Equilibrium equation of state of a hard sphere binary mixture at very large densities using replica exchange Monte Carlo simulations

We use replica exchange Monte Carlo simulations to measure the equilibrium equation of state of the disordered fluid state for a binary hard sphere mixture up to very large densities where standard Monte Carlo simulations do not easily reach thermal equilibrium. For the moderate system sizes we use (up to N = 100), we find no sign of a pressure discontinuity near the location of dynamic glass singularities extrapolated using either algebraic or simple exponential divergences, suggesting they do not correspond to genuine thermodynamic glass transitions. Several scenarios are proposed for the fate of the fluid state in the thermodynamic limit.     

Communication: Monte Carlo calculation of the exchange energy

In recent generalized Kohn-Sham (GKS) schemes for density functional theory (DFT) Hartree-Fock type exchange is important. In plane waves and grid approaches the high cost of exchange energy calculations makes these GKS considerably more expensive than Kohn-Sham DFT calculations. We develop a stochastic approach for speeding up the calculation of exchange for large systems. We show that stochastic error per particle does not grow and can even decrease with system size (at a given number of iterations). We discuss several alternative approaches and explain how these ideas can be included in the GKS framework.     

Monte Carlo simulation of hard spheroids

We present Monte Carlo simulations of the equation of state and radial distribution function for a model fluid composed of hard spheroids.     

Canonical and micro-canonical analysis of folding of trpzip2: An all-atom replica exchange Monte Carlo simulation study

The density of states of trpzip2, a β-hairpin peptide, has been explored at all-atom level. Replica exchange Monte Carlo method was used for sufficient sampling over a wide range of temperature. Micro-canonical analysis was performed to confirm that the phase transition behavior of this two-state folder is first-order-like. Canonical analysis of heat capacity suggests that hydrogen bonding interaction exerts a considerable positive influence on folding cooperativity, in contrast, hydrophobic interaction is insufficient for high degree of folding cooperativity. Furthermore, we explain physical nature of the folding process from free energy landscape perspective and extensively analyse hydrogen bonding and stacking energy.     

Comparing three stochastic search algorithms for computational protein design: Monte Carlo,replica exchange Monte Carlo,and a multistart,steepest‐descent heuristic

Computational protein design depends on an energy function and an algorithm to search the sequence/conformation space. We compare three stochastic search algorithms: a heuristic, Monte Carlo (MC), and a Replica Exchange Monte Carlo method (REMC). The heuristic performs a steepest‐descent minimization starting from thousands of random starting points. The methods are applied to nine test proteins from three structural families, with a fixed backbone structure, a molecular mechanics energy function, and with 1, 5, 10, 20, 30, or all amino acids allowed to mutate. Results are compared to an exact, “Cost Function Network” method that identifies the global minimum energy conformation (GMEC) in favorable cases. The designed sequences accurately reproduce experimental sequences in the hydrophobic core. The heuristic and REMC agree closely and reproduce the GMEC when it is known, with a few exceptions. Plain MC performs well for most cases, occasionally departing from the GMEC by 3–4 kcal/mol. With REMC, the diversity of the sequences sampled agrees with exact enumeration where the latter is possible: up to 2 kcal/mol above the GMEC. Beyond, room temperature replicas sample sequences up to 10 kcal/mol above the GMEC, providing thermal averages and a solution to the inverse protein folding problem. © 2016 Wiley Periodicals, Inc.     

Diffusion Monte Carlo study of the equation of state of solid ortho-D2

The authors present results of diffusion Monte Carlo calculations for a system of solid ortho-D2 at different densities, for pressure ranging from 0 up to 350 MPa. They compare the equation of state obtained using two of the most used effective intermolecular potentials, i.e., the Silvera-Goldman and the Buck potentials, with experimental data, in order to assess the validity of the model interactions. The Silvera-Goldman potential has been found to provide a satisfactory agreement with experimental results, showing that, as opposed to what recently found for p-H2, three-body forces can be efficiently accounted for by an effective two-body term.     

Monte Carlo simulations of two-dimensional hard core lattice gases

Monte Carlo simulations are used to study lattice gases of particles with extended hard cores on a two-dimensional square lattice. Exclusions of one and up to five nearest neighbors (NN) are considered. These can be mapped onto hard squares of varying side length, lambda (in lattice units), tilted by some angle with respect to the original lattice. In agreement with earlier studies, the 1NN exclusion undergoes a continuous order-disorder transition in the Ising universality class. Surprisingly, we find that the lattice gas with exclusions of up to second nearest neighbors (2NN) also undergoes a continuous phase transition in the Ising universality class, while the Landau-Lifshitz theory predicts that this transition should be in the universality class of the XY model with cubic anisotropy. The lattice gas of 3NN exclusions is found to undergo a discontinuous order-disorder transition, in agreement with the earlier transfer matrix calculations and the Landau-Lifshitz theory. On the other hand, the gas of 4NN exclusions once again exhibits a continuous phase transition in the Ising universality class-contradicting the predictions of the Landau-Lifshitz theory. Finally, the lattice gas of 5NN exclusions is found to undergo a discontinuous phase transition.     

Monte Carlo study of four dimensional binary hard hypersphere mixtures

A multithreaded Monte Carlo code was used to study the properties of binary mixtures of hard hyperspheres in four dimensions. The ratios of the diameters of the hyperspheres examined were 0.4, 0.5, 0.6, and 0.8. Many total densities of the binary mixtures were investigated. The pair correlation functions and the equations of state were determined and compared with other simulation results and theoretical predictions. At lower diameter ratios the pair correlation functions of the mixture agree with the pair correlation function of a one component fluid at an appropriately scaled density. The theoretical results for the equation of state compare well to the Monte Carlo calculations for all but the highest densities studied.     

Molten globule state in homopolymers:A Monte Carlo study

Simple models of polymer chains were based on a simple cubic lattice. The model chains were star‐branched with f = 3 and f = 6 branches. The attractive potential between polymer segments was introduced to study the properties of polymer chains in the different temperature regimes. The computer simulations were carried out by means of the dynamic Monte Carlo method. It was found that contrary to recent real experiments, the ratio of the radius of gyration to the hydrodynamic radius did not exhibit a maximum near the coil‐globule transition but decreased monotonically with the temperature. The distribution of polymer‐polymer contacts and their lifetimes were also studied. It appeared that in homopolymer chains the lifetimes of these contacts were very short. At low temperatures contacts were distributed over the entire chain and at high temperatures only contacts that were close to the chain survived longer times.     

Thermodynamic derivative properties and densities for hyperbaric gas condensates: SRK equation of state predictions versus Monte Carlo data

The ability of Soave–Redlich–Kwong cubic equation of state (SRK EoS) to predict densities and thermodynamic derivative properties such as thermal expansivity, isothermal compressibility, calorific capacity, and Joule–Thompson coefficients, for two gas condensates over a wide range of pressures (up to 110 MPa) was studied. The predictions of the EoS were compared to Monte Carlo simulation data obtained by Lagache et al. [M.H. Lagache, P. Ungerer, A. Boutin, Fluid Phase Equilibr. 220 (2004) 221]. Two completely different alpha functions for the SRK EoS attractive term were used and their respective effects on the predictions of such properties were analyzed. Also, two different forms of the crossed terms of the attractive parameter, a_ij, and three expressions of the crossed terms of the repulsive parameter, b_ij, were combined in different ways, and predictions were carried out. Little sensitivity of the properties on the chosen alpha function, except for the calorific capacities, was found in the systems studied. The most commonly used combination rules to model phase behavior of reservoir fluids, i.e. geometric and arithmetic forms of a_ij and b_ij, respectively, predicted very deficient results for these fluids at extreme conditions, specially for density calculations.     

Crystal nucleation in binary hard sphere mixtures: a Monte Carlo simulation study

We present calculations of the nucleation barrier during crystallization in binary hard sphere mixtures under moderate degrees of supercooling using Monte Carlo simulations in the isothermal-isobaric semigrand ensemble in conjunction with an umbrella sampling technique. We study both additive and negatively nonadditive binary hard sphere systems. The solid-fluid phase diagrams of such systems show a rich variety of behavior, ranging from simple spindle shapes to the appearance of azeotropes and eutectics to the appearance of substitutionally ordered solid phase compounds. We investigate the effect of these types of phase behavior upon the nucleation barrier and the structure of the critical nucleus. We find that the underlying phase diagram has a significant effect on the mechanism of crystal nucleation. Our calculations indicate that fractionation of the species upon crystallization increases the difficulty of crystallization of fluid mixtures and in the absence of fractionation (azeotropic conditions) the nucleation barrier is comparable to pure fluids. We also calculate the barrier to nucleation of a substitutionally ordered compound solid. In such systems, which also show solid-solid phase separation, we find that the phase that nucleates is the one whose equilibrium composition is closer to the composition of the fluid phase.     

Inhomogeneous fluids of colloidal hard dumbbells: fundamental measure theory and Monte Carlo simulations

Recently, a density functional theory for hard particles with shape anisotropy was developed, the extended deconvolution fundamental measure theory (edFMT). We apply edFMT to hard dumbbells, arguably the simplest non-convex shape and readily available experimentally in the form of colloids. We obtain good agreement between edFMT and Monte Carlo simulations for fluids of dumbbells in a slit and for the same system under gravity. This indicates that edFMT can be successfully applied to nearly all colloidal shapes, not just for the convex shapes for which edFMT was originally derived. A theory, such as edFMT, that allows a fast and general way of mapping the phase behavior of anisotropic colloids, can act as a useful guide for the design of colloidal shapes for various applications.     

Revisiting the phase diagram of hard ellipsoids

In this work, the well-known Frenkel-Mulder phase diagram of hard ellipsoids of revolution [D. Frenkel and B. M. Mulder, Mol. Phys. 55, 1171 (1985)] is revisited by means of replica exchange Monte Carlo simulations. The method provides good sampling of dense systems and so, solid phases can be accessed without the need of imposing a given structure. At high densities, we found plastic solids and fcc-like crystals for semi-spherical ellipsoids (prolates and oblates), and SM2 structures [P. Pfleiderer and T. Schilling, Phys. Rev. E 75, 020402 (2007)] for x : 1-prolates and 1 : x-oblates with x ≥ 3. The revised fluid-crystal and isotropic-nematic transitions reasonably agree with those presented in the Frenkel-Mulder diagram. An interesting result is that, for small system sizes (100 particles), we obtained 2:1- and 1.5:1-prolate equations of state without transitions, while some order is developed at large densities. Furthermore, the symmetric oblate cases are also reluctant to form ordered phases.     

On the equation of state of hard chain molecules

The chain-of-rotators (COR) equation of state developed by Chien, Greenkorn, and Chao makes an assumption on the hard chain partition function based on results for monomers and dimers, i.e., spheres and dumbbells. Here this assumption is checked for trimers by comparison with the results of Boubik's hard convex body equation. It turns out that the COR assumption is, in general, a good approximation. Its quality depends somewhat on the bond length and the bond angle which it does not consider. The agreement is especially good for angles somewhat less than 90°.     

Monte Carlo computation of ground‐state energy derivatives

Monte Carlo is a simple technique, which uses random numbers to compute ground‐state energies of small molecules (and quantum systems in general). The results always have a small statistical error, which poses a major obstacle when estimating properties defined as ground‐state‐energy derivatives (such as the molecule's geometry, its vibrational frequencies, polarizabilities, etc.). In this article, we present and demonstrate an approach that makes an accurate Monte–Carlo estimation of such derivatives possible. This is achieved by realizing that the simulation constitutes an autocorrelated stochastic process, whose proper analysis then enables us to estimate various energy derivatives as a combination of total correlation between readily computable quantities. The resulting procedure is a natural extension of the usual Monte Carlo algorithm for computing the ground‐state energy, with relatively small computational overhead. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Excess energy and equation of state of fluids with hard-core potential models from a second-order Monte Carlo perturbation theory

Monte Carlo simulations in the NVT ensemble of the reference hard-sphere fluid have been performed to obtain the “exact” first- and second-order terms in the inverse temperature expansion of the free energy of fluids with hard-core potentials. The results have been used to obtain parametrizations of the free energy of fluids with Sutherland potentials with variable range as well as for a fluid with a hard-core Lennard–Jones potential. The results for the excess energy and the equation of state are compared with simulation data available in the literature for these fluids.     

Osmotic pressure,atomic pressure and the virial equation of state of polymer solutions: Monte Carlo simulations of a bead-spring model

A recently introduced coarse-grained model of polymer chains is studied analyzing various contributions to the pressure as obtained from the virial theorem as a function of chain length N, temperature T and density ϕ. The off-lattice model of the polymer chains has anharmonic springs between the beads, but of finite extensibility, and the Morse-type interaction between beads is repulsive at very short distances and attractive at intermediate distances. Solvent molecules are not explicitly included. It is found that the covalent forces along the chain (modelled by the spring potentials) contribute a negative term to the pressure, irrespective of temperature, which vanishes linearly in ϕ as ϕ → 0. In contrast, both contributions to the pressure due to intrachain nonbonded forces and due to forces between different chains change sign from high temperatures (T ≫ θ, θ the theta-temperature) where they are positive, to low temperature where both parts of the pressure become negative. It is shown that the total pressure has the expected behavior with temperature near the θ-temperature, i.e., Δp ≡ p_tot − k_B · T_p ∼ (T − θ). We study also the concentration and chainlength dependence of the various contributions to the pressure in the good solvent regime and interpret them with scaling predictions.     

Reversible folding simulation by hybrid Hamiltonian replica exchange

Reversible foldings of a beta-hairpin peptide, chignolin, by recently invented hybrid Hamiltonian replica exchange molecular dynamics simulations based on Poisson-Boltzmann model in explicit water are demonstrated. Initiated from extended structures the peptide folded and unfolded a couple of times in seven out of eight replica trajectories during 100 nanoseconds simulation. The folded states have the lowest all-atom root mean squared deviation of 1.3 A with respect to the NMR structures. At T=300 K the occurrence of folded states was converged to 62% during 80 ns simulation which agrees well with experimental data. Especially, a detailed structural evolution map was constructed based on 800,000 structural snapshots and from where a unique folding doorway emerges. Compared with 130 ns standard replica exchange simulation using 24 replicas on the same system, the hybrid Hamiltonian replica exchange molecular dynamics simulation presents consistent results.