Coarse graining of slow variables in dynamic simulations of soft matter

A new Brownian dynamics model is presented to describe the coarse grain dynamics of particles with long-lived memory. Instead of solving a set of generalized Langevin equations we introduce a set of variables describing the slowly fluctuating thermodynamic state of the ignored degrees of freedom. These variables give rise to additional transient forces on the simulated particles, whose interpretation provides a new way of thinking about memory effects in soft-matter physics. We illustrate the proposed method by simulating shear thinning of synthetic resins.\u

Domain formation and growth in spinodal decomposition of a binary fluid by molecular dynamics simulations

The two initial stages of spinodal decomposition of a symmetric binary Lennard-Jones fluid have been simulated by molecular dynamics simulations, using a hydrodynamics-conserving thermostat. By analyzing the growth of the average domain size R(t) with time, a satisfactory agreement is found with the R(t)t1/3 Lifshitz-Slyozov growth law for the early diffusion-driven stage of domain formation in a quenched homogeneous mixture. In the subsequent stage of viscous-dominated growth, the mean domain size appears to follow the linear growth law predicted by Siggia

Repeated segregation and energy dissipation in an axially segregated granular bed

Discrete element simulations were used to study the segregation behaviour in a bed of bidisperse granules in a rotating drum. In the final state the large particles ended up in the upper part of the bed near the vertical walls. In order to arrive at this state, the system went through two cycles of structural changes, on top of which fast oscillations were observed between an axially segregated and a somewhat more mixed state. These oscillations were sustained by different angles of repose near the vertical walls and in the middle of the bed. Concomitantly with the structural changes, the system's energy dissipation went through two cycles after which it settled in the state requiring the least work of all traversed states, suggesting that the granular bed strives for minimal dissipation

Kayaking and wagging of liquid crystals under shear: Comparing director and mesogen motions

Rod-like colloids in dense solutions perform collective orientational motions under shear flow. The periodic tumbling motions of the director, i.e. the average orientation of the rods, are commonly characterized as kayaking, wagging and flow-aligning, in order of increasing shear rate. Our event-driven Brownian dynamics simulations of rigid spherocylinders reproduce these three distinct director motions, but also clearly show, for the first time, that the individual mesogens are kayaking at all shear rates. The synchrony of the mesogens's motions gradually decreases with increasing shear rate, which at a critical shear rate causes a transition of the apparent collective motion from kayaking to wagging. The rods's persistent kayaking also explains the continuity of the tumbling period at this transition and the smooth change from wagging to flow-aligning observed at higher shear rates

Molecular dynamics simulation of amphiphilic membrane and wormlike micelles: a multi-scale modelling approach to the design of visco-elastic surfactant solutions

Bilayer membranes and wormlike micelles have been studied using molecular–dynamics simulations. The structure of the worm is analysed in terms of radial density distribution functions, and mechanical properties such as the elastic modulus are calculated. From an analysis of the fluctuation spectra of the tensionless states, we have calculated bending rigidities. Micelles consisting of coarse–grained (CG) model surfactants are studied in order to map the properties of the atomistic micelle. We optimize the CG model with respect to the structure factor S(q) of the atomistic micelle. The mechanical properties thus obtained will be used as input for a mesoscopic model of wormlike micelles where the persistence length is the smallest length–scale

Vapour-liquid coexistence in many-body dissipative particle dynamics

Many-body dissipative particle dynamics is constructed to exhibit vapour-liquid coexistence, with a sharp interface, and a vapour phase of vanishingly small density. In this form, the model is an unusual example of a soft-sphere liquid with a potential energy built out of local-density dependent one-particle self energies. The application to fluid mechanics problems involving free surfaces is illustrated by simulation of a pendant drop.Comment: 8 pages, 6 figures, revtex

Stochastic-dynamical thermostats for constraints and stiff restraints

A broad array of canonical sampling methods are available for molecular simulation based on stochastic-dynamical perturbation of Newtonian dynamics, including Langevin dynamics, Stochastic Velo- city Rescaling, and methods that combine Nosé-Hoover dynamics with stochastic perturbation. In this article we discuss several stochastic-dynamical thermostats in the setting of simulating systems with holonomic constraints. The approaches described are easily implemented and facilitate the recovery of correct canonical averages with minimal disturbance of the underlying dynamics. For the purpose of illustrating our results, we examine the numerical application of these methods to a simple atomic chain, where a Fixman term is required to correct the thermodynamic ensemble

Solvent Effect on the Isomerization Rate of Calix[4]arene Studied by Molecular Dynamics Simulations

The isomerization rates of a calix[4]arene in benzene and in chloroform have been calculated by using molecular dynamics simulations. The reaction coordinate that is employed is based on the unstable normal mode at the saddle point of the potential energy surface. The free energy as a function of this coordinate has been calculated by means of umbrella sampling. Comparison of the free energies in the solvents with those in vacuum reveals that both solvents destabilize the paco conformation and stabilize the transition state region. In chloroform the calix[4]arene shows a stronger preference for the cone conformation than in benzene or in vacuum. The isomerization rate has been determined by the reactive flux method. In benzene the transmission coefficient is about a third higher than in chloroform. The calculated rates are in perfect agreement with experimental data