Constant pressure molecular dynamics: Instantaneous external stress tensor in systems with periodic boundary conditions

A stress tensor for systems with periodic boundary conditions is presented, which is different from the wellknown Irving-Kirkwood expression. It is shown that it represents the external stress for particles initially in one of the cells of the periodic system. The statistical properties of the pressure, derived from the stress tensor, are discussed. It is demonstrated that this pressure can be used to simulate a constant pressure - constant enthalpy ensemble. Constant pressure computer simulations on the basis of the proposed stress tensor are free of artificial parameters and the internal pressure is not constrained, in contrast to previously existing constant pressure simulation schemes.     

How does the ambiguity of the electronic stress tensor influence its ability to reveal the atomic shell structure

The electronic stress tensor is not uniquely defined. Therefore, shell indicators stemming from the quantum stress tensor may inherit this ambiguity. Based on a general formula of the stress tensor this ambiguity can be described by an external parameter λ. Two functions derived from the quantum stress tensor have been evaluated according to their ability to serve as shell indicators. The influence of λ is analyzed and the consequences for the representation of the atomic shell structure are discussed in detail. It is found that the trace of the stress tensor does not fully reveal the atomic shell structure. In contrast, the scaled trace (whereby the scaling function is proportional to the Thomas-Fermi kinetic energy density) produces fairly good representation of the atomic shell structure over a wide range of λ values.     

A simple, direct derivation and proof of the validity of the SLLOD equations of motion for generalized homogeneous flows

We present a simple and direct derivation of the SLLOD equations of motion for molecular simulations of general homogeneous flows. We show that these equations of motion (1) generate the correct particle trajectories, (2) conserve the total thermal momentum without requiring the center of mass to be located at the origin, and (3) exactly generate the required energy dissipation. These equations of motion are compared with the g-SLLOD and p-SLLOD equations of motion, which are found to be deficient. Claims that the SLLOD equations of motion are incorrect for elongational flows are critically examined and found to be invalid. It is confirmed that the SLLOD equations are, in general, non-Hamiltonian. We derive a Hamiltonian from which they can be obtained in the special case of a symmetric velocity gradient tensor. In this case, it is possible to perform a canonical transformation that results in the well-known DOLLS tensor Hamiltonian.     

How does the ambiguity of the electronic stress tensor influence its ability to serve as bonding indicator

The electronic stress tensor is not uniquely defined. Possible bonding indicators originating from the quantum stress tensor may inherit this ambiguity. Based on a general formula of the stress tensor this ambiguity can be described by an external parameter λ for indicators derived from the scaled trace of the stress tensor (whereby the scaling function is proportional to the Thomas–Fermi kinetic energy density). The influence of λ is analyzed and the consequences for the representation of chemical bonding are discussed in detail. It is found that the scaled trace of the stress tensor may serve as suitable bonding indicator over a wide range of λ values, excluding the value range between ?0.15 and ?0.48. Focusing on the eigenvalues of the stress tensor, it is found that the sign of the eigenvalues heavily depends on the chosen representation of the stress tensor. Therefore, chemical bonding analyses which are based on the interpretation of the eigenvalue sign (e.g., the spindle structure) are strongly dependent on the chosen form of the stress tensor. © 2014 Wiley Periodicals, Inc.     

Stress anisotropy induced by periodic boundary conditions

Finite size effects due to periodic boundary conditions are investigated using computer simulations in the canonical ensemble. We study liquids with densities corresponding to typical liquid coexistence densities, and temperatures between the triple and critical points. The components of the pressure tensor are computed in order to analyze the finite size effects arising from the size and geometry of the simulation box. Two different box geometries are considered: cubic and parallelepiped. As expected the pressure tensor is isotropic in cubic boxes, but it becomes anisotropic for small noncubic boxes. We argue this is the origin of the anomalous behavior observed recently in the computation of the surface tension of liquid-vapor interfaces. Otherwise, we find that the bulk pressure is sensitive to the box geometry when small simulation boxes are considered. These observations are general and independent of the model liquid considered. We report results for liquids interacting through short range forces, square well and Lennard-Jones, and also long range Coulombic interactions. The effect that small surface areas have on the surface tension is discussed, and some preliminary results at the liquid vapor-interface for the square well potential are given.     

Approximate first passage time distribution for barrier crossing in a double well under fractional Gaussian noise

The distribution of waiting times, f(t), between successive turnovers in the catalytic action of single molecules of the enzyme beta-galactosidase has recently been determined in closed form by Chaudhury and Cherayil [J. Chem. Phys. 125, 024904 (2006)] using a one-dimensional generalized Langevin equation (GLE) formalism in combination with Kramers' flux-over-population approach to barrier crossing dynamics. The present paper provides an alternative derivation of f(t) that eschews this approach, which is strictly applicable only under conditions of local equilibrium. In this alternative derivation, a double well potential is incorporated into the GLE, along with a colored noise term representing protein conformational fluctuations, and the resulting equation transformed approximately to a Smoluchowski-type equation. f(t) is identified with the first passage time distribution for a particle to reach the barrier top starting from an equilibrium distribution of initial points, and is determined from the solution of the above equation using local boundary conditions. The use of such boundary conditions is necessitated by the absence of definite information about the precise nature of the boundary conditions applicable to stochastic processes governed by non-Markovian dynamics. f(t) calculated in this way is found to have the same analytic structure as the distribution calculated by the flux-over-population method.     

Osmotic stress tensor in charge stabilized colloidal crystals

Osmotic stress tensor is introduced to describe the osmotic pressure in colloidal crystals within the framework of the theory of the Poisson-Boltzmann equation. The osmotic stress tensor is related to the fundamental stress tensor, which is associated with the Poisson-Boltzmann equation. It is shown that the osmotic stress tensor can be determined for colloidal crystals with arbitrary structures, as well as for media that are described by cell models. The general results are exemplified by spherical and cylindrical cell models.     

Effect of softness of the potential on the stress anisotropy in liquids

We have performed molecular dynamics simulations of dense liquids using nonconformal and Gaussian potential models. We investigate the effect of the softness of the potential on the pressure tensor of liquids and dense fluids when the simulations are carried out using parallelepiped cells. The combination of periodic boundary conditions and small cross sectional areas induces an anisotropy in the diagonal components of the pressure tensor. This anisotropy results in an artificial stress in the system that has to be taken into account in simulations of explicit interfaces, where the artificial stress introduces errors in the computation of the surface tension. At high liquid densities the stress anisotropy exhibits an oscillatory dependence with the cross sectional area of the simulation box. We find that the softness of the potential has a dramatic effect on the amplitude of the oscillations, which can be significantly reduced in soft potentials, such as those used in the modeling of hydrocarbon liquids or polymers.     

Local thermodynamic derivation of Young's equation

A derivation of Young's equation based on the energy balance near the contact line is presented. Our proposal is rigorous and avoids the errors identified in the usual local derivation. It is valid under very general conditions (for any geometry, in a gravitational field and for compressive fluids). Deviations of the contact angle from Young's equation are discussed in several cases: surfaces of high curvature and line tension. Finally, the relationship between surface tensions and surface energies comes as an additional, natural result. Our derivation also provides a new physical insight into the equilibrium of forces acting near the contact line. Its local character makes the recourse to integral analysis unnecessary, which results in a great simplification when compared to other general treatments.     

Contact line motion in confined liquid-gas systems: Slip versus phase transition

In two-phase flows, the interface intervening between the two fluid phases intersects the solid wall at the contact line. A classical problem in continuum fluid mechanics is the incompatibility between the moving contact line and the no-slip boundary condition, as the latter leads to a nonintegrable stress singularity. Recently, various diffuse-interface models have been proposed to explain the contact line motion using mechanisms missing from the sharp-interface treatments in fluid mechanics. In one-component two-phase (liquid-gas) systems, the contact line can move through the mass transport across the interface while in two-component (binary) fluids, the contact line can move through diffusive transport across the interface. While these mechanisms alone suffice to remove the stress singularity, the role of fluid slip at solid surface needs to be taken into account as well. In this paper, we apply the diffuse-interface modeling to the study of contact line motion in one-component liquid-gas systems, with the fluid slip fully taken into account. The dynamic van der Waals theory has been presented for one-component fluids, capable of describing the two-phase hydrodynamics involving the liquid-gas transition [A. Onuki, Phys. Rev. E 75, 036304 (2007)]. This theory assumes the local equilibrium condition at the solid surface for density and also the no-slip boundary condition for velocity. We use its hydrodynamic equations to describe the continuum hydrodynamics in the bulk region and derive the more general boundary conditions by introducing additional dissipative processes at the fluid-solid interface. The positive definiteness of entropy production rate is the guiding principle of our derivation. Numerical simulations based on a finite-difference algorithm have been carried out to investigate the dynamic effects of the newly derived boundary conditions, showing that the contact line can move through both phase transition and slip, with their relative contributions determined by a competition between the two coexisting mechanisms in terms of entropy production. At temperatures very close to the critical temperature, the phase transition is the dominant mechanism, for the liquid-gas interface is wide and the density ratio is close to 1. At low temperatures, the slip effect shows up as the slip length is gradually increased. The observed competition can be interpreted by the Onsager principle of minimum entropy production.     

A microscopic theory of interfacial hydrodynamics

The exact evolution equations for the conserved densities of a one-component two-phase fluid are reduced, in each bulk phase to the corresponding linearized hydrodynamic equations and at the interface, to boundary conditions, relating the jump in the stress tensor and heat current to surface excess thermodynamic and surface transport properties.     

Grand canonical Monte Carlo simulations of water in protein environments

The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in open equilibrium with a large system serving as a bulk reservoir. It is shown that the influence of the bulk reservoir can be represented as a many-body potential of mean force acting on the atoms located inside the subvolume. The grand canonical Monte Carlo (GCMC) algorithm, augmented by a number of technical advances to increase the acceptance of insertion attempts, is implemented, and tested for simple systems. In particular, the method is illustrated in the case of a pure water box with periodic boundary conditions. In addition, finite spherical systems of pure water and containing a dialanine peptide, are simulated with GCMC while the influence of the surrounding infinite bulk is incorporated using the generalized solvent boundary potential [W. Im, S. Berneche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)]. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated.     

Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy

We analyze the electronic structure of molecules which may exist in gas phase of chemical vapor deposition process for GeSbTe alloy using the electronic stress tensor, with special focus on the chemical bonds between Ge, Sb, and Te atoms. We find that, from the viewpoint of the electronic stress tensor, they have intermediate properties between alkali metals and hydrocarbon molecules. We also study the correlation between the bond order which is defined based on the electronic stress tensor, and energy‐related quantities. We find that the correlation with the bond dissociation energy is not so strong while one with the force constant is very strong. We interpret these results in terms of the energy density on the “Lagrange surface,” which is considered to define the boundary surface of atoms in a molecule in the framework of the electronic stress tensor analysis. © 2015 Wiley Periodicals, Inc.     

Rovibrational molecular hamiltonian in mixed bond-angle and umbrella-like coordinates

A new exact quantum mechanical rovibrational Hamiltonian operator for molecules exhibiting large amplitude inversion and torsion motions is derived. The derivation is based on a division of a molecule into two parts: a frame and a top. The nuclei of the frame only are used to construct a molecular system of axes. The inversion motion of the frame is described in the umbrella-like coordinates, whereas the torsion motion of the top is described by the nonstandard torsion angle defined in terms of the nuclear vectors and one of the molecular axes. The internal coordinates chosen take into account the properties of the inversion and torsion motions. Vibrational s and rotational Omega vectors obtained for the introduced internal coordinates determine the rovibrational tensor G defined by simple scalar products of these vectors. The Jacobian of the transformation from the Cartesian to the internal coordinates considered and the G tensor specify the rovibrational Hamiltonian. As a result, the Hamiltonian for penta-atomic molecules like NH2OH with one inverter is presented and a complete set of the formulas necessary to write down the Hamiltonian of more complex molecules, like NH2NH2 with two inverters, is reported. The approach considered is essentially general and sufficiently simple, as demonstrated by derivation of a polyatomic molecule Hamiltonian in polyspherical coordinates, obtained by other methods with much greater efforts.     

Phase equilibria and interfacial tension of fluids confined in narrow pores

Correlation between phase behaviors of a Lennard-Jones fluid in and outside a pore is examined over wide thermodynamic conditions by grand canonical Monte Carlo simulations. A pressure tensor component of the confined fluid, a variable controllable in simulation but usually uncontrollable in experiment, is related with the pressure of a bulk homogeneous system in equilibrium with the confined system. Effects of the pore dimensionality, size, and attractive potential on the correlations between thermodynamic properties of the confined and bulk systems are clarified. A fluid-wall interfacial tension defined as an excess grand potential is evaluated as a function of the pore size. It is found that the tension decreases linearly with the inverse of the pore diameter or width.     

Generalized nematostatics

The generalized equations of bulk and interfacial nematostatics in terms of the tensor order parameter are derived using calculus of variations, taking into account long and short range nematic bulk free energies as well as anchoring and saddle-splay surface free energies. A general expression for the surface stress tensor order parameter for a nematic liquid crystal/isotropic fluid (NLC/I) interface has been derived, and found to represent normal, shear, and bending stresses. It is shown that the surface stress tensor is asymmetric. It is also found that anchoring energy contributes to bending and normal stresses, while saddle-splay energy contributes to normal and shear stresses. The rotational identifies governing the bulk and surface stress tensors are derived and used to show that the equations of nematostatics are fully consistent with the general balance equations of polar fluids. The equations presented provide a theoretical framework for solving interfacial problems involving NLCs that is applicable to cases where variations in liquid crystalline order and saddle-splay energy play significant roles.     

Generalized nematostatics

The generalized equations of bulk and interfacial nematostatics in terms of the tensor order parameter are derived using calculus of variations, taking into account long and short range nematic bulk free energies as well as anchoring and saddle-splay surface free energies. A general expression for the surface stress tensor order parameter for a nematic liquid crystal/isotropic fluid (NLC/I) interface has been derived, and found to represent normal, shear, and bending stresses. It is shown that the surface stress tensor is asymmetric. It is also found that anchoring energy contributes to bending and normal stresses, while saddle-splay energy contributes to normal and shear stresses. The rotational identifies governing the bulk and surface stress tensors are derived and used to show that the equations of nematostatics are fully consistent with the general balance equations of polar fluids. The equations presented provide a theoretical framework for solving interfacial problems involving NLCs that is applicable to cases where variations in liquid crystalline order and saddle-splay energy play significant roles.     

Transformation properties of many-electron wave functions with special attention to the relation between pair-correlated DODS and configuration interaction

A method is presented that leads to a simple derivation of the explicit relation between pair-correlated DODS schemes (e.g., the alternant molecular orbital method and the extended valence bond method) and configuration interaction. This result is based on a reduction formula for the representations of the general linear group, GL(m), carried by the N-electron function space. Generally, this paper deals with the effect of “partitioned” orbital transformations on states with “local” permutation symmetry.     

Boundary conditions in local electrostatics algorithms

We study the simulation of charged systems in the presence of general boundary conditions in a local Monte Carlo algorithm based on a constrained electric field. We first show how to implement constant-potential, Dirichlet boundary conditions by introducing extra Monte Carlo moves to the algorithm. Second, we show the interest of the algorithm for studying systems which require anisotropic electrostatic boundary conditions for simulating planar geometries such as membranes.