Mesoscopic Simulation Method Research Articles

Autocatalytic reaction dynamics in systems crowded by catalytic obstacles

Reaction and diffusion dynamics in systems crowded by catalytic obstacles are investigated using a particle-based mesoscopic simulation method. The focus of the work is on effects of correlations induced by the presence of the catalytic obstacles and solvent collective modes. As an example, a system is considered where the reaction A + C → B + C takes place on the surfaces of the C catalytic obstacles, while the autocatalytic reaction A + B → 2 A occurs in the bulk of the solution. It is shown that mean-field, mass-action rate laws break down and fail to describe the reaction dynamics for large volume fractions of obstacles. The influence of hydrodynamics on the reaction and diffusion dynamics is also studied.

A 2-D mesoscopic model coupling mechanical and diffusion for electromigration in thin films

Electromigration is an important mechanism of deformation and failure in miniaturized electronics materials. In this paper, a 2-D mesoscopic simulation method is developed for analyzing electromigration-induced stress in thin films and finite element method is implemented for solution. Numerical simulations are compared with theoretical result and comparisons validate the model. The method has advantage in describing boundary conditions for constrained diffusion when focusing on creep process of thin films.

Cooperation of sperm in two dimensions: Synchronization, attraction, and aggregation through hydrodynamic interactions

Sperm swimming at low Reynolds number have strong hydrodynamic interactions when their concentration is high in vivo or near substrates in vitro. The beating tails not only propel the sperm through a fluid, but also create flow fields through which sperm interact with each other. We study the hydrodynamic interaction and cooperation of sperm embedded in a two-dimensional fluid by using a particle-based mesoscopic simulation method, multiparticle collision dynamics. We analyze the sperm behavior by investigating the relationship between the beating-phase difference and the relative sperm position, as well as the energy consumption. Two effects of hydrodynamic interaction are found, synchronization and attraction. With these hydrodynamic effects, a multisperm system shows swarm behavior with a power-law dependence of the average cluster size on the width of the distribution of beating frequencies.

Multicomponent dissipative particle dynamics: Formulation of a general framework for simulations of complex fluids

AbstractThe dissipative particle dynamics mesoscopic simulation method is analyzed thoroughly by identifying the scaling factors necessary to simulate a multicomponent system. A new framework of general expressions is derived relating the parameters in the system to their dimensionless quantities. The consistent non‐dimensionalization used in this paper serves to connect the previous models in the literature. When the scaling factors are based on the solvent in a multicomponent system, the system of equations reduces to the well‐known Groot and Warren model. Validation results for ideal, simple and binary immiscible fluids are presented and compared with established results from the literature. The framework established herein is an important step toward the practical application of dissipative particle dynamics for the analysis of complex fluid systems. Copyright © 2008 John Wiley & Sons, Ltd.

Ordered Packing of Soft Discoidal System

A novel mesoscopic simulation method is adopted to study the ordered packing of the anisotropic disklike particles with a soft repulsive interaction, which possesses a modified anisotropic conservative force type used in dissipative particle dynamics. We examine the influence of the shape of the particles, the angular width of the repulsion, and the strength of the repulsion on the packing structures. Specifically, an ordered hexagonal columnar structure is obtained in our simulations. Our study demonstrates that an anisotropic repulsive potential between soft discoidal particles is sufficient to produce a relatively ordered hexagonal columnar structure.

Spontaneous Formation of Complex Micelles from a Homogeneous Solution

We present an extensive computer simulation study of structure formation in amphiphilic block copolymer solutions after a quench from a homogeneous state. By using a mesoscopic field-based simulation method, we are able to access time scales in the range of a second. A "phase diagram" of final structures is mapped out as a function of the concentration and solvent philicity of the copolymers. A rich spectrum of structures is observed, ranging from spherical and rodlike micelles and vesicles to toroidal and net-cage micelles. The dynamical pathways leading to these structures are analyzed in detail, and possible ways to control the structures are discussed briefly.

Simulation of tetraetherlipids on solid surfaces – an extension of the DPD-model

Glyceroldialkylnomizoltetraetherlipid (GDNT) is a tetraetherlipid that can be extracted from archaebacteria and that is known for its antifouling capabilities [1]. Therefore it is of interest to find out whether solid surfaces can be coated with this material in order to generate resistant devices for water analytics. Recently we developed a new mesoscopic molecular modelling computer simulation method from the Dissipative Particle Dynamics (DPD) method [2] useful for simulations of specific dynamical processes at the microsecond and micrometer scale. This unique technique, called Molecular-Fragment-Dynamics (MFD), can be generally applied to surfactants, polymers, nanoparticles and complex mixtures in materials and life science simulation studies [3]. In MFD the molecule is divided into different regions of molecular fragments. Therefore, the MFD scheme overcomes the limitations of classic atomic scale simulations. This method has been applied to a system of GDNT in three different solvents (e.g. cyclohexane, chloroform and carbon tetrachlorine) at the interface with a solid borofloate substrate. Goal of the study was to find out at which concentration of GDNT and in which solvent the best levels of aggregation could be reached and how such coated surfaces look like. The results of the study will be presented on the poster with pictures and graphs.

Electroosmosis in homogeneously charged micro- and nanoscale random porous media

Electroosmosis in homogeneously charged micro- and nanoscale random porous media has been numerically investigated using mesoscopic simulation methods which involve a random generation-growth method for reproducing three-dimensional random microstructures of porous media and a high-efficiency lattice Poisson–Boltzmann algorithm for solving the strongly nonlinear governing equations of electroosmosis in three-dimensional porous media. The numerical modeling and predictions of EOF in micro- and nanoscale random porous media indicate that the electroosmotic permeability increases monotonically with the porosity of porous media and the increasing rate rises with the porosity as well; the electroosmotic permeability increases with the average solid particle size for a given porosity and with the bulk ionic concentration also; the proportionally linear relationship between the electroosmotic permeability and the zeta potential on solid surfaces breaks down for high zeta potentials. The present predictions agree well with the available experimental data while some results deviate from the predictions based on the macroscopic theories.

Computer simulation of aqueous block copolymer assemblies: Length scales and methods

AbstractAtomistic, coarse‐grain, and mesoscopic computer simulation methods applied recently to the study of block copolymer assemblies in solution are reviewed. At the atomic level, particle‐based simulations have provided insight into specific interactions such as hydrogen bonding between polymer and water. Coarse‐grain models have given a generalized view of the conformations of polymer chains in solvents of different qualities by grouping clusters of atoms into effective interaction sites. Mesoscopic self‐consistent field theory allows for the study of the phase diagram of block copolymers in water using a mean‐field continuum description. Advances in and results with these methodologies are presented along with present challenges. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1907–1918, 2006

Computer simulation of surface modification with ion beams

Niobium surface modification dynamics treated by cluster ion irradiation was studied based on atomistic and mesoscopic simulation methods and the results were compared to experiments. A surface smoothening method was proposed consisting of a treatment of the Nb cavity surfaces by accelerated gas (argon) cluster ion beams (GCIB) that is capable of reducing the surface roughness up to the theoretical limit.

Application of Preisach model to adsorption–desorption hysteresis

We are developing mesoscopic simulation methods to model surface phenomena. Mesoscopic level links microscopic description of physicochemical systems with macroscopic observables. Recent progress in mathematical theory of hysteresis provides tools to realise such link in the realm of adsorption–desorption hysteresis. The general methodology can be also applied to other classes of surface phenomena (e.g. pattern formation as a result of coupling of elementary bistable elements).

Constant-pressure simulations with dissipative particle dynamics

Dissipative particle dynamics (DPD) is a mesoscopic simulation method for studying hydrodynamic behavior of complex fluids. Ideally, a mesoscopic model should correctly represent the thermodynamic and hydrodynamic properties of a real system beyond certain length and time scales. Traditionally defined DPD quite successfully mimics hydrodynamics but is not flexible enough to accurately describe the thermodynamics of a real system. The so-called multibody DPD (MDPD) is a pragmatic extension of the classical DPD that allows one to prescribe the thermodynamic behavior of a system with only a small performance impact. In an earlier paper [S. Y. Trofimov, E. L. F. Nies, and M. A. J. Michels, J. Chem. Phys. 117, 9383 (2002)] we much improved the accuracy of the MDPD model for strongly nonideal systems, which are of most practical interest. The ability to correctly reproduce the equation of state of realistic systems in turn makes simulations at constant pressure sensible and useful. This situation of constant-pressure conditions is very common in experimental studies of (soft) condensed matter but has so far remained unexplored with the traditional DPD. Here, as a proof of concept, we integrate a modified version of the Andersen barostat into our improved MDPD model and make an evaluation of the performance of the new model on a set of single- and multicomponent systems. The modification of the barostat suppresses the "unphysical" volume oscillations after a sudden pressure change and simplifies the equilibration of the system.

Molecular Modeling on the Binary Blend Compatibility of Poly(vinyl alcohol) and Poly(methyl methacrylate): An Atomistic Simulation and Thermodynamic Approach

Computer simulations play an important role in designing new polymers as well as in predicting properties of existing polymers. In this paper, the blend compatibility of poly(vinyl alcohol) (PVA) with poly(methyl methacrylate) (PMMA) was studied over the wide range of compositions allowed by the atomistic and mesoscopic simulation methods. The Flory-Huggins interaction parameter, chi, of the blends computed using the atomistic simulation confirmed the blend compatibility for compositions containing >60 wt % of PVA. This observation was further supported by differential scanning calorimetric experiments. Solubility parameters of the polymers obtained from the simulation procedure were in good agreement with those of the literature data. Simulation results were further supported by the spectral and solution property measurements. From the atomistic simulations, chi versus concentration plots were constructed, which showed trends similar to those experimentally measured melting temperature versus concentration. The chi values for the blends, which satisfied the criteria of miscibility of two polymers by the atomistic simulation, agreed quite well with the solubility criteria related to order parameters calculated from the mesoscopic simulation. Kinetics of phase separation was examined via density profiles calculated using the MesoDyn approach for incompatible blends. The length and time scales spanned by these simulations were found to be relevant to the real application scales. The free energy computed in the mesoscopic simulation for blends reached equilibrium, particularly when the simulation was performed at a higher time step, indicating the stability of the blend system at certain compositions.

Mesoscopic simulation of the crossing dynamics at an entanglement point of surfactant threadlike micelles

The crossing dynamics at an entanglement point of surfactant threadlike micelles in an aqueous solution was studied using a mesoscopic simulation method, dissipative particle dynamics, with a coarse-grained surfactant model. The possibility of a phantom crossing, which is the relaxation mechanism for the pronounced viscoelastic behavior of surfactant threadlike micellar solution, was investigated. When two threadlike micelles were encountered at an entanglement point under the condition close to thermal equilibrium, they fused to form a four-armed branch point. Then, a phantom crossing reaction occurred occasionally, or one micelle was cut down at the branch point. Increasing the repulsive forces between hydrophilic parts of the surfactants, fusion occurred less and the threadlike micelle was frequently broken down at an entanglement point. In these three schemes (a phantom crossing cut down at the branch point, and break down at the entanglement point), the breakage occurs at somewhere along the threadlike micelle. The breakage is considered as an essential process in the relaxation mechanism, and a phantom crossing can be seen as a special case of these processes. To explain the experimental evidence that a terminal of threadlike micelles is scarcely observed, a mechanism was also proposed where the generated terminal merges into the connected micelle part between two entanglement points due to the thermal motion.

Hydrodynamic and Brownian Fluctuations in Sedimenting Suspensions

We use a mesoscopic computer simulation method to study the interplay between hydrodynamic and Brownian fluctuations during steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.1-15. Even when the hydrodynamic interactions are an order of magnitude weaker than Brownian forces, they still induce backflow effects that dominate the reduction of the average sedimentation velocity with increasing particle packing fraction. Velocity fluctuations, on the other hand, begin to show nonequilibrium hydrodynamic character for Pe>1.

A Procedure for Molecular Electronic State Calculation in Inhomogeneous Materials

A possible procedure for calculating the molecular electronic states in mesoscopic inhomogeneous structures is explained based on the results of simulations on different spatial scales. Electrostatic potential is discussed as an essential factor to connect the electronic characteristics of different scales. The procedure is demonstrated by applying the results of hierarchical simulations on the structural formula of a polyelectrolyte (Nafion, a DuPont trademark) molecule to the electronic state calculations for a hydronium ion in a hydrated Nafion membrane via the mesoscopic structure of the membrane. The mesoscopic simulation method adopted here is dissipative particle dynamics (DPD), which is a coarse graining simulation method with dissipative and randomly fluctuating force terms. A mixed basis function method is introduced for electronic state calculations in inhomogeneous fields as a combination of Gaussian basis functions and shape functions of the finite element method (FEM) for expressing electronic wavefunctions. The procedure of the multi-scale simulation represents a practical example of ones reproducing electronic structural information within a mesoscopic inhomogeneous structure.

Mesoscale Computer Simulations on the Phase Behavior of the Non-Ionic Surfactant C12E5

Abstract Dissipative Particle Dynamics is a mesoscopic simulation method which allows to predict the self-assembly of amphiphilic polymers and surfactants. It was possible to reproduce the phase behavior of the non-ionic surfactant C12E5 in water. The three different phases L1, La and L2 could be characterized with Dissipative Particle Dynamics.

Phase behavior of amphiphilic polymers: A dissipative particles dynamics study

Dissipative particle dynamics is a mesoscopic simulation method which allows one to predict the self-assembly of amphiphilic polymers and surfactants. It was possible to reproduce the formation of microemulsions of the oil/water (o/w), water/oil (w/o), and L3-type of C10E4 in water and n-decane with excellent accuracy. We are able to predict the experimentally not investigated emulsion formation of a poly(ethylene butylene)–poly(ethylene oxide) in water and methylcyclohexane.

Mesoscopic Simulation for the Drying Process of Polymer Films

A mesoscopic simulation method is presented to predict the drying behavior of polymer films using a dissipative particle dynamics method (DPD) with a simple model for evaporation. A gas phase is set above the polymer solution, and then evaporation of the solvent particle is calculated with appropriate parameters which lead solvent particles to prefer the gas phase rather than the polymer solution. A solvent particle that moves into the gas phase is considered as a gas particle after being determined as having evaporated. An effective mass is considered, so as to represent the relatively slower motion of the polymer particle compared to the solvent particle and the dependence of solvent diffusivity on its concentration in a polymer solution. A time-dependent profile of solvent concentration throughout the polymer film was successfully calculated, and skin formation, which indicates significant concentration gradients on the surface of the polymer film, was also observed.

Thermodynamic consistency in dissipative particle dynamics simulations of strongly nonideal liquids and liquid mixtures

Dissipative particle dynamics (DPD) is a mesoscopic simulation method for studying hydrodynamic behavior of complex fluids. Ideally, a mesoscopic model should correctly represent the thermo- and hydrodynamic properties of a real system beyond certain length and time scales. Traditionally defined DPD quite successfully mimics hydrodynamics, but is not flexible enough to accurately describe the thermodynamics of a real system. The so-called “multibody” DPD (MDPD) is a pragmatic extension of the classical DPD that allows one to prescribe the thermodynamic behavior of a system with only a small performance impact. Here we present a practical improvement to the “multibody” DPD model and test it on a number of single-component examples. We also generalize MDPD to multicomponent systems, which are an important target of DPD studies. The improved model provides a correction for particle correlations in strongly nonideal systems that were neglected in the original MDPD model. The implications of the coarse-graining procedure on the MDPD are discussed.