Semi-bottom-up coarse graining of water based on microscopic simulations

The generalized dissipative particle dynamics (DPD) equation derived from the generalized Langevin equation under Markovian approximations is used to simulate coarse-grained (CG) water cells. The mean force and the friction coefficients in the radial and transverse directions needed for DPD equation are obtained directly from the all atomistic molecular dynamics (AAMD) simulations. But the dissipative friction forces are overestimated in the Markovian approximation, which results in wrong dynamic properties for the CG water in the DPD simulations. To account for the non-Markovian dynamics, a rescaling factor is introduced to the friction coefficients. The value of the factor is estimated by matching the diffusivity of water. With this semi-bottom-up mapping method, the radial distribution function, the diffusion constant, and the viscosity of the coarse-grained water system computed with DPD simulations are all in good agreement with AAMD results. It bridges the microscopic level and mesoscopic level with consistent length and time scales.     

The dynamics of solid substance formation in strongly supersaturated media

Proceeding from the idea of the isolation of a substance from a supersaturated medium as the nucleation, growth, and aggregation of substance particles, a kinetic equation for changes in the particle state distribution function corresponding to the experimental data was obtained. The equation satisfying the requirement of the conservation of the number of new phase particles was simplified to the Liouville, Fokker-Planck, Farkas, and Zel’dovich equations.     

Operator splitting algorithm for isokinetic SLLOD molecular dynamics

We apply an operator splitting method to develop a simulation algorithm that has complete analytical solutions for the Gaussian thermostated SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] for a system under shear. This leads to a homogeneous algorithm for performing both equilibrium and nonequilibrium isokinetic molecular dynamics simulation. The resulting algorithm is computationally efficient. In particular, larger integration time steps can be used compared to simulations with regular Gaussian thermostated SLLOD equations of motion. The utility and accuracy of the algorithm are demonstrated through application to the Weeks-Chandler-Anderson fluid. Although strict conservation of the kinetic energy suppresses thermal fluctuations in the system, this algorithm does not allow simulations at lower shear rates than those normally afforded by older nonequilibrium molecular dynamics simulations.     

Mesoscale simulation of polymer reaction equilibrium: combining dissipative particle dynamics with reaction ensemble Monte Carlo. I. Polydispersed polymer systems

We present a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics (RxDPD) method, for studying reaction equilibrium of polymer systems. The RxDPD method combines elements of dissipative particle dynamics (DPD) and reaction ensemble Monte Carlo (RxMC), allowing for the determination of both static and dynamical properties of a polymer system. The RxDPD method is demonstrated by considering several simple polydispersed homopolymer systems. RxDPD can be used to predict the polydispersity due to various effects, including solvents, additives, temperature, pressure, shear, and confinement. Extensions of the method to other polymer systems are straightforward, including grafted, cross-linked polymers, and block copolymers. To simulate polydispersity, the system contains full polymer chains and a single fractional polymer chain, i.e., a polymer chain with a single fractional DPD particle. The fractional particle is coupled to the system via a coupling parameter that varies between zero (no interaction between the fractional particle and the other particles in the system) and one (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the DPD equations of motion, accompanied by changes in the coupling parameter. The coupling-parameter changes are either accepted with a probability derived from the grand canonical partition function or governed by an equation of motion derived from the extended Lagrangian. The coupling-parameter changes mimic forward and reverse reaction steps, as in RxMC simulations.     

Porous agglomerates in the general linear flow field

We calculate the flow within and around a porous spherical agglomerate suspended in the general linear flow field, and also the flow induced by its rotation. We use the Stokes equations exterior to the particle and the Brinkman equations inside it. The effect of particle permeability on the flow is expressed via the Brinkman parameter beta = r(0)/square root of k, where r0 is particle radius and k is its permeability. With translational creeping motion of porous spheres in a quiet fluid investigated by Debye and Bueche [P. Debye, A.M. Bueche, J. Chem. Phys. 16 (6) (1943) 573-579], this study provides information necessary for investigating dynamics of porous particles moving in creeping shear flows under the action of external forces and torques. The agglomerate flow field solutions are used to calculate the effective viscosity of a dilute suspension of porous solid aggregates, which generalizes the well-known Einstein's equation for solid suspensions. The agglomerate effective viscosity diameter is proposed which allows using the Einstein's formula evaluation of the agglomerates suspension viscosity.     

Nonequilibrium simulations of filled polymer networks: searching for the origins of reinforcement and nonlinearity

We present nonequilibrium dissipative particle dynamics (DPD) simulations of cross-linked elastomers containing solid filler particles at 30% volume fraction. We study systematically the effect of the morphology (dispersed or aggregated particles) and of the effective particle-particle interactions. In addition, we have experimented by replacing the standard harmonic DPD bonds with other potential functions, conceived to deal with the finite extensibility of the polymer chains and the possibility of a slow equilibrium between strongly and weakly adsorbed chains at the rubber-filler interface. The simulation results shed some light on the basic mechanisms of rubber reinforcement, including the nonlinearity and history dependence commonly known as "Payne effect" and "Mullins effect."     

Effects of the bead-bead potential on the restricted rotational diffusion of nonrigid macromolecules

The influence of the bead-bead interaction on the rotational dynamics of macromolecules which are immersed into a solution has been investigated by starting from the microscopic theory of the macromolecular motion, i.e., from a Fokker-Planck equation for the phase-space distribution function. From this equation, we then derived an explicit expression for the configuration-space distribution function of a nonrigid molecule which is immobilized on a surface. This function contains all the information about the interaction among the beads as well as the effects from the surrounding solvent particles and from the surface. For the restricted rotational motion, the dynamics of the macromolecules can now be characterized in terms of a rotational diffusion coefficient as well as a radial distribution functions. Detailed computations for the rotational diffusion coefficient and the distribution functions have been carried out for HOOKEAN, finitely extensible nonlinear elastic, and a DNA type bead-bead interaction.     

Structure of mass, momentum, and energy transfer equations under highly nonequilibrium conditions

The structure of mass, momentum, and energy transfer equations under highly non-equilibrium conditions is considered when the traditional assumption of nonequilibrium thermodynamics (the local equilibrium condition) is violated. The derived transfer equations based on particle mass, momentum, and the law of energy conservation are related to heterogeneous systems with arbitrary density, i.e., for three aggregate states and their interfaces. Fluxes of the mentioned properties are described at the atomic-molecular level by nonequilibrium discrete unary and binary distribution functions (in the lattice gas model) with regard to interparticle potential interactions of system components. It is found that the total set of local transfer equations consists of five modified mass, momentum, and energy transfer equations for each of the system sites, and of 15 new equations describing the correlated characteristics of the density, rate, and temperature for the sites of a pair. The relationship between the derived equations and previous theories is discussed.     

Artifacts in dynamical simulations of coarse-grained model lipid bilayers

With special focus on dissipative particle dynamics simulations of anisotropic and complex soft matter, such as lipid bilayers in water, we have investigated the occurrence of artifacts in the results obtained from dynamical simulations of coarse-grained particle-based models. The particles are modeled by beads that interact via soft repulsive conservative forces (as defined in dissipative particle dynamics simulations), harmonic bond potentials, as well as bending potentials imparting stiffness to the lipid tails. Two different update schemes are investigated: dissipative particle dynamics with a velocity-Verlet-like integration scheme [G. Besold, I. Vattulainen, M. Karttunen, and J. M. Polson, Phys. Rev. E 63, R7611 (2000)] and Lowe-Andersen thermostatting [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] with the standard velocity-Verlet integration algorithm. By varying the integration time step, we examine various physical quantities, in particular pressure profiles and kinetic bead temperatures, for their sensitivity to artifacts caused by the specific combination of integration technique and the thermostat. We then propose a simple fingerprint method that allows monitoring the presence of simulation artifacts.     

Effect of internal viscosity on Brownian dynamics of DNA molecules in shear flow

The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. A stochastic model is derived on the basis of the balance equation for forces acting on the chain. The Euler method is applied to the solution of the model. The extensions of DNA molecules for different Weissenberg numbers are analyzed. Comparison with the experimental results available in the literature is carried out to estimate the contribution of the effect of internal viscosity.     

Flow-alignment and rheology of polymer melts: Computation of the single-link orientational distribution function

The single-link orientational distribution function and the space-averaged stresses in the fluid are computed for the case of steady shear flow of polymer melts. The computation is achieved with Galerkin's method with spherical harmonics and Euler polynomials as trial functions. The stress components become power functions of shear rate when the latter is large. The single-link orientational distribution function f solves the Fokker-Planck equation subject to a boundary condition for f at the chain ends. A solution is obtained for every shear rate and ratio of the orientational and one-dimensional diffusion coefficient. It is demonstrated that the Fokker-Planck equation with appropriate boundary condition is useful in order to predict the flow-alignment and stresses in good agreement with experimental data as well as with recent results of a nonequilibrium molecular dynamics computer simulation on polymer melts.     

Approximation of functions of Lipschitz class and solution of Fokker-Planck equation by two-dimensional Legendre wavelet operational matrix

In this paper, Lipschitz class of two-variables is considered. This is the genralization of well-known Lipschitz class of functions. A new estimator of functions belonging to generalized Lipschitz class has been obtained. Also, the solutions for the Fokker-Planck equations have been obtained for two different cases by two-dimensional Legendre wavelet operational matrix method. The approximated solutions of the time-and space-Fokker Planck equation have been compared with the exact solutions and the solutions obtained by homotopy perturbation method. The proposed scheme is simple, effective and suitable for the solution of Fokker-Planck equation.

     

Transient molecular dynamics simulations of liquid viscosity for nonpolar and polar fluids

A transient molecular dynamics (TMD) method for obtaining fluid viscosity is extended to multisite, force-field models of both nonpolar and polar liquids. The method overlays a sinusoidal velocity profile over the peculiar particle velocities and then records the transient decay of the velocity profile. The viscosity is obtained by regression of the solution of the momentum equation with an appropriate constitutive equation and initial and boundary conditions corresponding to those used in the simulation. The transient velocity decays observed appeared to include both relaxation and retardation effects. The Jeffreys viscoelastic model was found to model accurately the transient responses obtained for multisite models for n-butane, isobutane, n-hexane, water, methanol, and 1-hexanol. TMD viscosities obtained for saturated liquids over a wide range of densities agreed well for the polar fluids, both with nonequilibrium molecular dynamics (NEMD) results using the same force-field models and with correlations based on experimental data. Viscosities obtained for the nonpolar fluids agreed well with the experimental and NEMD results at low to moderate densities, but underpredicted experimental values at higher densities where shear-thinning effects and viscous heating may impact the TMD simulations.     

Dynamics of swelling/contracting hard spheres surmised by an irreversible Langevin equation

The diffusion of molecules through uniform homogeneous materials can readily be described by Brownian motion or generalizations thereof. The further generalization of these models to describe molecular diffusion through heterogeneous and nonstationary solvents is much less understood. Phenomenological nonstationary generalizations of the generalized Langevin equation (GLE) have earlier been developed satisfying the fluctuation-dissipation relationship in quasi-equilibrium limits while exhibiting somewhat complex behavior away from equilibrium. This reduced-dimensional representation should be capable of describing the diffusion of a particle through a colloidal suspension whose average particle size is tuned by an external driving force such as pH. A simple particle model of such a process involves the motion of a hard-sphere particle in an explicit environment of swelling hard spheres. The velocity autocorrelation functions observed in a large number of simulations of the particle model under various swelling rates agree precisely with those of a single form of the nonstationary phenomenological model. Though this procedure is not an explicit projection of the mechanical system onto the nonstationary GLE, it does show that the latter correctly describes the dynamics of the projected coordinate--namely, diffusion of the solute--under nonequilibrium conditions. Both nonequilibrium solvent models lead to behavior reminiscent of beta-relaxation processes at packing fractions substantially below that of the glass transition.     

Constitutive equations for the flow behavior of entangled polymeric systems: application to star polymers

A semimicroscopic derivation is presented of equations of motion for the density and the flow velocity of concentrated systems of entangled polymers. The essential ingredient is the transient force that results from perturbations of overlapping polymers due to flow. A Smoluchowski equation is derived that includes these transient forces. From this, an equation of motion for the polymer number density is obtained, in which body forces couple the evolution of the polymer density to the local velocity field. Using a semimicroscopic Ansatz for the dynamics of the number of entanglements between overlapping polymers, and for the perturbations of the pair-correlation function due to flow, body forces are calculated for nonuniform systems where the density as well as the shear rate varies with position. Explicit expressions are derived for the shear viscosity and normal forces, as well as for nonlocal contributions to the body force, such as the shear-curvature viscosity. A contribution to the equation of motion for the density is found that describes mass transport due to spatial variation of the shear rate. The two coupled equations of motion for the density and flow velocity predict flow instabilities that will be discussed in more detail in a forthcoming publication.     

Shear viscosity of molten alkali halides from equilibrium and nonequilibrium molecular-dynamics simulations

The shear viscosity of molten NaCl and KCl was calculated through equilibrium (EMD) and nonequilibrium molecular-dynamics (NEMD) simulations in the canonical (N,V,T) ensemble. Two rigid-ion potentials were investigated, namely, the Born-Mayer-Huggins-Tosi-Fumi potential and the Michielsen-Woerlee-Graaf-Ketelaar potential with the parameters proposed by Ladd. The NEMD simulations were performed using the SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] with a Gaussian isokinetic thermostat and the results are compared with those obtained from Green-Kubo EMD (N,V,T) simulations and experimental shear viscosity data. The NEMD zero strain rate shear viscosity, eta(0), was obtained by fitting a simplified Carreau-type equation and by application of mode-coupling theory, i.e., a eta-gamma(1/2) linear relationship. The values obtained from the first method are found to be significantly lower than those predicted by the second. The agreement between the EMD and NEMD results with experimental data is satisfactory for the two potentials investigated. The ion-ion radial distribution functions obtained with the two rigid-ion potentials for both molten salts are discussed in terms of the differences between the two models.     

Polarizable particle aggregation under rotating magnetic fields using scattering dichroism

We used scattering dichroism to study the dynamics of dipolar chains induced in magnetorheological suspensions under rotating magnetic fields. Both the dichroism (proportional to the total number of aggregated particles) and the phase lag show different behavior below and above a cross-over frequency. The cross-over frequency depends linearly on both the square of the magnetization and the inverse of the viscosity. The Mason number (ratio of viscous to magnetic forces) governs the dynamics. Therefore, there is a cross-over Mason number below which the dichroism remains almost constant and above which the rotation of the field prevents the particle aggregation process from taking place. Our experimental results have been compared with particle dynamics simulations showing good agreement.     

The Stern-Gerlach experiment and the effects of spin relaxation

The classical Stern-Gerlach experiment is analyzed with an emphasis on the spin dynamics. The central question asked is whether there occurs a relaxation of the spin angular momentum during the time the particle passes through the Stern-Gerlach magnet. We examine in particular the transverse relaxation, involving angular momentum exchange between the spin of the particles and the spins of the magnet. A method is presented describing relaxation effects at an individual particle level. This leads to a stochastic equation of motion for the spins. This is coupled to a classical equation of motion for the particle translation. The experimental situation is then modeled through simulations of individual trajectories using two sets of parameter choices and three different sets of initial conditions. The two main conclusions are: (A) if the coupling between the magnet and the spin is solely described by the Zeeman interaction with the average magnetic field the simulations show a clear disagreement with the experimental observation of Stern and Gerlach. (B) If one, on the other hand, also allows for a T(2) relaxation time shorter than the passage time one can obtain a practically quantitative agreement with the experimental observations. These conclusions are at variance with the standard textbook explanation of the Stern-Gerlach experiment.     

On Coarse-Graining by the Inverse Monte Carlo Method: Dissipative Particle Dynamics Simulations Made to a Precise Tool in Soft Matter Modeling

We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD) simulations, which are then used in coarse-grained dissipative particle dynamics (DPD) simulations. Here, the effective potentials were obtained by applying the inverse Monte Carlo method [Lyubartsev and Laaksonen, Phys. Rev. E. 52, 3730 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. In our first application of the method, the effective potentials were used in DPD simulations of aqueous NaCl solutions. With the same computational effort we were able to simulate systems of one order of magnitude larger than the MD simulations. The results from the MD and DPD simulations are in excellent agreement.