Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. II. Simulation results

The results of a series of constant pressure and temperature molecular-dynamics (MD) simulation studies based on the rigorous shell particle formulation of the isothermal-isobaric (NpT) ensemble are presented. These MD simulations validate the newly proposed constant pressure equations of motion in which a "shell" particle is used to define uniquely the volume of the system [M. J. Uline and D. S. Corti, J. Chem. Phys. (to be published), preceding paper]. Ensemble averages obtained with the new MD NpT algorithm match the ensemble averages obtained using the previously derived shell particle Monte Carlo NpT method [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. In addition, we also verify that the Hoover NpT MD algorithm [W. G. Hoover, Phys. Rev. A 31, 1695 (1985); 34, 2499 (1986)] generates the correct ensemble averages, though only when periodic boundary conditions are employed. The extension of the shell particle MD algorithm to multicomponent systems is also discussed, in which we show for equilibrium properties that the identity of the shell particle is completely arbitrary when periodic boundary conditions are applied. Self-diffusion coefficients determined with the shell particle equations of motion are also identical to those obtained in other ensembles. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the effects of the shell particle on the dynamics of the system. Overall, the shell particle MD algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium MD methods.     

Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. III. Discontinuous potentials

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.     

Molecular simulation of dendrimers and their mixtures under shear: comparison of isothermal-isobaric (NpT) and isothermal-isochoric (NVT) ensemble systems

Flow properties of dendrimers are studied with the aid of nonequilibrium molecular dynamics techniques. Simulations are performed in the NpT ensemble using the NpT-SLLOD algorithm [P. J. Davis and D. J. Evans, J. Chem. Phys. 100, 541 (1994)] and are compared to the results from simulations performed in the NVT ensemble reported earlier [J. T. Bosko, B. D. Todd, and R. J. Sadus, Chem. Phys. 121, 12050 (2004)]. Shear thickening observed at high strain rates vanishes in systems kept under constant pressure. Also the exponents in the power-law dependencies of the viscosity and the normal stress coefficients change. The variations are significant only at high strain rates and do not affect largely microscopic properties such as shape, alignment, or rotation of molecules. The NpT-SLLOD algorithm has been applied to study various systems including dendrimers in solution and their blends with linear chain molecules of the same molecular mass, and some results for these systems are presented.     

Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)] relates the work done on a system during a nonequilibrium transformation to the free energy difference between the final and the initial state of the transformation. Recently, the authors have derived the Crooks equation for systems in the canonical ensemble thermostatted by the Nose-Hoover or Nose-Hoover chain method [P. Procacci et al., J. Chem. Phys. 125, 164101 (2006)]. That proof is essentially based on the fluctuation theorem by Evans and Searles [Adv. Phys. 51, 1529 (2002)] and on the equations of motion. Following an analogous approach, the authors derive here the Crooks equation in the context of molecular dynamics simulations of systems in the isothermal-isobaric (NPT) ensemble, whose dynamics is regulated by the Martyna-Tobias-Klein algorithm [J. Chem. Phys. 101, 4177 (1994)]. Their present derivation of the Crooks equation correlates to the demonstration of the Jarzynski identity for NPT systems recently proposed by Cuendet [J. Chem. Phys. 125, 144109 (2006)].     

Molecular nitrogen-N2 properties: the intermolecular potential and the equation of state

Quantum mechanical (QM) high precision calculations were used to determine N(2)-N(2) intermolecular interaction potential. Using QM numerical data the anisotropic potential energy surface was obtained for all orientations of the pair of the nitrogen molecules in the rotation invariant form. The new N(2)-N(2) potential is in reasonably good agreement with the scaled potential obtained by van der Avoird et al. using the results of Hartree-Fock calculations [J. Chem. Phys. 84, 1629 (1986)]. The molecular dynamics (MD) of the N(2) molecules has been used to determine nitrogen equation of state. The classical motion of N(2) molecules was integrated in rigid rotor approximation, i.e., it accounted only translational and rotational degrees of freedom. Fincham [Mol. Simul. 11, 79 (1993)] algorithm was shown to be superior in terms of precision and energy stability to other algorithms, including Singer [Mol. Phys. 33, 1757 (1977)], fifth order predictor-corrector, or Runge-Kutta, and was therefore used in the MD modeling of the nitrogen pressure [S. Krukowski and P. Strak, J. Chem. Phys. 124, 134501 (2006)]. Nitrogen equation of state at pressures up to 30 GPa (300 kbars) and temperatures from the room temperature to 2000 K was obtained using MD simulation results. Results of MD simulations are in very good agreement (the error below 1%) with the experimental data on nitrogen equation of state at pressures below 1 GPa (10 kbars) for temperatures below 1800 K [R. T. Jacobsen et al., J. Phys. Chem. Ref. Data 15, 735 (1986)]. For higher temperatures, the deviation is slightly larger, about 2.5% which still is a very good agreement. The slightly larger difference may be attributed to the vibrational motion not accounted explicitly by rigid rotor approximation, which may be especially important at high temperatures. These results allow to obtain reliable equation of state of nitrogen for pressures up to 30 GPa (300 kbars), i.e., close to molecular nitrogen stability limit, determined by Nellis et al. [Phys. Rev. Lett. 53, 1661 (1984)].     

Comment on "Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2-" [J. Chem. Phys. 122, 074314 (2005)

We discuss the computational results of the "Theoretical study of the photoinduced transfer among the ground state and two metastable states in [Fe(CN)5NO]2-" [J. Chem. Phys. 122, 074314 (2005)] with respect to our previously reported polarized absorption study on the metastable states SI and SII in Na2[Fe(CN)5NO]2H2O [D. Schaniel, J. Schefer, B. Delley, M. Imlau, and Th. Woike, Phys. Rev. B 66, 085103 (2002)].     

Pressure derivatives in the classical molecular-dynamics ensemble

The calculation of thermodynamic state variables, particularly derivatives of the pressure with respect to density and temperature, in conventional molecular-dynamics simulations is considered in the frame of the comprehensive treatment of the molecular-dynamics ensemble by Lustig [J. Chem. Phys. 100, 3048 (1994)]. This paper improves the work of Lustig in two aspects. In the first place, a general expression for the basic phase-space functions in the molecular-dynamics ensemble is derived, which takes into account that a mechanical quantity G is, in addition to the number of particles, the volume, the energy, and the total momentum of the system, a constant of motion. G is related to the initial position of the center of mass of the system. Secondly, the correct general expression for volume derivatives of the potential energy is derived. This latter result solves a problem reported by Lustig [J. Chem. Phys. 109, 8816 (1998)] and Meier [Computer Simulation and Interpretation of the Transport Coefficients of the Lennard-Jones Model Fluid (Shaker, Aachen, 2002)] and enables the correct calculation of the isentropic and isothermal compressibilities, the speed of sound, and, in principle, all higher pressure derivatives. The derived equations are verified by calculations of several state variables and pressure derivatives up to second order by molecular-dynamics simulations with 256 particles at two state points of the Lennard-Jones fluid in the gas and liquid regions. It is also found that it is impossible for systems of this size to calculate third- and higher-order pressure derivatives due to the limited accuracy of the algorithm employed to integrate the equations of motion.     

Hard spheres revisited: accurate calculation of the solid-liquid interfacial free energy

We revise the earlier [R. L. Davidchack and B. B. Laird, Phys. Rev. Lett. 85, 4751 (2000)] direct calculation of the hard sphere solid-liquid interfacial free energy by the cleaving walls method. The revisions of the method include modified interactions with the cleaving walls and the use of a nonequilibrium work measurements approach, which allows for a more robust control of the accuracy of the obtained results. We find that the new values are lower compared to the original ones, which is consistent with the more recent indirect estimates based on extrapolation from the soft-sphere results [R. L. Davidchack and B. B. Laird, Phys. Rev. Lett. 94, 086102 (2005)], as well as those obtained using the capillary fluctuations method [R. L. Davidchack, J. R. Morris, and B. B. Laird, J. Chem. Phys. 125, 094710 (2006)].     

Theoretical interpretation of Grimme's spin-component-scaled second order Møller-Plesset theory

It is shown that spin-component-scaled second order M?ller-Plesset theory proposed by Grimme [J. Chem. Phys. 118, 9095 (2003)] can be interpreted as a two-parameter scaling of the zero order Hamiltonian, a generalization of the approach reported by Feenberg [Phys. Rev. 103, 1116 (1956)].     

Adding salt to an aqueous solution of t-butanol: is hydrophobic association enhanced or reduced?

Recent neutron scattering experiments on aqueous salt solutions of amphiphilic t-butanol by Bowron and Finney [Phys. Rev. Lett. 89, 215508 (2002); J. Chem. Phys. 118, 8357 (2003)] suggest the formation of t-butanol pairs, bridged by a chloride ion via O-H...Cl- hydrogen bonds, leading to a reduced number of intermolecular hydrophobic butanol-butanol contacts. Here we present a joint experimental/theoretical study on the same system, using a combination of molecular dynamics (MD) simulations and nuclear magnetic relaxation measurements. Both MD simulation and experiment clearly support the more classical scenario of an enhanced number of hydrophobic contacts in the presence of salt, as it would be expected for purely hydrophobic solutes. [T. Ghosh et al., J. Phys. Chem. B 107, 612 (2003)]. Although our conclusions arrive at a structurally completely distinct scenario, the molecular dynamics simulation results are within the experimental error bars of the Bowron and Finney data.     

The free energy of the metastable supersaturated vapor via restricted ensemble simulations

Pressure, excess chemical potential, and excess free energy, with respect to ideal gas data at different densities of the supersaturated Lennard-Jones particle vapor at the reduced temperature 0.7 are obtained by the restricted canonical ensemble Monte Carlo simulation method [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)]. The excess free energy values depend upon the constraints imposed on the system with local minima exhibited for densities below the spinodal density and monotonic variation for densities larger than the spinodal density. The results are compared with a molecular dynamics simulation study [A. Linharton et al., J. Chem. Phys. 122, 144506 (2005)] on the same system. The current study verifies the conclusion drawn by the simulation work that clustering of Lennard-Jones atoms exists even in the vicinity of spinodal. Our method gives an alternative to molecular dynamic simulations for the determination of equilibrium properties of a metastable fluid, especially close to the spinodal, and does not require a very large system to carry out the simulation.     

Statistical mechanical theory for steady state systems. VI. Variational principles

Several variational principles that have been proposed for nonequilibrium systems are analyzed. These include the principle of minimum rate of entropy production due to Prigogine [Introduction to Thermodynamics of Irreversible Processes (Interscience, New York, 1967)], the principle of maximum rate of entropy production, which is common on the internet and in the natural sciences, two principles of minimum dissipation due to Onsager [Phys. Rev. 37, 405 (1931)] and to Onsager and Machlup [Phys. Rev. 91, 1505 (1953)], and the principle of maximum second entropy due to Attard [J. Chem.. Phys. 122, 154101 (2005); Phys. Chem. Chem. Phys. 8, 3585 (2006)]. The approaches of Onsager and Attard are argued to be the only viable theories. These two are related, although their physical interpretation and mathematical approximations differ. A numerical comparison with computer simulation results indicates that Attard's expression is the only accurate theory. The implications for the Langevin and other stochastic differential equations are discussed.     

Revisiting the Frenkel-Ladd method to compute the free energy of solids: the Einstein molecule approach

In this paper a new method to evaluate the free energy of solids is proposed. The method can be regarded as a variant of the method proposed by Frenkel and Ladd [J. Chem. Phys. 81, 3188 (1984)]. The main equations of the method can be derived in a simple way. The method can be easily implemented within a Monte Carlo program. We have applied the method to determine the free energy of hard spheres in the solid phase for several system sizes. The obtained free energies agree within the numerical uncertainty with those obtained by Polson et al. [J. Chem. Phys. 112, 5339 (2000)]. The fluid-solid equilibria has been determined for several system sizes and compared to the values published previously by Wilding and Bruce [Phys. Rev. Lett. 85, 5138 (2000)] using the phase switch methodology. It is shown that both the free energies and the coexistence pressures present a strong size dependence and that the results obtained from free energy calculations agree with those obtained using the phase switch method, which constitutes a cross-check of both methodologies. From the results of this work we estimate the coexistence pressure of the fluid-solid transition of hard spheres in the thermodynamic limit to be p*=11.54(4), which is slightly lower than the classical value of Hoover and Ree (p*=11.70) [J. Chem. Phys. 49, 3609 (1968)]. Taking into account the strong size dependence of the free energy of the solid phase, we propose to introduce finite size corrections, which allow us to estimate approximately the free energy of the solid phase in the thermodynamic limit from the known value of the free energy of the solid phase with N molecules. We have also determined the free energy of a Lennard-Jones solid by using both the methodology of this work and the finite size correction. It is shown how a relatively good estimate of the free energy of the system in the thermodynamic limit is obtained even from the free energy of a relatively small system.     

A proper approach for nonequilibrium molecular dynamics simulations of planar elongational flow

We present nonequilibrium molecular dynamics simulations of planar elongational flow (PEF) by an algorithm proposed by Tuckerman et al. [J. Chem. Phys. 106, 5615 (1997)] and theoretically elaborated by Edwards and Dressler [J. Non-Newtonian, Fluid Mech. 96, 163 (2001)], which we shall call the proper-SLLOD algorithm, or p-SLLOD for short. [For background on names of algorithms see W. G. Hoover, D. J. Evans, R. B. Hickman, A. J. C. Ladd, W. T. Ashurst, and B. Moran, Phys. Rev. A 22, 1690 (1980) and D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984).] We show that there are two sources for the exponential growth in PEF of the total linear momentum of the system in the contracting direction, which has been previously observed using the so-called SLLOD algorithm. The first comes from the SLLOD algorithm itself, and the second from the implementation of the Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)] boundary conditions. Using the p-SLLOD algorithm (to eliminate the first source) implemented with our simulation strategy (to eliminate the second) in PEF simulations, we no longer observe the exponential growth. By analyzing the equations of motion, we also demonstrate that both the SLLOD and the DOLLS algorithms are intrinsically unsuitable for representing a nonequilibrium system with elongational flow. However, the p-SLLOD algorithm has a rigorously canonical structure in laboratory phase space, and thus can represent a nonequilibrium system not only for elongational flow but also for a general flow.     

The free energy of the metastable supersaturated vapor via restricted ensemble simulations. II. Effects of constraints and comparison with molecular dynamics simulations

Extensive restricted canonical ensemble Monte Carlo simulations [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)] were performed. Pressure, excess chemical potential, and excess free energy with respect to ideal gas data were obtained at different densities of the supersaturated Lennard-Jones (LJ) vapor at reduced temperatures from 0.7 to 1.0. Among different constraints imposed on the system studied, the one with the local minimum of the excess free energy was taken to be the approximated equilibrium state of the metastable LJ vapor. Also, a comparison of our results with molecular dynamic simulations [A. Linhart et al., J. Chem. Phys. 122, 144506 (2005)] was made.     

Diffusion in linear porous media with periodic entropy barriers: A tube formed by contacting spheres

The problem of transport in quasi-one-dimensional periodic structures has been studied recently by several groups [D. Reguera et al., Phys. Rev. Lett.96, 130603 (2006); P. S. Burada et al., Phys. Rev. E75, 051111 (2007); B. Q. Ai and L. G. Liu, ibid.74, 051114 (2006); B. Q. Ai et al., ibid.75, 061126 (2007); B. Q. Ai and L. G. Liu, J. Chem. Phys.126, 204706 (2007); 128, 024706 (2008); E. Yariv and K. D. Dorfman, Phys. Fluids19, 037101 (2007); N. Laachi et al., Europhys. Lett.80, 50009 (2007); A. M. Berezhkovskii et al., J. Chem. Phys.118, 7146 (2003); 119, 6991 (2003)]. Using the concept of "entropy barrier" [R. Zwanzig, J. Phys. Chem.96, 3926 (1992)] one can classify such structures based on the height of the entropy barrier. Structures with high barriers are formed by chambers, which are weakly connected with each other because they are connected by small apertures. To escape from such a chamber a diffusing particle has to climb a high entropy barrier to find an exit that takes a lot of time [I. V. Grigoriev et al., J. Chem. Phys.116, 9574 (2002)]. As a consequence, the particle intrachamber lifetime tau(esc) is much larger than its intrachamber equilibration time, tau(rel), tau(esc)>tau(rel). When the aperture is not small enough, the intrachamber escape and relaxation times are of the same order and the hierarchy fails. This is the case of low entropy barriers. Transport in this case is analyzed in the works of Schmid and co-workers, Liu and co-workers, and Dorfman and co-workers, while the work of Berezhkovskii et al. is devoted to diffusion in the case of high entropy barriers.     

Exact analytical evaluation of time dependent transmission coefficient from the method of reactive flux for an inverted parabolic barrier

The paper demonstrates an elegant way of combining the normal mode analysis and the method of reactive flux to evaluate the time dependent transmission coefficient for a classical particle coupled to a set of harmonic oscillators, surmounting a one dimensional barrier. The author's analysis reproduces the results of Kohen and Tannor [J. Chem. Phys. 103, 6013 (1995)] and Bao [J. Chem. Phys. 124, 114103 (2006)]. Moreover the use of normal mode analysis has a better physical meaning.     

Projection of two-dimensional diffusion in a curved midline and narrow varying width channel onto the longitudinal dimension

This study focuses on the derivation of a general effective diffusion coefficient to describe the two-dimensional (2D) diffusion in a narrow and smoothly asymmetric channel of varying width, in the simple diffusional motion of noninteracting pointlike particles under no external field. We present a generalization to the case of an asymmetric channel using the projection method introduced earlier by Kalinay and Percus [J. Chem. Phys. 122, 204701 (2005); and Phys. Rev. E 74, 041203 (2006)] to project the 2D diffusion equation into an effective one-dimensional generalized Fick-Jacobs equation. The expression for the diffusion coefficient given in Eq. (23) is our main result. This expression is a more general effective diffusion coefficient for narrow channels in 2D, which contains the well-known previous results as special cases, namely, those obtained by Bradley [Phys. Rev. E 80, 061142 (2009)], and more recently by Berezhkovskii and Szabo [J. Chem. Phys. 135, 074108 (2011)]. Finally, we study some specific 2D asymmetric channel configurations to test and show the broader applicability of Eq. (23).