thermostat extended Lagrangian propagation in the context of the polarizable force field based on classical Drude oscillators, the statistical mechanics of a dual-temperature canonical ensemble is formulated. The conditions for dynamically maintaining the dual-temperature properties in the case of the classical Drude oscillator are analyzed using the generalized Langevin equation.

A recently proposed extended Hamiltonian approach to switching interaction potentials is generalized to enable adaptive partitioning molecular dynamics simulations. Switching is performed along a fictitious classical degree of freedom whose value determines the mixing ratio of the two potentials on a time scale determined by its associated mass. We propose to choose this associated fictitious mass adaptively so as to ensure a constant time scale for all switching processes. For different model systems, including a harmonic oscillator and a Lennard-Jones fluid, we investigate the window of switching time scales that guarantees the conservation of the extended Hamiltonian for a large number of switching events. The methodology is first applied in the microcanonical ensemble and then generalized to the canonical ensemble using a Nosé-Hoover chain thermostat. It is shown that the method is stable for thousands of consecutive switching events during a single simulation, with constant temperature and a conserved extended Hamiltonian. A slight modification of the original Hamiltonian is introduced to avoid accumulation of small numerical errors incurred after each switching process.

We introduce a method to construct the interface potential from a series of molecular dynamics simulations conducted within the canonical ensemble. The interface potential provides the surface excess free energy associated with the growth of a fluid film from a surface. We collect the force that the fluid exerts on the surface (disjoining pressure) at a series of film thicknesses. These force data are then integrated to obtain the interface potential. “Spreading” and “drying” versions of the general approach are considered. The spreading approach focuses on the growth of a thin liquid film from a solid substrate in a mother vapor. The drying approach focuses on the growth of a thin vapor film on a solid substrate in a mother liquid. The methods provide a means to compute the contact angle of a fluid droplet in contact with the surface. The general method is applied to two model systems: (1) a monatomic Lennard-Jones fluid in contact with atomistically detailed face centered cubic (FCC) substrate and (2) TIP4P/2005 water in contact with a rigid silica surface. For the Lennard-Jones model system, we generate results with both the drying and spreading methods at various temperatures and substrate strengths. These results are compared to those from previous simulation studies. For the water system, the drying method is used to obtain wetting properties over a range of temperatures. The water system also highlights challenges associated with application of the spreading method within the framework pursued here.We introduce a method to construct the interface potential from a series of molecular dynamics simulations conducted within the canonical ensemble. The interface potential provides the surface excess free energy associated with the growth of a fluid film from a surface. We collect the force that the fluid exerts on the surface (disjoining pressure) at a series of film thicknesses. These force data are then integrated to obtain the interface potential. “Spreading” and “drying” versions of the general approach are considered. The spreading approach focuses on the growth of a thin liquid film from a solid substrate in a mother vapor. The drying approach focuses on the growth of a thin vapor film on a solid substrate in a mother liquid. The methods provide a means to compute the contact angle of a fluid droplet in contact with the surface. The general method is applied to two model systems: (1) a monatomic Lennard-Jones fluid in contact with atomistically detailed face centered cubic (FCC) substrate and (2) T...

We present an extension of the locally enhanced sampling method. A restraint potential is introduced to drive the many-replica system to the canonical ensemble corresponding to the physical, single-replica system. Convergence properties are demonstrated using a model rugged two-dimensional potential, for which sampling by conventional equilibrium molecular dynamics is inefficient. Restrained locally enhanced sampling (RLES) is found to explore the space of configurations with an efficiency comparable to that of temperature replica exchange. To demonstrate the potential of RLES for realistic applications, the method is used to fold the 12-residue tryptophan zipper miniprotein in explicit solvent. The RLES algorithm can be incorporated into existing LES implementations with minor code modifications.

Shape anisotropy of colloidal particles can give rise to complex intermolecular interactions that determine particle packing and phase behavior. The vapor-liquid coexistence curves of attractive rough particles display a shift when compared to attractive smooth spherical particles. We use Integral Equation Theory (IET) to determine the vapor-liquid spinodal phase diagram of smooth and rough colloidal particles interacting through square-well attraction. Additionally, we use Gibbs Ensemble Monte Carlo (GEMC) simulations to locate their vapor-liquid coexistence curves. We model a rough colloidal particle as a spherical core with small beads embedded on its surface. The critical point of smooth spherical particle systems predicted by theory and simulations is in quantitative agreement. An increase in surface roughness due to an increase in either the number of beads or the diameter of the beads has a modest effect on the local structure of the system in the supercritical region. In contrast, increasing surface roughness consistently shifts the vapor-liquid coexistence curves to higher temperatures. The critical temperature is found to be a quadratic function of the number of beads. At a fixed bead size and number of beads, the critical temperature does not vary with the arrangement of beads on the core. Both IET and GEMC simulations predict that unlike critical temperatures, critical packing fractions vary non-monotonically with surface roughness. We find that the feasibility and accuracy of the integral equation theory depend sensitively on the chosen closure combination.

We introduce new Langevin-type equations describing the rotational and translational motion of rigid bodies interacting through conservative and non-conservative forces, and hydrodynamic coupling. In the absence of non-conservative forces the Langevin-type equations sample from the canonical ensemble. The rotational degrees of freedom are described using quaternions, the lengths of which are exactly preserved by the stochastic dynamics. For the proposed Langevin-type equations, we construct a weak 2nd order geometric integrator which preserves the main geometric features of the continuous dynamics. The integrator uses Verlet-type splitting for the deterministic part of Langevin equations appropriately combined with an exactly integrated Ornstein-Uhlenbeck process. Numerical experiments are presented to illustrate both the new Langevin model and the numerical method for it, as well as to demonstrate how inertia and the coupling of rotational and translational motion can introduce qualitatively distinct behaviours., 13 pages main text, 5 pages supplementary material, 10 figures, includes links to mp4 video files

We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method. We applied this method to a β-hairpin mini protein, chignolin. In this simulation, we observed not only the folded state but also the misfolded state. We calculated the temperature and pressure dependence of the fractions on the folded, misfolded, and unfolded states. Differences in partial molar enthalpy, internal energy, entropy, partial molar volume, and heat capacity were also determined and agreed well with experimental data. We observed a new phenomenon that misfolded chignolin becomes more stable under high-pressure conditions. We also revealed this mechanism of the stability as follows: TYR2 and TRP9 side chains cover the hydrogen bonds that form a β-hairpin structure. The hydrogen bonds are protected from the water molecules that approach the protein as the pressure increases.

Values of the fifth virial coefficient, compressibility factors, and fluid-fluid coexistence curves of binary asymmetric nonadditive mixtures of hard disks are reported. The former correspond to a wide range of size ratios and positive nonadditivities and have been obtained through a standard Monte Carlo method for the computation of the corresponding cluster integrals. The compressibility factors as functions of density, derived from canonical Monte Carlo simulations, have been obtained for two values of the size ratio ($q=0.4$ and $q=0.5$), a value of the nonadditivity parameter $\Delta=0.3$), and five values of the mole fraction of the species with the biggest diameter ($x_1=0.1$, $0.3$, $0.5$, $0.7$, and $0.9$). Some points of the coexistence line relative to the fluid-fluid phase transition for the same values of the size ratios and nonadditivity parameter have been obtained from Gibbs Ensemble Monte Carlo simulations. A comparison is made between the numerical results and those that follow from some theoretical equations of state., Comment: 11(+4) pages, 11 figures; Supplemental Material included

When an important process of a molecular system occurs via a combination of two or more rare events, which occur almost independently to one another, computational sampling for the important process is difficult. Here, to sample such a process effectively, we developed a new method, named the "multi-dimensional Virtual-system coupled Monte Carlo (multi-dimensional-VcMC)" method, where the system interacts with a virtual system expressed by two or more virtual coordinates. Each virtual coordinate controls sampling along a reaction coordinate. By setting multiple reaction coordinates to be related to the corresponding rare events, sampling of the important process can be enhanced. An advantage of multi-dimensional-VcMC is its simplicity: Namely, the conformation moves widely in the multi-dimensional reaction coordinate space without knowledge of canonical distribution functions of the system. To examine the effectiveness of the algorithm, we introduced a toy model where two molecules (receptor and its ligand) bind and unbind to each other. The receptor has a deep binding pocket, to which the ligand enters for binding. Furthermore, a gate is set at the entrance of the pocket, and the gate is usually closed. Thus, the molecular binding takes place via the two events: ligand approach to the pocket and gate opening. In two-dimensional (2D)-VcMC, the two molecules exhibited repeated binding and unbinding, and an equilibrated distribution was obtained as expected. A conventional canonical simulation, which was 200 times longer than 2D-VcMC, failed in sampling the binding/unbinding effectively. The current method is applicable to various biological systems.

Supersaturated steam modeled by the Gaussian charge polarizable model [P. Paricaud, M. Předota, and A. A. Chialvo, J. Chem. Phys. 122, 244511 (2005)] and BK3 model [P. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)] has been simulated at conditions occurring in steam turbines using the multiple-particle-move Monte Carlo for both the homogeneous phase and also implemented for the Gibbs ensemble Monte Carlo molecular simulation methods. Because of these thermodynamic conditions, a specific simulation algorithm has been developed to bypass common simulation problems resulting from very low densities of steam and cluster formation therein. In addition to pressure-temperature-density and orthobaric data, the distribution of clusters has also been evaluated. The obtained extensive data of high precision should serve as a basis for development of reliable molecular-based equations for properties of metastable steam.

A huge gap in time between the experiment and the atomistic simulation restricts us from accessing a realistic glass structure, because the glass state is highly dependent on the cooling rate. In this study, to improve computational efficiency, we propose a simple but effective procedure, which enables us to explore a deeper basin in the energy landscape of glassy materials without a substantial increase in the computational cost. This method combines canonical ensemble molecular dynamics (MD) and energy minimization while controlling the stress of the MD system, and it is called the quasi-slow-quenching (QSQ) method. Herein, we measured the performance of the QSQ method using a binary silicate, (SiO2)80(Na2O)20, and we observed that a more stable configuration can be obtained in comparison with the conventional isobaric-isothermal MD method. The stable glass model appears to possess a lower glass transition temperature (Tg), confirming that the QSQ method finds a deeper local minimum closer to the super-cooled glass state. We also conducted further validation tests for various oxide glasses, including silicate, borate, phosphate, and their mixtures, and we verified that the QSQ method consistently enables the glassy materials to attain energetically more stable configurations and denser structures.

Properly simulating nonequilibrium phenomena such as thermal transport and shock wave propagation in complex condensed matter systems require the conservation of system’s internal energy. This precludes the application of the coarse-grained (CG) generalized Langevin equation (GLE) dynamics due to the presence of dissipative interactions. Attempts to address this issue have been pursued both phenomenologically and from entropy-based first principles for dissipative particle dynamics (DPD, a Markovian variant of the CG GLE dynamics) by introducing an energy conserving extension of DPD (DPD-E). We present here a rigorous microscopic derivation of two energy conserving variants of the CG GLE dynamics by extending the CG equations of motion to include the GLE for certain internal energy observables of the microscopic system. We consider two choices of such observables: the total internal energy and a set of internal energies of the CG particles. The derivation is performed using the Mori-Zwanzig projection operator method in the Heisenberg picture for time evolution of thermodynamic expectations and the recently introduced interpretation of the Zwanzig projection operator [S. Izvekov, J. Chem. Phys. 146(12), 124109 (2017)] which allows an exact calculation of the memory and projected terms. We begin with equilibrium conditions and show that the GLE dynamics for the internal energy observables is purely dissipative. Our extension of the GLE dynamics to quasiequilibrium conditions (necessary to observe heat transport) is based on the generalized canonical ensemble approach and transport equation using the nonequilibrium statistical operator (NSO) method. We derive closed microscopic expressions for conductive heat transfer coefficients in the limit of neglecting dissipation in heat transfer and in the lowest order of deviation from equilibrium. After employing the Markov approximation, we compare the equations of motion to the published DPD-E equations. Our equations contain additional energy transfer terms not reported in the previous works. Additionally, we show that, despite neglecting dissipative processes in heat transport, the heat transfer coefficients and random force are related in a way reminiscent of the fluctuation-dissipation relation. The formalism presented here is sufficiently general for the rigorous formulation of the GLE dynamics for arbitrary microscopic phase space observables as well as sampling different microscopic ensembles in CG simulations.Properly simulating nonequilibrium phenomena such as thermal transport and shock wave propagation in complex condensed matter systems require the conservation of system’s internal energy. This precludes the application of the coarse-grained (CG) generalized Langevin equation (GLE) dynamics due to the presence of dissipative interactions. Attempts to address this issue have been pursued both phenomenologically and from entropy-based first principles for dissipative particle dynamics (DPD, a Markovian variant of the CG GLE dynamics) by introducing an energy conserving extension of DPD (DPD-E). We present here a rigorous microscopic derivation of two energy conserving variants of the CG GLE dynamics by extending the CG equations of motion to include the GLE for certain internal energy observables of the microscopic system. We consider two choices of such observables: the total internal energy and a set of internal energies of the CG particles. The derivation is performed using the Mori-Zwanzig projection ope...

The elasticity of dsDNA molecules is investigated by Monte Carlo simulations based on a coarse-grained model of DNA. The force-displacement (f-r) curves are computed under the constraints of the constant force (Gibbs) or the constant length (Helmholtz) ensemble. Particular attention was paid to the compressional (negative) and weak tensile forces. It was confirmed that simulations using the vector Gibbs ensemble fail to represent the compression behavior of polymers. Simulations using the scalar Gibbs protocol resulted in a qualitatively correct compressional response of DNA provided that the quadratic averages of displacements were employed. Furthermore, a well-known shortcoming of the popular Marko-Siggia relation for DNA elasticity at weak tensile forces is elucidated. Conversely, the function f-r from the simulation at the constant length constraint, as well as the new closed-form expressions, provides a realistic depiction of the DNA elasticity over the wide range of negative and positive forces. Merely a qualitative resemblance of the compression functions f-r predicted by the employed approaches supports the notion that the elastic response of DNA molecules may be greatly affected by the specifics of the experimental setups and the kind of averaging of the measured variable.

In this article, we present a molecular thermodynamic study of a system of N particles contained within a volume V and interacting via a hard-core pair potential with an attractive interaction according to the Wolf model for charged systems. This variable-range potential is characterized by three parameters: the repulsive hard-core diameter σ, the energy-well depth ϵ, and the inverse range α; a fourth parameter of the model is a cut-off distance xc that depends on α according to the relation xc = 2/α. Two equations of state (EOSs) are presented and derived from thermodynamic perturbation theory and Monte Carlo (MC) simulation data. The first EOS is given by the standard Zwanzig's high-temperature expansion of the Helmholtz free energy, where the first three perturbation terms a1, a2, and a3 were obtained from MC simulations in the canonical ensemble (NVT) and parameterized as functions of α and the reduced density of particles ρ* = Nσ3/V. The second EOS was obtained from the discrete perturbation theory applied to a discrete representation of the Wolf potential. Results for pressures, internal energies, and isochoric heat capacities are compared to the MC computer simulation data of the Wolf system, including vapor-liquid coexistence curves, for different values of α. Overall, both EOSs give a very good representation of the thermodynamic properties of the Wolf fluid when 0.3 ≤ α ≤ 1.0 and 0.05 ≤ ρ* ≤ 0.8. Since the Yukawa fluid can reproduce information of screened ionic interactions, we discuss the equivalence between the Wolf and Yukawa fluids in the context of equivalent systems in liquid theory.

In this paper, equilibrium properties of structure II hydrates of hydrogen were determined from Monte Carlo simulations in the isothermal-isobaric Gibbs ensemble. Water and hydrogen molecules are described by the TIP4P/Ice and Silvera-Goldman models, respectively. The use of the Gibbs ensemble has many key advantages for the simulation of hydrates. By the separation of hydrogen vapor and hydrate phases into their own domains, coupled with transfer moves of hydrogen molecules between domains, cage occupancies were determined. Furthermore, the choice of this ensemble also allows equilibrium lattice constants and guest molecule chemical potentials to be straightforwardly estimated. Results for hydrogen mass fractions indicate reasonable agreement with prior simulation data and theoretical models, while detailed analysis of cage occupancy distributions and neighboring cage pair occupancy combinations gives valuable insight into the behavior of this hydrate at the inter-cage scale. These results will aid in the construction of theoretical models, for which knowledge of the occupancy of neighboring cages is of great importance. In support of previous experimental and theoretical works, we also find evidence of double occupancy of a few small cages inside of the hydrate stability zone, albeit at very high pressures; approximately 0.1% of small cages are doubly occupied at 300 MPa, for temperatures of 225 K and 250 K.

Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical integration may distort such assumption. Fortunately, backward error analysis allows us to identify the quantity that is actually subject to equipartition. This is related to a shadow Hamiltonian, which coincides with the specified Hamiltonian only when the time-step size approaches zero. This paper deals with discretization effects in a straightforward way. With a small computational overhead, we obtain refined versions of the kinetic and potential energies, whose sum is a suitable estimator of the shadow Hamiltonian. Then, we tune the thermostatting procedure by employing the refined kinetic energy instead of the conventional one. This procedure is shown to reproduce a canonical ensemble compatible with the refined system, as opposed to the original one, but canonical averages regarding the latter can be easily recovered by reweighting. Water, modeled as a rigid body, is an excellent test case for our proposal because its numerical stability extends up to time steps large enough to yield pronounced discretization errors in Verlet-type integrators. By applying our new approach, we were able to mitigate discretization effects in equilibrium properties of liquid water for time-step sizes up to 5 fs., accepted manuscript

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems.

In this study, Boltzmann inversion is applied in conjunction with molecular dynamics simulations to derive inter-molecular potential for protein lysozyme in aqueous solution directly from experimental static structure factor. The potential has a soft repulsion at short distances and an attraction well at intermediate distances that give rise to the liquid-liquid phase separation. Moreover, Gibbs ensemble Monte Carlo simulations demonstrate that a non-spherical description of lysozyme is better suited to correctly reproduce the experimentally observed properties of such a phase separation. Our findings shed new light on the common problem in molecular and cell biology: “How to model proteins in their natural aqueous environments?”

The instantaneous and centroid triplet structure factors, S(3)(k1,k2), of liquid (one-center) para-hydrogen are computed on the crystallization line for temperatures T/K ≤ 33. The focus is on salient equilateral and isosceles features, and the methods utilized are path integral Monte Carlo (PIMC) simulations and Ornstein-Zernike (OZ) integral equations, which involve Jackson-Feenberg convolution (JF3) and other distinct closures. Long path integral simulation runs are carried out in the canonical ensemble, so as to obtain sufficiently accurate direct PI triplet results. Conclusions are drawn regarding general triplet structure features and the role and usefulness of the OZ closures. The equilateral features are studied in more detail, and one finds that (a) PIMC results point to the existence of regularity in the centroid main peak amplitudes; (b) some of the studied closures give qualitative descriptions for wave numbers below k ≈ 1 A−1, but they all fail to describe the main peak amplitude regions (1.75 < k/A−1 < 2.5); and (c) JF3 plays the role of a limit closure that is valid for increasing wave numbers (k ≥ 2.6 A−1). In addition, representative isosceles PI features turn out to be reasonably bounded (within Δk = 0.1 A−1) by those of some closures.

The theoretical framework to evaluate small-angle scattering (SAS) profiles for multi-component macromolecular solutions is re-examined from the standpoint of molecular simulations in the grand-canonical ensemble, where the chemical potentials of all species in solution are fixed. This statistical mechanical ensemble resembles more closely scattering experiments, capturing concentration fluctuations that arise from the exchange of molecules between the scattering volume and the bulk solution. The resulting grand-canonical expression relates scattering intensities to the different intra- and intermolecular pair distribution functions, as well as to the distribution of molecular concentrations on the scattering volume. This formulation represents a generalized expression that encompasses most of the existing methods to evaluate SAS profiles from molecular simulations. The grand-canonical SAS methodology is probed for a series of different implicit-solvent, homogeneous systems at conditions ranging from dilute to concentrated. These systems consist of spherical colloids, dumbbell particles, and highly flexible polymer chains. Comparison of the resulting SAS curves against classical methodologies based on either theoretical approaches or canonical simulations (i.e., at a fixed number of molecules) shows equivalence between the different scattering intensities so long as interactions between molecules are net repulsive or weakly attractive. On the other hand, for strongly attractive interactions, grand-canonical SAS profiles deviate in the low- and intermediate-q range from those calculated in a canonical ensemble. Such differences are due to the distribution of molecules becoming asymmetric, which yields a higher contribution from configurations with molecular concentrations larger than the nominal value. Additionally, for flexible systems, explicit discrimination between intra- and inter-molecular SAS contributions permits the implementation of model-free, structural analysis such as Guinier's plots at high molecular concentrations, beyond what the traditional limits are for such analysis.

Isomerization kinetics of molecules in the gas phase naturally falls on the microcanonical ensemble of statistical mechanics, which for small systems might significantly differ from the more traditional canonical ensemble. In this work, we explore the examples of cis-trans isomerization in butane and bibenzyl and to what extent the fully atomistic rate constants in isolated molecules can be reproduced by coarse-graining the system into a lower dimensional potential of mean force (PMF) along a reaction coordinate of interest, the orthogonal degrees of freedom acting as a canonical bath in a Langevin description. Time independent microcanonical rate constants can be properly defined from appropriate state residence time correlation functions; however, the resulting rate constants acquire some time dependence upon canonical averaging of initial conditions. Stationary rate constants are recovered once the molecule is placed into a real condensed environment pertaining to the canonical ensemble. The effective one-dimensional kinetics along the PMF, based on appropriately chosen inertia and damping parameters, quantitatively reproduces the atomistic rate constants at short times but deviates systematically over long times owing to the neglect of some couplings between the system and the bath that are all intrinsically present in the atomistic treatment. In bibenzyl, where stronger temperature effects are noted than in butane, the effective Langevin dynamics along the PMF still performs well at short times, indicating the potential interest of this extremely simplified approach for sampling high-dimensional energy surfaces and evaluating reaction rate constants.

The phase behavior of complex fluid mixtures is of continuing interest, but obtaining the phase diagram from computer simulations can be challenging. In the Gibbs ensemble method, for example, each of the coexisting phases is simulated in a different cell, and ensuring the equality of chemical potentials of all components requires the transfer of molecules from one cell to the other. For complex fluids such as polymers, successful insertions are rare. An alternative method is to simulate both coexisting phases in a single simulation cell, with an interface between them. The challenge here is that the interface position moves during the simulation, making it difficult to determine the concentration profile and coexisting concentrations. In this work, we propose a new method for single cell simulations that uses a spatial concentration autocorrelation function to (spatially) align instantaneous concentration profiles from different snapshots. This allows one to obtain average concentration profiles and hence the coexisting concentrations. We test the method by calculating the phase diagrams of two systems: the Widom-Rowlinson model and the symmetric blends of freely jointed polymer molecules for which phase diagrams from conventional methods are available. Excellent agreement is found, except in the neighborhood of the critical point where the interface is broad and finite size effects are important. The method is easy to implement and readily applied to any mixture of complex fluids.

In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential. We analyze the behavior of the confined system for several supercritical temperatures as a function of variation of molecular parameters: potential range λ, bulk densities ρb*, pore width H, cutoff range interaction rc*, and range of the potential and depth of the particle-wall (λw, ew*). Additionally, we include predictions for liquid-vapor coexistence of bulk associative particles and how their critical properties are modified by the presence of associative sites in the molecule. The molecular simulation data presented in this work are of prime importance to the development of theoretical approaches for inhomogeneous fluids as classical density functional theory. The simulation results presented here are resourceful for predicting adsorption isotherms of real associating fluids such as water.

The stability of the body-centered cubic (bcc) solid phase of classical hard spheres is of intrinsic interest and is also relevant to the development of perturbation theories for bcc solids of other model systems. Using canonical ensemble Monte Carlo, we simulated systems initialized in a perfect bcc lattice at various densities in the solid region. We observed that the systems rapidly evolved into one of four structures that then persisted for the duration of the simulation. Remarkably, one of these structures was identified as cI16, a cubic crystalline structure with 16 particles in the unit cell, which has recently been observed experimentally in lithium and sodium solids at high pressures. The other three structures do not exhibit crystalline order but are characterized by common patterns in the radial distribution function and bond-orientational order parameter distribution; we refer to them as bcc-di, with i ranging from 1 to 3. We found similar outcomes when employing any of the three single occupancy cell (SOC) restrictions commonly used in the literature. We also ran long constant-pressure simulations with box shape fluctuations initiated from bcc and cI16 initial configurations. At lower pressures, all the systems evolved to defective face-centered cubic (fcc) or hexagonal close-packed (hcp) structures. At higher pressures, most of the systems initiated as bcc evolved to cI16 with some evolving to defective fcc/hcp. High pressure systems initiated from cI16 remained in that structure. We computed the chemical potential of cI16 using the Einstein crystal reference method and found that it is higher than that of fcc by ∼0.5kT-2.5kT over the pressure range studied, with the difference increasing with pressure. We find that the undistorted bcc solid, even with constant-volume and SOC restrictions applied, is so mechanically unstable that it is unsuitable for consideration as a metastable phase or as a reference system for studying bcc phases of other systems. On the other hand, cI16 is a mechanically stable structure that can spontaneously emerge from a bcc starting point but it is thermodynamically metastable relative to fcc or hcp.

A rigorous statistical analysis is presented for Gibbs ensemble Monte Carlo simulations. This analysis reduces the uncertainty in the critical point estimate when compared with traditional methods found in the literature. Two different improvements are recommended due to the following results. First, the traditional propagation of error approach for estimating the standard deviations used in regression improperly weighs the terms in the objective function due to the inherent interdependence of the vapor and liquid densities. For this reason, an error model is developed to predict the standard deviations. Second, and most importantly, a rigorous algorithm for nonlinear regression is compared to the traditional approach of linearizing the equations and propagating the error in the slope and the intercept. The traditional regression approach can yield nonphysical confidence intervals for the critical constants. By contrast, the rigorous algorithm restricts the confidence regions to values that are physically sensible. To demonstrate the effect of these conclusions, a case study is performed to enhance the reliability of molecular simulations to resolve the n-alkane family trend for the critical temperature and critical density.

In a molecular dynamics (MD) simulation, various thermostat algorithms, including Langevin dynamics (LD), Nose-Hoover (NH), and weak-coupling (WC) thermostats, can be used to keep the simulation temperature constant. A canonical ensemble is generated by the use of LD and NH, while the nature of the ensemble produced by WC has not yet been identified. A few years ago, it was shown that when using a WC thermostat with particular values of the temperature coupling time for liquid water at ambient temperature and pressure, the distribution of the potential energy is less wide than the canonical one. This led to an artifact in temperature replica-exchange molecular dynamics (T-REMD) simulations in which the potential energy distributions appear not to be equal to the ones of standard MD simulations. In this paper, we re-investigate this problem. We show that this artifact is probably due to the ensemble generated by WC being incompatible with the T-REMD replica-exchange criterion, which assumes a canonical configurational ensemble. We also show, however, that this artifact can be reduced or even eliminated by particular choices of the temperature coupling time of WC and the replica-exchange time period of T-REMD, i.e., when the temperature coupling time is chosen very close to the MD time step or when the exchange time period is chosen large enough. An attempt to develop a T-REMD replica-exchange criterion which is likely to be more compatible with the WC configurational ensemble is reported. Furthermore, an exchange criterion which is compatible with a microcanonical ensemble is used in total energy REMD simulations.

We study a system of few colloids confined in a small spherical cavity by event driven molecular dynamics simulations in the canonical ensemble. The colloidal particles interact through a short range square-well potential, which takes into account the basic elements of attraction and excluded-volume repulsion of the interaction among colloids. We analyze the structural and thermodynamic properties of this few-body confined system in the framework of the theory of inhomogeneous fluids. Pair correlation functions and density profiles across the cavity are used to determine the structure of the system and the spatial characteristics of its inhomogeneities. Pressure on the walls, internal energy and surface quantities such as surface tension and adsorption are also analyzed for the whole range of densities, temperatures and number of particles considered. We have characterized the structure of systems from 2 to 6 confined particles as function of density and temperature, identifying the distinctive qualitative behaviors all over the thermodynamic plane $T-\rho$ in a few-particle equivalence to phase diagrams of macroscopic systems. Applying the extended law of corresponding states the square well interaction is mapped to the Asakura-Oosawa model for colloid-polymer mixtures. We link explicitly the temperature in the confined square-well fluid to the equivalent packing fraction of polymers in the Asakura-Oosawa model. Using this approach we study the confined system of few colloids in a colloid-polymer mixture., Comment: 17 pages, 2 tables, and 17 figures

Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble.

© 2015 AIP Publishing LLC. The effects of confinement on colloidal self-assembly in the case of fixed number of confined particles are studied in the one dimensional lattice model solved exactly in the grand canonical ensemble (GCE) in Pękalski et al. [J. Chem. Phys. 142, 014903 (2015)]. The model considers a pair interaction defined by a short-range attraction plus a longer-range repulsion. We consider thermodynamic states corresponding to self-assembly into clusters. Both fixed and adaptive boundaries are studied. For fixed boundaries, there are particular states in which, for equal average densities, the number of clusters in the GCE is larger than in the canonical ensemble. The dependence of pressure on density has a different form when the system size changes with fixed number of particles and when the number of particles changes with fixed size of the system. In the former case, the pressure has a nonmonotonic dependence on the system size. The anomalous increase of pressure for expanding system is accompanied by formation of a larger number of smaller clusters. In the case of elastic confining surfaces, we observe a bistability, i.e., two significantly different system sizes occur with almost the same probability. The mechanism of the bistability in the closed system is different to that of the case of permeable walls, where the two equilibrium system sizes correspond to a different number of particles.

We show that for solids the effective Hessian matrix, averaged over the canonical ensemble, can be calculated from the force covariance matrix. This effective Hessian reduces to the standard Hessian as the temperature approaches zero, while at finite temperatures it implicitly includes anharmonic corrections. As a case study, we calculate the effective Hessians and the corresponding normal mode eigenvectors and frequencies for the crystalline organic explosives pentaerythritol tetranitrate and α-1,3,5-trinitro-1,3,5-triazacyclohexane. The resulting normal mode frequencies are compared to those obtained by diagonalizing the standard Hessian matrix of second derivatives in Cartesian displacements about the potential energy minimum. Effects of temperature and statistical noise on the effective Hessians and normal mode frequencies are discussed.

Nucleation of bubbles and droplets is of fundamental interest in science and technology and has been widely investigated through experiments, theory, and simulations. Giving the rare event nature of these phenomena, nucleation simulations are computationally costly and require the use of a limited number of particles. Moreover, they are often performed in the canonical ensemble, i.e., by fixing the total volume and number of particles, to avoid the additional complexities of implementing a barostat. However, cavitation and droplet formation take place differently depending on the ensemble. Here, we analyze the importance of finite-size effects in cavitation and droplet formation. We present simple formulas which predict the finite-size corrections to the critical size, the nucleation barrier, and the nucleation rates in the canonical ensemble very accurately. These results can be used to select an appropriate system-size for simulations and to get a more precise evaluation of nucleation in complex substances, by using a small number of molecules and correcting for finite-size effects.

Off-lattice Monte Carlo simulations in the canonical ensemble are used to study polymer-particle interactions in nanocomposite materials. Specifically, nanoscale interactions between long polymer chains (N=550) and strongly adsorbing colloidal particles of comparable size to the polymer coils are quantified and their influence on nanocomposite structure and dynamics investigated. In this work, polymer-particle interactions are computed from the integrated force-distance curve on a pair of particles approaching each other in an isotropic polymer medium. Two distinct contributions to the polymer-particle interaction potential are identified: a damped oscillatory component that is due to chain density fluctuations and a steric repulsive component that arises from polymer confinement between the surfaces of approaching particles. Significantly, in systems where particles are in a dense polymer melt, the latter effect is found to be much stronger than the attractive polymer bridging effect. The polymer-particle interaction potential and the van der Waals potential between particles determine the equilibrium particle structure. Under thermodynamic equilibrium, particle aggregation is observed and there exists a fully developed polymer-particle network at a particle volume fraction of 11.3%. Near-surface polymer chain configurations deduced from our simulations are in good agreement with results from previous simulation studies.

We propose Lennard-Jones potential parameters for interatomic interactions of linear and branched alkanes based on matching the results of Gibbs ensemble simulations of vapor-liquid equilibria to experimental data. The alkane model is similar as in the OPLS-AA [W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225 (1996)], but multiple atom types for carbon based on the number of covalently bonded hydrogen atoms are necessary to accurately reproduce liquid densities and enthalpies of vaporization with the errors of 2.1% and 3.3%, respectively, for hydrocarbons of various chain lengths and structures. We find that the attraction energies of the carbon atoms are almost proportional to the number of covalent hydrogen atoms with each increasing the carbon energy parameter by ≈0.033 kcal/mol. Though the present force field outperforms the OPLS-AA force field for alkanes we studied, systematic deviations for vapor pressures are still observed with errors of 15%–30%, and critical temperatures are slightly underestimated. We think that these shortcomings are probably due to the inadequacy of the two-parameter Lennard-Jones potential, and especially its behavior at short distances.

Gibbs ensemble Monte Carlo simulations were used to test the ability of intermolecular pair potentials derived ab initio from quantum mechanical principles, enhanced by Axilrod-Teller triple-dipole interactions, to predict the vapor-liquid phase equilibria of pure neon, pure argon, and the binary mixtures neon-argon and argon-krypton. The interaction potentials for Ne-Ne, Ar-Ar, Kr-Kr, and Ne-Ar were taken from literature; for Ar-Kr a different potential has been developed. In all cases the quantum mechanical calculations had been carried out with the coupled-cluster approach [CCSD(T) level of theory] and with correlation consistent basis sets; furthermore an extrapolation scheme had been applied to obtain the basis set limit of the interaction energies. The ab initio pair potentials as well as the thermodynamic data based on them are found to be in excellent agreement with experimental data; the only exception is neon. It is shown, however, that in this case the deviations can be quantitatively explained by quantum effects. The interaction potentials that have been developed permit quantitative predictions of high-pressure phase equilibria of noble-gas mixtures.

A simple statistical theory of irreversible processes in a subsystem coupled to (or "interrupted" by) a stochastic bath is formulated. The theory does not explicitly invoke time scale separation that underlies the standard description of nonequilibrium phenomena and is intrinsic to the concept of quasiequilibrium in the canonical ensemble. Arbitrary statistics and speed of bath fluctuations are straightforwardly treated by the theory. Except in the case of an extremely slow, nonequilibrium bath, the ultimate statistics of interrupted escape are shown to be Poisson, which is solely a consequence of the stationary nature of interactions in a sufficiently dense system. In the limit of a fast bath, the corresponding relaxation rate is shown to equal the initial rate of decay, thus validating a wide class of Golden Rate type expressions at long times. This true exponentiality thus appears when the time scale separation takes place. The theory also applies to a number of specific phenomena including transport in a fluctuating or disordered medium, gated reactions, the line shape theory, and the quantum Zeno effect. The general nature of motional narrowing phenomena is demonstrated and related to the bath mediated slowing down of a decay process with a nearly deterministic uninterrupted escape probability. The corresponding survival probability is shown also to exhibit discernible oscillations around the exponential background. Mathematical tools necessary for using the theory in specific applications are exposed in some detail.

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

We present a density functional theory for inhomogeneous fluids at constant external pressure. The theory is formulated for a volume-dependent density, n(r,V), defined as the conjugate variable of a generalized external potential, nu(r,V), that conveys the information on the pressure. An exact expression for the isothermal-isobaric free-energy density functional is obtained in terms of the corresponding canonical ensemble functional. As an application we consider a hard-sphere system in a spherical pore with fluctuating radius. In general we obtain very good agreement with simulation. However, in some situations a peak develops in the center of the cavity and the agreement between theory and simulation becomes worse. This happens for systems where the number of particles is close to the magic numbers N=13, 55, and 147.

The global phase behavior ~i.e., vapor-liquid and fluid-solid equilibria! of rigid linear Lennard-Jones ~LJ! chain molecules is studied. The phase diagrams for three-center and five-center rigid model molecules are obtained by computer simulation. The segment-segment bond lengths are L5s, so that models of tangent monomers are considered in this study. The vapor-liquid equilibrium conditions are obtained using the Gibbs ensemble Monte Carlo method and by performing isobaric-isothermal NPT calculations at zero pressure. The phase envelopes and critical conditions are compared with those of flexible LJ molecules of tangent segments. An increase in the critical temperature of linear rigid chains with respect to their flexible counterparts is observed. In the limit of infinitely long chains the critical temperature of linear rigid LJ chains of tangent segments seems to be higher than that of flexible LJ chains. The solid-fluid equilibrium is obtained by Gibbs–Duhem integration, and by performing NPT simulations at zero pressure. A stabilization of the solid phase, an increase in the triple-point temperature, and a widening of the transition region are observed for linear rigid chains when compared to flexible chains with the same number of segments. The triple-point temperature of linear rigid LJ chains increases dramatically with chain length. The results of this work suggest that the fluid-vapor transition could be metastable with respect to the fluid-solid transition for chains with more than six LJ monomer units.

A common strategy for mapping coexistence curves is to employ multi-canonical (MUCA) sampling to simulate along a macrostate path connecting two phases. Central to this approach is the task of accurately calculating the importance weights used in the MUCA procedure, which are needed for both effective sampling and accurate determination of phase boundaries. The purpose of this study is to develop a strategy for determining the importance weights that is built upon Bennett's optimized acceptance ratio method. This approach is shown to be closely related to transition matrix schemes, and is used to compute the vapor-liquid equilibrium of a Lennard-Jones fluid and the liquid-liquid equilibrium of a n-hexane/n-perfluorohexane mixture. For the Lennard-Jones system, the importance weights as a function of the number of particles "N" (at fixed temperature and volume) are obtained by using Bennett's method to estimate free energy differences between N and N+1 particle systems over the desired range of N values. In this application, the method is found to perform slightly better than a related transition matrix scheme. For the n-hexane/n-perfluorohexane liquid mixture, the method is designed to obtain weights as a function of composition (for fixed temperature, pressure, and total number of particles); in this case, the method is found to outperform the Gibbs ensemble approach.

Grand canonical and canonical ensemble Monte Carlo simulation methods are used to study the structure and phase behavior of Lennard-Jones fluids confined between the parallel (100) planes of the face centered cubic crystal. Ultra thin slit pores of the width allowing for the formation of only two adsorbate layers are considered. It is demonstrated that the structure of adsorbed phases is very sensitive to the wall-wall separation and to the strength of the fluid-wall potential. It is also shown that the structure of low temperature (solid) phases strongly depends on the fluid density. In particular, when the surface field is sufficiently strong, then the high density phases may exhibit a domain wall structure, quite the same as found in monolayer films adsorbed at a single substrate wall. On the other hand, the weakening of the surface potential leads to the regime in which only the hexagonally ordered bilayer structure is stable. The phase diagrams for a series of systems are estimated. It is shown that, depending on the pore width and the temperature, the condensation leads to the formation of the commensurate or incommensurate phases. The incommensurate phases may have the domain-wall or the hexagonal structure depending on the pore width and the strength of the fluid-wall potential.

We report a new method for calculating the Wigner transform of the Boltzmann operator in the canonical ensemble. The transform is accomplished by writing the Boltzmann operator in a semiharmonic form, utilizing the variational centroid effective frequencies introduced by Feynman and Kleinert (FK). The approximate many-body Wigner transformed Boltzmann operator is then utilized with a linearized path integral (LPI) representation for correlation functions. It is shown that this new FK-LPI method is capable of calculating quite accurately the short time behavior of linear and highly nonlinear correlation functions for low temperature Lennard-Jones model systems and that it is vastly superior to classical dynamics. The feasibility of the FK-LPI method for large systems is illustrated by considering a model liquid composed of 32 oxygen molecules with periodic boundary conditions. Initial conditions for molecular dynamics are obtained from its Boltzmann Wigner transform and the FK-LPI method is shown to describe correctly the zero-point motion of the liquid. The effective frequency representation of the Wigner transformed thermal density operator provides an efficient way of sampling nonclassical initial conditions for molecular-dynamics simulations more generally. Applications to vibrational energy relaxation and rate constant calculations in complex molecular systems are discussed.

The equilibrium thermodynamics of confined linear homopolymers between two impenetrable walls was investigated by means of Monte Carlo simulations in the canonical ensemble with the parallel tempering algorithm. The influence of confinement and chain size on the potential energy, heat capacity, radius of gyration, and the end-to-end distance was investigated as a function of temperature. A bead–spring model was used to simulate the chains. Two conformational changes were observed regardless of the differences in confinement of chain size: The coil-to-globule transition that resembles the gas to liquid transition and the liquidlike to solidlike transition. An additional transition between solid states was also observed for the smallest chain size studied (16 beads). Results indicate a shift of the coil-to-globule transition temperature to lower values as the slit width approaches the two-dimensional case (wall separation equal to bead diameter), and to higher temperature regions as the chain length increas...

By implementing the parallel-tempering algorithm to the canonical ensemble, the conformational changes of an isolated Ac–W(RAAAR)5A–NH2 model peptide were determined. The interparticle interactions were modeled using a minimalist potential, i.e., a beadlike model that uses harmonic oscillators to describe covalent interactions and modified Lennard-Jones potentials to model nonbonding interactions. In particular, the interactions between arginines are modeled by repulsive interactions, causing a stabilization of the alpha-helix structure at low temperatures. The conformational changes were identified by anomalies in the constant volume heat capacity as a function of temperature. Namely, the temperature at which the constant volume heat capacity reached a maximum in the transition region was associated with the temperature at which a conformational change occurred. The transitions were also characterized by computing the radius of gyration of the peptide and the most probable isomeric structure obtained at ...

The vapor–liquid equilibria of pure krypton were calculated by Gibbs ensemble Monte Carlo simulation using two different ab initio pair potentials. One pair potential was obtained from coupled-cluster calculations, using the CCSD(T) level of theory and two successive correlation consistent basis sets, aug-cc-pVTZ and -pVQZ. The resulting pair potentials were extrapolated to obtain the basis set limit of the interaction energies. The second ab initio potential was taken from literature. It is shown that the coupled-cluster potential leads to a quantitative prediction of second virial coefficients, vapor pressures, and orthobaric densities, if Axilrod–Teller triple-dipole potentials are included in the simulations.

Canonical ensemble Monte Carlo simulations of 55-atom Morse clusters are used to study the effect of the range of the pair interaction on the cluster melting transition. Several different structural indicators are employed to monitor the solid-liquid transition and to locate the melting and freezing temperatures. The behavior of Landau free energy curves in the solid-liquid phase coexistence regime is correlated with the distribution of inherent minima sampled by the system. The melting transition temperatures, the width of the phase coexistence regime, and the internal energy change on melting are shown to increase with decreasing range of the pair interaction, which parallels the behavior seen in bulk Morse systems. Unlike in the case of bulk melting, cluster melting falls into three distinct categories based on the range of the pair interaction: (i) a rigidity transition in long-range systems with a low density of metastable states, (ii) the cluster analogue of bulk melting where the system transits from the basin of an ordered global minima into a set of metastable, amorphous packing minima, and (iii) transition from a set of defected solid-like minima into a set of amorphous packing minima.

The global phase diagram (i.e., vapor–liquid and fluid–solid equilibrium) of two-center Lennard-Jones (2CLJ) model molecules of bond length L=σ has been determined by computer simulation. The vapor–liquid equilibrium conditions are obtained using the Gibbs ensemble Monte Carlo method and by performing isobaric-isothermal NPT calculations at zero pressure. In the case of the solid phase, two close-packed solidstructures are considered: In the first structure, the molecules are located in layers and all molecular axes point in the same direction; and in the second structure, the atoms form a close-packed arrangement but the molecular axes of the diatomic molecules have random orientations. It is shown that at the vapor–liquid–solid triple-point temperature, the orientationally disordered solid is the stable structure for the solid phase of this model. The vapor–liquid-disordered solid triple-point temperature of the 2CLJ model, with bond length L=σ, is located at T*=0.650(4). This is very close to the triple-point temperature of the Lennard-Jones monomer system (T*=0.687). At very low temperatures, the ordered solid is the stable phase. The vapor-ordered solid-disorderedsolid triple point is situated at T*=0.282. The simulation data are compared to Wertheim’s first-order thermodynamic perturbation theory (TPT1) for the fluid and solid phases. It is found that Wertheim’s TPT1 not only provides an accurate description of the equation of state in both the fluid and solid phases, but also provides accurate values of the free energies. The prediction of Wertheim’s TPT1 for the global phase diagram of the 2CLJ model shows excellent agreement with the simulation results, illustrating the possibility of using Wertheim’s perturbation theory to determine not only the vapor–liquid equilibria but also the global phase diagram of simple chain model molecules.

We present a systematic numerical study of the phase behavior of square-well fluids with a "patchy" short-ranged attraction. In particular, we study the effect of the size and number of attractive patches on the fluid–fluid coexistence. The model that we use is a generalization of the hard sphere square well model. The systems that we study have a stronger tendency to form gels than the isotropic square-well system. For this reason, we had to combine Gibbs ensemble simulations of the fluid–fluid coexistence with a parallel tempering scheme. For moderate directionality, changes of the critical density and the width of coexistence curves are small. For strong directionality, however, we find clear deviations from the extended law of corresponding states: in contrast to isotropic attractions, the critical point is not characterized by a universal value of the reduced second virial coefficient. Furthermore, as the directionality increases, multiparticle bonding affects the critical temperature. We discuss implications for the phase behavior, and possibly crystallization, of globular proteins.

Three distinct liquid–liquid coexistence regions were observed for ST2 model water by restricted ensemble Monte Carlo simulations of the isotherms of homogenized systems and by phase equilibria simulations in the Gibbs ensemble. The lowest density liquid–liquid transition meets the liquid–vapor phase transition at a triple point and ends in a metastable critical point. A percolation analysis evidences, that the phase separations at the lowest and highest densities can be attributed to the separation of differently coordinated water molecules. The densities of the obtained four phases of supercooled water correlate with experimentally observed densities of amorphous ice.